National Coverage Analysis (NCA) Decision Memo

Next Generation Sequencing (NGS) for Medicare Beneficiaries with Advanced Cancer

CAG-00450R

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Decision Summary

A.  The Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a CLIA-certified laboratory, when ordered by a treating physician and when all of the following requirements are met:

  1. The patient has:
    • ovarian or breast cancer; and
    • a clinical indication for germline (inherited) testing for hereditary breast or ovarian cancer; and
    • a risk factor for germline (inherited) breast or ovarian cancer; and
    • not been previously tested with the same germline test using NGS for the same germline genetic content.
  2. The diagnostic laboratory test using NGS must have all of the following:
    • Food and Drug Administration (FDA) approval or clearance; and
    • results provided to the treating physician for management of the patient using a report template to specify treatment options.

B.  Other

Medicare Administrative Contractors (MACs) may determine coverage of Next Generation Sequencing (NGS) as a diagnostic laboratory test when performed in a CLIA-certified laboratory, when ordered by a treating physician, when results are provided to the treating physician for management of the patient and when the patient has:

  • any cancer diagnosis; and
  • a clinical indication for germline (inherited) testing of hereditary cancers; and
  • a risk factor for germline (inherited) cancer; and
  • not been previously tested with the same germline test using NGS for the same germline genetic content.

We are making other technical, clarifying, and conforming changes in Section 90.2 of the National Coverage Determinations Manual.  We are clarifying the existing policy related to diagnostic tests for Somatic (Acquired) Cancer. 

See Appendix B for the draft manual language.

For ease of the reader, this National Coverage Determination (NCD) is only applicable to diagnostic lab tests using NGS for somatic (acquired) and germline (inherited) cancer.  Medicare Administrative Contractors (MACs) may determine coverage of diagnostic lab tests using NGS for RNA sequencing and protein analysis.  MACs also have discretion to determine coverage of diagnostic lab tests using NGS for any non-cancer (e.g., infectious disease and heart disease) use.  These uses are outside the scope of this NCD.

Decision Memo

TO:		Administrative File: CAG-00450R

FROM:	Tamara Syrek Jensen, JD
		Director,
		Coverage and Analysis Group

		Joseph Chin, MD, MS
		Deputy Director, Coverage and Analysis Group

		Melissa A. Evans, PhD, MSAE
		Director, Division of Policy & Evidence Review 

		Lori Ashby, MA
		Deputy Director, Division of Policy & Evidence Review

		Andrew Ward, PhD, MPH
		Director, Evidence Development Division

		James Rollins, MD, PhD
		Medical Officer

		Carl Li, MD, MPH
		Medical Officer

		Kimberly Long
		Lead Analyst    

SUBJECT:	National Coverage Determination for Diagnostic Laboratory Tests using Next Generation Sequencing (NGS) for Medicare Beneficiaries 
with Germline (Inherited) Cancer 

DATE:		January 27, 2020

I.   Decision

A.  The Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a CLIA-certified laboratory, when ordered by a treating physician and when all of the following requirements are met:

  1. The patient has:
    • ovarian or breast cancer; and
    • a clinical indication for germline (inherited) testing for hereditary breast or ovarian cancer; and
    • a risk factor for germline (inherited) breast or ovarian cancer; and
    • not been previously tested with the same germline test using NGS for the same germline genetic content.
  2. The diagnostic laboratory test using NGS must have all of the following:
    • Food and Drug Administration (FDA) approval or clearance; and
    • results provided to the treating physician for management of the patient using a report template to specify treatment options.

B.  Other

Medicare Administrative Contractors (MACs) may determine coverage of Next Generation Sequencing (NGS) as a diagnostic laboratory test when performed in a CLIA-certified laboratory, when ordered by a treating physician, when results are provided to the treating physician for management of the patient and when the patient has:

  • any cancer diagnosis; and
  • a clinical indication for germline (inherited) testing of hereditary cancers; and
  • a risk factor for germline (inherited) cancer; and
  • not been previously tested with the same germline test using NGS for the same germline genetic content.

We are making other technical, clarifying, and conforming changes in Section 90.2 of the National Coverage Determinations Manual.  We are clarifying the existing policy related to diagnostic tests for Somatic (Acquired) Cancer. 

See Appendix B for the draft manual language.

For ease of the reader, this National Coverage Determination (NCD) is only applicable to diagnostic lab tests using NGS for somatic (acquired) and germline (inherited) cancer.  Medicare Administrative Contractors (MACs) may determine coverage of diagnostic lab tests using NGS for RNA sequencing and protein analysis.  MACs also have discretion to determine coverage of diagnostic lab tests using NGS for any non-cancer (e.g., infectious disease and heart disease) use.  These uses are outside the scope of this NCD.

II.  Background

Throughout this document we use numerous acronyms, some of which are not defined as they are presented in direct quotations.  Please find below a list of these acronyms and corresponding full terminology:

ACCE - Analytical validity, clinical validity, clinical utility, ethical, legal and social implications of genetic testing
ACS - The American Cancer Society
AD - Lung adenocarcinoma
ADSQ - Adenosquamous carcinoma
AHRQ - Agency for Healthcare Research and Quality
AKT - Protein kinase B
ALK - Anaplastic lymphoma receptor tyrosine kinase
AMVAC - Accelerated methotrexate, vinblastine, doxorubicin, and cisplatin
ANOVA - Analysis of Variance
ARID1A - AT-Rich Interaction Domain 1A
ASCO - American Society of Clinical Oncology
ATC - Anaplastic thyroid carcinoma
ATM - Ataxia telangiectasia, mutated
BC – Breast Cancer
BRAF - B-Raf, proto-oncogene B-Raf, v-Raf murine sarcoma viral oncogene homolog B
BRCA1 - BReast CAncer gene 1
BRCA2 - BReast CAncer gene 2
BSC - Best supportive care
BTC - Biliary tract cancer
CAP - College of American Pathologists
CCND1 - Cyclin D1
CD8 - Cluster of Differentiation 8
CDKN2A - Cyclin-dependent kinase inhibitor 2A
CED - Coverage with Evidence Development
cfDNA - Cell Free DNA
CFR - Code of Federal Regulations
CGH - Comparative Genomic Hybridization
CGP - Comprehensive Genomic Profile
CHEK2 – Checkpoint Kinase 2 CI - Confidence Interval
CLIA - Clinical Laboratory Improvement Amendments
CMS - Centers for Medicare & Medicaid Services
CNA - Copy Number Alteration
COSMIC - Catalogue Of Somatic Mutations In Cancer, database
CR - Complete Response
CRC - Colorectal cancer
CRGAs - Clinically relevant genomic alterations
CS - Current smoker
cSCC - Cutaneous squamous cell carcinoma
CTCAE - Common Terminology Criteria for Adverse Events
ctDNA - circulating tumor DNA
CTEP - NIH-NCI Cancer Therapy Evaluation Program
CTNNB1 - Catenin Beta 1
c-kit - proto-oncogene c-Kit
DAB - Departmental Appeals Board
DFS - Disease-free survival
DNA - Deoxyribonucleic acid
DOT - Duration of treatment
EC - Endometrial cancer
EGFR - Epidermal growth factor receptor
EHCCA - Extrahepatic cholangiocarcinoma
EOC - Epithelial Ovarian Carcinoma
ER - Estrogen receptor
ERBB2 - Receptor Tyrosine-Protein Kinase Erb-B2
ES - Ex-smoker
F1CDx - FoundationOne CDx™
FANCC - Fanconi Anemia Complementation Group C
FBXW7 - F-Box And WD Repeat Domain Containing 7
FDA - Food and Drug Administration
FFPE - formalin-fixed paraffin embedded
FGFR - Fibroblast growth factor receptor
FIGO - International Federation of Gynecology and Obstetrics
FISH - Fluorescence in-situ hybridization
FLT3 - Fms-like tyrosine kinase 3
FR - Federal Register
GA - Genomic Alteration
GTB - Genomic Tumor Board
GTR - NIH Genetic Testing Registry
HHS - U.S. Department of Health and Human Services
HR - Hazard Ratio
HR - Homologous Recombination
IHC - Immunohistochemical
IOM - Institute of Medicine
IQR - Interquartile range
LADC - Lung Adenocarcinoma
LDT - Laboratory Developed Test
MAC - Medicare Administrative Contractor
MLPA - Multiplex Ligation-dependent Probe Amplification
MM - Malignant Mesotheliomas
MRD - Minimal Residual Disease
MSI - Microsatellite Instability
MTB - Molecular Tumor Board
NCA - National Coverage Analysis
NCCN - National Comprehensive Cancer Network
NCD - National Coverage Determination
NCI - National Cancer Institute
NGS - Next Generation Sequencing
NICE - National Institute for Health Care Excellence
NIH - National Institutes of Health
ORR - Objective Response Rate
OS - Overall Survival
PD - Progressive Disease
PFS - Progression Free Survival
PR - Partial Response
PR – Progesterone Receptor
QOL - Quality of Life
RECIST - Response Evaluation Criteria in Solid Tumors
RR - Response Rate
RRR - Relative Response Ratio
S.D. - Standard Deviation
SD - Stable Disease
SEER - Surveillance, Epidemiology, and End Results Program
SWOG - NCI supported organization conducting clinical trials in adult cancers
TCGA - The Cancer Genome Atlas
TKI - Tyrosine Kinase Inhibitor
TMB - Tumor Mutational Burden
TNBC – Triple Negative Breast Cancer
TTF - Time to Treatment Failure
US - United States
WES - Whole Exome Sequencing

A.  What is cancer?

Cancer is the second leading cause of death in the United States (Siegel, 2019).  In 2019, breast cancer was the most common cause of cancer and accounted for 30% of all new cancer diagnoses in women.  Breast cancer was the second leading and ovarian cancer was the fifth leading cause of death due to cancer among women.  For women above 60 years of age in 2016, breast cancer was the second leading cause of cancer death (Siegel, 2019).

Hereditary cancer is estimated to account for 5–10% of cancer diagnoses (Kulkarni, 2016).  It is estimated that between 5% and 10% of all new cases of breast cancer can be attributed to mutations in germline breast cancer susceptibility genes, including BRCA1 and BRCA2 (Hilgart, 2012).  Approximately 9–24% of women with ovarian cancer are carrying germline mutations in BRCA1 and BRCA2 (Committee on Practice Bulletins–Gynecology, Committee on Genetics, Society of Gynecologic Oncology, 2017).

Cancer is a collection of related diseases during which normal cells behave abnormally to grow and divide without control, which can lead to invasion and spread into surrounding tissues.  Malignant cancer cells can form solid masses distinct from benign tumors and are likely less developed than nearby mature healthy cells.  These malignant tumors may influence the surrounding microenvironment to further growth and development of the tumor or evade normal immune-mediated responses.

There are other collections of related diseases in which normal cells proliferate or behave abnormally but are not cancer.  Hyperplasia is an increase in the number of normal cells in an organ or tissue.  Dysplasia is the presence of abnormal cells in an otherwise normal organ or tissue.  Carcinoma in situ is an increase in the number of abnormal cells in an otherwise normal organ or tissue.  Carcinoma in situ is distinct from cancer as these abnormal cells have not spread into normal tissue.

Cancer is the result of genetic changes to deoxyribonucleic acid (DNA) that can be inherited or acquired during the lifetime.  While each cancer may have unique genetic changes that could vary among cells of the same tumor type, there are certain mutations that commonly cause cancer, including mutations to tumor suppressor genes, DNA repair genes, or proto-oncogenes.  Moreover, metastatic cancer cells and cells of the original cancer usually have some molecular features in common, such as the presence of changes to specific chromosomes containing DNA.

Hereditary cancers are caused by inherited mutations.  These mutations are also called germline mutations because they occur in the parent's egg or sperm cells, which are also called germ cells.  Another type of mutation is called a somatic mutation which differs from inherited or germline mutations.  Somatic mutations are present in cancer cells.  Somatic mutations cannot be inherited because they do not occur in the parent’s egg or sperm cells, and are acquired.

By knowing if a cancer patient has an inherited cancer it could lead to change in management compared to a patient with an acquired cancer.  For example, there are a number of different types of breast cancer, some are inherited.  Knowing whether the patient has an inherited cancer can change clinical management and benefit the patient.

In this decision memorandum, the terms "germline" and "inherited" and "hereditary" will be used interchangeably.  The term "familial" is about relating to or occurring in a family or its members.

People with hereditary cancer predisposition possess a germline mutation in a gene critical to cell cycle regulation, the DNA damage repair process or angiogenesis (the development of new blood vessels) regulation.  In addition to germline mutations, acquired mutations accrue and accumulate, expanding in clonal populations, such that cell growth becomes de-regulated, de-differentiated and tumors are formed.  (Kulkarni, 2016).

Risk Factors for Hereditary (or Germline) Breast and Ovarian Cancer

The American College of Obstetrician and Gynecologists’ criteria for further genetic evaluation for hereditary (germline) breast and ovarian cancer are as follows:

  • Women affected with one or more of the following have an increased likelihood of having an inherited predisposition to breast and ovarian, tubal, or peritoneal cancer and should be offered genetic testing:
    –  Epithelial ovarian, tubal, or peritoneal cancer
    –  Breast cancer at age 45 years or less
    –  Breast cancer and have a close relative with breast cancer at age 50 years or less or close relative with epithelial ovarian, tubal, or peritoneal cancer at any age
    –  Breast cancer at age 50 years or less with a limited or unknown family history
    –  Breast cancer and have two or more close relatives with breast cancer at any age
    –  Breast cancer and have two or more close relatives with pancreatic cancer or aggressive prostate cancer
    –  Two breast cancer primaries, with the first diagnosed before age 50 years
    –  Triple-negative breast cancer at age 60 years or less
    –  Breast cancer and Ashkenazi Jewish ancestry at any age
    –  Pancreatic cancer and have two or more close relatives with breast cancer; ovarian, tubal, or peritoneal cancer; pancreatic cancer; or aggressive prostate cancer
  • Women unaffected with cancer, but with one or more of the following have an increased likelihood of having an inherited predisposition to breast and ovarian, tubal, or peritoneal cancer and should be offered genetic testing:
    –  A first-degree or several close relatives that meet one or more of the aforementioned criteria
    –  A close relative carrying a known BRCA1 or BRCA2 mutation
    –  A close relative with male breast cancer

(Committee on Practice Bulletins–Gynecology, Committee on Genetics, Society of Gynecologic Oncology, 2017).

Clinical Indications for Hereditary (or Germline) Breast and Ovarian Cancer

Clinical indications are different from risk factors.  A risk factor is a variable associated with an increased risk of a disease, such as age, gender, or family history of disease but does not have signs or symptoms of the disease.  In clinical medicine, a clinical indication, unlike a risk factor, is a sign, symptom, laboratory test result, or medical condition, or a combination of these indications, that leads to the recommendation of a treatment, laboratory test, or procedure for a disease or condition.  Risk assessment models for breast cancer use both risk factors and clinical indications to estimate the risk of breast cancer over time and aid in determining the risk of testing positive for pathogenic BRCA1 or BRCA2 variants.  Risk models for breast cancer use combinations of family history as a risk factor (BRCAPRO, Myriad, Claus, Boadicea, or Tyrer Cuzick), hormonal risk factors (Tyrer Cuzick or Gail), and the clinical indications related to pathologic factors such as atypical hyperplasia (Gail) or atypical hyperplasia/lobular carcinoma-in-situ (Tyrer Cuzick).  The Gail model is not appropriate for identifying patients at high risk of hereditary disease, as it only accounts for first-degree female relatives with breast cancer, thereby ignoring male breast cancer, second-degree relatives, ovarian cancer, and paternal family history, all of which are critical in identifying patients for genetic testing. (Clifford et al., 2016).

B.  Diagnosis of Cancer

In most cases, examination of malignant tumors includes sampling the abnormal cells with a biopsy procedure, which may be performed with a needle, endoscope or during surgery.  Clinical laboratory services involve the biological, microbiological, serological, chemical, immunohematological, hematological, biophysical, cytological, pathological, or other examination of materials derived from the human body for the diagnosis, prevention, or treatment of a disease or assessment of a medical condition.

To provide genetic information about the normal or abnormal cells sampled, including genetic alterations (GAs), additional diagnostic tests using specialized techniques may also be performed.

More recently, sequencing technology such as NGS to read the order of nucleotide molecules on DNA has improved to more effectively provide detailed information on multiple types of GAs simultaneously.  The NGS oncology panel tests also provide patients and their providers a more comprehensive genetic profile of cancer and information relevant to potential cancer treatments.  NGS oncology panel tests hold potential for patients and providers in optimizing (personalizing) therapies that target specific characteristics of individual patient cancers.  However, it is important that these tests produce valid results that are useful in guiding therapies to improve outcomes for patients with germline cancer.

NGS-based tests may encompass the following steps: (a) specimen collection, processing, and storage, (b) DNA extraction, (c) DNA processing and library preparation, (d) generation of sequence reads and base calling, (e) sequence alignment/mapping, (f) variant calling, (g) variant annotation and filtering, (h) variant evaluation and assertion, and (i) generation of test report (FDA, 2018).

C.  Clinical Utility

When we have made national coverage determinations for other diagnostic tests, we have considered the evidence to support utility of the diagnostic test in the hierarchical framework of Fryback and Thornbury (1991) where Level 2 addresses diagnostic accuracy, sensitivity, and specificity of the test; Level 3 focuses on whether the information produces change in the physician's diagnostic thinking; Level 4 concerns the effect on the patient management plan and Level 5 measures the effect of the diagnostic information on patient outcomes (for example, overall survival), in this case, in patients with germline (inherited) cancer.

III. History of Medicare Coverage

CMS issued an NCD on March 16, 2018, establishing the first national coverage policy for NGS.  In general, the NCD provides national coverage for diagnostic laboratory tests using NGS that have FDA approval or clearance as a companion in vitro diagnostic for patients with recurrent, relapsed, refractory, metastatic, or advanced cancers, an FDA approved or cleared indication for use in that patient’s cancer, and results provided to the treating physician for management of the patient using a report template to specify treatment options.

Effective for services performed on or after March 16, 2018, the Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, when ordered by a treating physician, and when all of the following requirements are met:

  1. Patient has:
    • either recurrent, relapsed, refractory, metastatic, or advanced stage III or IV cancer; and,
    • either not been previously tested using the same NGS test for the same primary diagnosis of cancer, or repeat testing using the same NGS test only when a new primary cancer diagnosis is made by the treating physician; and,
    • decided to seek further cancer treatment (e.g., therapeutic chemotherapy).
  2. The diagnostic laboratory test using NGS must have:
    • Food & Drug Administration (FDA) approval or clearance as a companion in vitro diagnostic; and,
    • an FDA-approved or -cleared indication for use in that patient’s cancer; and,
    • results provided to the treating physician for management of the patient using a report template to specify treatment options.

Since there is an existing NCD for NGS, this review is a reconsideration of the current policy.  The current policy is codified in section 90.2 of the Medicare National Coverage Determination Manual (Pub. 100-03).  Section 90.2 of the NCD Manual is included in Appendix C.

A.  Current Request

CMS initiated this national coverage determination (NCD) to reconsider the evidence available for NGS tests of germline (inherited) mutations to identify those with inherited cancer who may benefit from targeted treatments based on results of the test. 

B.  Benefit Category

Medicare is a defined benefit program.  For an item or service to be covered by the Medicare program, it must fall within one of the statutorily defined benefit categories as outlined in the Act.  For NGS, the following statute is applicable to coverage:

Under §1861(s)(2)(C) diagnostic services

Under §1861(s)(3) diagnostic laboratory tests, and other diagnostic tests

This may not be an exhaustive list of all applicable Medicare benefit categories for this item or service.

IV. Timeline of Recent Activities


Date Action
April 29, 2019 CMS opens an NCA for Initial 30-day public comment period begins.
May 29, 2019 First public comment period ends.  CMS receives 82 comments
October 29, 2019 Proposed Decision Memorandum posted.  30-day public comment period begins.
November 28, 2019 30-day comment period ends. CMS receives 43 comments.

V.   Food and Drug Administration (FDA) Status

In the United States, NGS tests to diagnose disease or other conditions, a subset of in vitro diagnostic devices (IVD), are considered medical devices by the U.S. Food and Drug Administration (FDA).  Generally, IVDs may be subject to premarket and postmarket controls and categorization under the Clinical Laboratory Improvement Amendments (CLIA '88) of 1988.

At the time of posting of this decision memo, a list of nucleic acid-based tests that have been cleared or approved by the FDA may be found at this link: https://www.fda.gov/medical-devices/vitro-diagnostics/nucleic-acid-based-tests.

VI. General Methodological Principles

In general, when making national coverage determinations under section 1862(a)(1)(A), CMS evaluates relevant clinical evidence to determine whether or not the evidence is of sufficient quality to support a finding that an item or service falling within one or more benefit categories is reasonable and necessary for the diagnosis or treatment of illness or injury or to improve the functioning of a malformed body member.  The evidence may consist of external technology assessments, internal review of published and unpublished studies, recommendations from the Medicare Evidence Development & Coverage Advisory Committee (MEDCAC), evidence-based guidelines, professional society position statements, expert opinion, and public comments.

The critical appraisal of the evidence during a national coverage analysis enables us to determine to what degree we are confident that: 1) the specific assessment of a clinical question relevant to the coverage request can be answered conclusively; and 2) the intervention will improve health outcomes for Medicare beneficiaries.  An improved health outcome is one of several considerations in determining whether an item or service is reasonable and necessary.

A detailed account of the methodological principles of study design that the Agency utilizes to assess the relevant literature on a therapeutic or diagnostic item or service for specific conditions can be found in Appendix A.  In general, features of clinical studies that improve quality and decrease bias include the selection of a clinically relevant cohort, an appropriate comparison group, the consistent use of a single good reference standard, blinding of readers of the index test, and reference test results.

Public commenters sometimes cite the published clinical evidence and provide CMS with useful information.  Public comments that provide information based on unpublished evidence, such as the results of individual practitioners or patients, are less rigorous and of lower quality, and therefore less useful for making a coverage determination.  Public comments that contain personal health information will be redacted or, in some cases, will not be made available to the public.  CMS responds in detail to the public comments on a proposed national coverage determination when issuing the final decision memorandum.

VII. Evidence

A.   Introduction

This section provides a summary of the evidence we considered during our review.  The evidence reviewed to date includes the published medical literature on pertinent clinical research of NGS testing for patients with germline cancers.

B.  Discussion of Evidence

1.   Evidence Question(s)

Our review and analysis of the evidence on the clinical utility of NGS in patients with a germline mutation or inherited cancer is guided by the following question:

  • Does NGS as a diagnostic test, either to detect germline mutations or identify inherited cancers, improve health outcomes for Medicare beneficiaries with inherited cancers?

2.  External Technology Assessments

CMS did not request an external technology assessment (TA) on this issue.

3.  Internal Technology Assessment

Literature Search Methods

We searched PubMed (1965 to current date), the Agency for Healthcare Research and Quality (AHRQ), the Cochrane Collection, and the Institute of Medicine, as well as the source material for commentary, guidelines, and formal evidence-based documents published by professional societies.  Search terms included next generation sequencing (NGS), germline mutation or hereditary cancer, and mortality or survival.  We looked for: 1) studies that used NGS to evaluate the effect of germline mutations or hereditary cancers on mortality, 2) studies that used NGS to identify predictors of germline mutations or hereditary cancers, and 3) studies on clinical utility of NGS in predicting and improving health outcomes including mortality.  Our search terms included "next generation sequencing", "NGS", "multigene panel testing", "massively parallel sequencing", "high-throughput nucleotide sequencing", "germline mutation", "germline cancer", "germline tumor", "hereditary cancer", "inherited cancer", "inherited tumor", "inherited tumour", "outcome", "death", mortality", "fatal outcome", and "survival".  We excluded studies of analytic validity and clinical validity which did not have clinical outcomes.  Because they are not original clinical research studies, we excluded reviews and commentaries.  Molecular mechanistic studies were excluded.  The exclusion criteria included case series with less than 10 patients (n < 10), since these studies lack study power to detect postulated differences between study groups.

We reviewed a total of 24 clinical research studies.  We identified eight prospective cohort studies, seven retrospective historical cohort studies, three single group drug treatment clinical trials, two retrospective case control studies, two retrospective analyses of clinical databases housed in academic institutions, one analysis of a population based prospective longitudinal cohort, and one study of a group of adjuvant clinical trials.  We also reviewed references submitted to us by public commenters and performed a hand search of bibliographies of included articles to identify other pertinent articles.

Blair AB, Groot VP, Gemenetzis G, et al. BRCA1/BRCA2 Germline Mutation Carriers and Sporadic Pancreatic Ductal Adenocarcinoma. J Am Coll Surg. 2018 Apr;226 (4):630-637.e1.

The aim of the retrospective, single institution, case-control study was to investigate the association of BRCA1/BRCA2 germline mutations with survival in resected sporadic pancreatic ductal adenocarcinoma (PDAC), and to investigate the relation of platinum-based adjuvant chemotherapy with the survival of BRCA mutated patients with PDAC.  The study used NGS data from 658 patients, where BRCA1/BRCA2 germline mutated PDAC cases totaled 22 (3%) of cases at a hospital in Baltimore, Maryland, from 2000 to 2015.

The study demographics for the BRCA-mutated patients included median age 61 years, 86% Caucasian, 64% male, and 68% T3 stage.  For BRCA patients, 9% were T1 stage, 23% T2 stage, 68% T3 stage and 0% T4 stage.  The analysis included targeted sequencing that was performed on banked frozen tissue using Ion Torrent Proton platform for known pancreatic cancer susceptibility genes (BRCA2, ATM, PALB2, BRCA1, CDKN2A, MLH1, MSH2, PRSS1, STK11, and TP53), known cancer susceptibility genes (MSH6, PMS2, CDH1, RAD51C, RAD51D, BUB1B, and FANCJ), and candidate pancreatic susceptibility genes (FANCA, FANCC, FANCG, FANCL, ARID1A, RECQL4, XRCC2, XRCC3, ERCC4, TERT, BAP1, BUB1, BUB3, and RNF43).

The study found that BRCA1/BRCA2 mutations were associated with inferior median overall survival (OS) when compared with the matched (by age and tumor location) wild-type control group (20.2 vs 27.8 months, p = 0.034). The median disease-free survival (DFS) was shorter (8.4 vs 16.7 months for wild-type, p < 0.001) when compared with the matched wild-type controls.  Within the BRCA1/BRCA2 mutated group, having had platinum-based adjuvant chemotherapy (n = 10) was associated with better survival than alternative chemotherapy (n = 8) or no adjuvant therapy (n = 4) (31.0 vs 17.8 vs 9.3 months, respectively, p < 0.001).

The authors noted the retrospective study design, self-reporting of family history and treatment heterogeneity as limitations.  The authors concluded that carriers of a germline BRCA1/BRCA2 mutation with sporadic PDAC had a worse overall and disease-free survival after pancreatectomy and platinum-based chemotherapy regimens were associated with markedly improved survival relative to controls.

Brianese RC, Nakamura KDM, Almeida FGDSR, et al. BRCA1 deficiency is a recurrent event in early-onset triple-negative breast cancer: a comprehensive analysis of germline mutations and somatic promoter methylation. Breast Cancer Res Treat. 2018 Feb;167(3):803-814.

The aim of the study was to investigate germline or somatic events that might lead to BRCA1 impairment in triple-negative breast cancer and analyze the clinical implications associated with BRCA deficiency.  This retrospective historical cohort study used tumor tissues from 131 women with triple-negative breast cancer from an unselected cohort of triple-negative breast cancer samples in a biobank at a single institution in Brazil.

The study patients ranged in age from 18 to 87 years old, 93% were Caucasian and 77% had distant metastasis.  Next-generation sequencing for the BRCA1/2 genes using the Ampliseq™ BRCA1 and BRCA2 panel-Ion PGM Torrent, and multiplex ligation-dependent probe amplification (MLPA) for the BRCA1 gene were performed for mutation testing.  Patients diagnosed at 40 years of age or younger were considered to have an early age at diagnosis.

Results of the study revealed that germline variants were detected in 13.0% of all cases and accounted for 94.4% (17/18) of the pathogenic variants.  Hereditary triple- negative tumors were related to BRCA1 (88.2%, 15/17).  BRCA1 impairment by either germline or somatic events was significantly more frequent in young women (55% in those ≤ 40 years; 33% in those 41–50 years; 22% in those > 50 years of age; p = 0.007).  Trends, though not statistically significant, towards better overall survival (p = 0.081) and disease free survival (p = 0.074) were observed in BRCA1-impaired tumors compared with those in BRCA-proficient tumors.  For women with early-onset (diagnosed ≤ 40 years old) triple-negative breast cancer, there was significantly better overall survival (p = 0.046) and close to significantly better disease-free survival rates (p = 0.052) were observed in patients with BRCA1-impaired tumors compared to those in patients with BRCA proficient tumors.

As a limitation, the authors noted the potential influence of the use of clinical surveillance tools to measure the survival of patients with BRCA1 pathological variants.  The authors concluded that BRCA1 deficiency was recurrent in both sporadic and hereditary early onset (diagnosed ≤ 40 years old) triple-negative breast cancer in young Brazilian women and associated with improved survival, with most receiving chemotherapy.

Chen S, Cavazza E, Barlier C, et al. Beside P53 and PTEN: Identification of molecular alterations of the RAS/MAPK and PI3K/AKT signaling pathways in high-grade serous ovarian carcinomas to determine potential novel therapeutic targets. Oncol Lett. 2016 Nov;12(5):3264-3272.

The aim of the study was to identify targets that could provide access to innovative therapy for patients with high-grade serous ovarian carcinomas (HGSOCs).  The retrospective historical cohort study used data from 45 ovarian cancer patients who were treated at a French cancer institute.

The patients’ mean age was 59.1 years (range, 25-87 years), 42% had a family history of cancer, 11% were International Federation of Gynecology and Obstetrics (FIGO) tumor stage I-II, and 89% were FIGO stage III-IV.  All women received cytoreductive surgery and a platinum-based chemotherapy.  Breast cancer 1/2 (BRCA1/2) germline mutations were screened in 17 patients with a familial or personal history of cancer.  Somatic mutations of KRAS, NRAS, B-Raf, PIK3CA and MET were screened as putative sources of RAS/MAPK and PI3K/AKT signaling using NGS with Amplicon Variant Analyzer software on frozen tumor specimens obtained at diagnosis.

The results of the study revealed that seven BRCA germline mutations were identified in 17 patients tested due to a familial and/or personal history of ovarian or breast carcinoma.  The two-year progression free survival (PFS) rate was 28% (range, 16-42%) and five-year overall survival (OS) rate was 37% (range, 21-53%).  There was a trend for a longer PFS among patients belonging to the subgroup with a personal history of breast cancer (HR, 0.319; 95% CI, 0.097-1.045, p = 0.0592) or BRCA germline mutations (HR, 0.321; 95% CI, 0.098-1.054, p = 0.0610).  In the multivariate Cox proportional hazard model regression analysis, P53 overexpression (HR, 0.269; 95% CI, 0.102-0.708, p = 0.0078) and a personal history of breast cancer (HR, 0.168; 95% CI, 0.035-0.809, p = 0.0261) compared to not having the risk factor, were identified as predictive factors of a longer OS.

The authors acknowledged the limitation of a small sample size and concluded that in HGSOCs somatic genetic abnormalities can be detected using NGS as predictive markers for stratifying patients for appropriate therapy and provide molecular rationale for targeted therapies, potentially offering novel therapeutic opportunities to patients.

Deng M, Chen HH, Zhu X, et al. Prevalence and clinical outcomes of germline mutations in BRCA1/2 and PALB2 genes in 2769 unselected breast cancer patients in China. Int J Cancer. 2019 Feb 5 doi: 10.1002/ijc.32184. PMID: 30720863.

The aim of the study was to explore the effect of BRCA1/2 and PALB2 mutation status on clinical outcomes in patients with breast cancer.  The historical cohort study used data from a consecutive series of 2,769 ethnic Chinese women with breast cancer unselected for age at diagnosis or family history of breast cancer.  Analysis of blood samples from a DNA research bank in Zhejiang Province, China, included all of the exons and exon–intron boundaries of the BRCA1/2 and PALB2 detected with an Illumina HiSeq X10 Next Generation Sequencing Platform.  Early-onset breast cancer (EBC) was defined as breast cancer patients who were diagnosed with breast cancer at less than or equal to 40 years of age.

The mean age of BRCA1 carriers was 45.6 years (SD 9.5 years) and of BRCA2 carriers 45.2 years (SD 9.7 years).  Among BRCA1/2 carriers, 36.1% were Stage 1, 37.5% Stage 2, 23.6% Stage III, and 0.7% were Stage IV.  Among BRCA1/2 carriers, 83.4% received adjuvant therapy.  Results of the study revealed that BRCA1, BRCA2 and PALB2 mutations accounted for 2.7% (n = 74), 2.7% (n = 76), and 0.9% (n = 24), respectively.  The disease-free survival (DFS) of BRCA1 mutation carriers was statistically significantly lower than that of noncarriers (adjusted hazard ratio [HR] = 2.20, 95% confidence interval [CI] = 1.15–4.18, p=0.017).  No statistically significant difference was found for overall survival between BRCA1 (p=0.802) or BRCA2 (p=0.818) pathogenic mutation carriers and noncarriers.  In the early-onset breast cancer subgroup, in a univariable analysis, BRCA1 mutation carriers showed a notably worse DFS than noncarriers (HR = 2.44, 95% CI = 1.15–5.17, p = 0.020).  However, after adjusting for other prognostic features, there was no statistically significant difference in mortality between BRCA1 carriers and noncarriers (HR = 1.93, 95% CI = 0.58–6.36, p = 0.282).

Limitations included a short median follow up and that most cases were from eastern China.  The authors concluded that BRCA1 germline mutation status may be associated with a worse disease progression in patients with breast cancer, but risk of death was not different for BRCA1 or BRCA2 carriers compared to noncarriers.

de Souza Timoteo AR, Gonçalves AÉMM, Sales LAP, et al. A portrait of germline mutation in Brazilian at-risk for hereditary breast cancer. Breast Cancer Res Treat. 2018  Dec;172(3):637-646.

The aim of the study was to determine the clinical and molecular characteristics of germline mutations in patients at-risk for hereditary breast cancer, in a cohort study of patients referred to a hospital-based oncogenetic counseling service in Natal, Brazil.  Massively parallel sequencing (an all-in-one approach to sequencing) by the BROCA Test was applied to peripheral blood in 157 individuals, of whom 132 had breast cancer and 25 had a familial history of breast cancer, but did not have a diagnosis of cancer, selected according to National Comprehensive Cancer Network (NCCN) criteria for hereditary breast cancer.  The breast cancer affected population consisted of 131 women and one male patient. Genome-wide association studies (GWAS) were performed using TruSight Cancer Sequencing Panel or DNA sequencing was performed using the Ion PGM platform.  Mean age of the study population was not reported.

Results of the study revealed that 27 of the 157 patients had a germline mutation (27/157; 19.4%).  Nineteen germline variants were identified, 15 pathogenic and 4 VUS (Variants of Uncertain Significance) in 27 individuals (27/157; 17%, p< 0.0001) distributed among 7 genes, including BRCA1 (7/19; 37%) and BRCA2 (6/19; 31%) and 32% of the mutations were in moderate-risk genes ATM (2/19; 10.5%); and ATR; CDH1; MLH1 and MSH6 (1/19 and 5.4% each one). Cancer-affected patients with moderate- risk mutations presented a more aggressive phenotype, such as the bilateral cancer (25% vs. 13%, p=0.0305), high-grade tumors (79.2% vs. 46.3%, p=0.0001) and triple negative (lack of the expression of estrogen receptor, progesterone receptor and growth factor HER2) (50% vs. 22.4%, p<0.0001) phenotypes when comparing those with germline mutations to those without a mutation.  No difference in overall survival (OS) between those negative (n=73) and positive (n=20) for a germline mutation was observed (odds ratio [OR] 0.38, 95% confidence interval [CI] − 0.09 to 1.6, P =0.19), nor when comparing BRCA mutation patients (n=16) versus moderate- risk genes patients (n=4) (OR 0.59, CI 0.08–4.23, p=0.60).

The authors concluded that their work highlighted the main concern with using NGS to manage moderate-risk and VUS patients because limited guidelines are available.  However, as no difference in the five-year overall survival was observed between BRCA and moderate risk groups, the authors stated that selection of appropriate candidates for genetic testing must be based on the personal and familial characteristics that determine the individual’s prior probability of being a mutation carrier, and the potential benefits, limitations, and risks of genetic testing.

Fan C, Zhang J, Ouyang T, Li J, et al. RAD50 germline mutations are associated with poor survival in BRCA1/2-negative breast cancer patients. Int J Cancer. 2018 Oct 15;143(8):1935-1942.

The aim of the study was to investigate the clinical impact of RAD50 germline mutations in a large cohort of unselected breast cancer patients treated at a breast center hospital in Beijing, China.  RAD50 germline mutations were determined using next-generation sequencing on the blood of 7657 consecutive ethnic Chinese women with breast cancer (70.6% were Grade II).  The mean are of the patients was 51 years (range 19-98) years without BRCA1/2 mutations, and 73.1% were treated with either chemotherapy or endocrine therapy.  Sequencing was performed on a HiSeq 2500 platform.  A group of 5,000 healthy women served as the healthy controls.  These healthy controls came from the same geographical region as the studied patients.

Results of the study revealed that 26 out of 7,657 (0.34%) patients had RAD50 pathogenic mutations.  These mutations did not confer an increased risk of breast cancer in the studied patients compared to healthy controls (0.21% vs, 0.18%; odds ratios [OR], 1.16; 95% confidence interval [CI], 0.51–2.63; p = 0.72], however, multivariate analysis revealed that RAD50 pathogenic mutations were an independent unfavorable predictor of recurrence-free survival (RFS) (adjusted hazard ratio [HR] 2.66; 95% confidence interval [CI], 1.18–5.98; p = 0.018) and disease-specific survival (DSS; adjusted HR 4.36; 95% CI, 1.58–12.03; p = 0.004) comparing RAD50 carriers to non- carriers in the entire study cohort.

The limitations acknowledged by the authors included bias in study site selection in that the study population was hospital-based and follow-up in that the follow up was only for 50 months.  The authors concluded that RAD50 germline mutations were not associated with an increased risk of breast cancer, but suggests that breast cancers carrying a RAD50 mutation have an aggressive phenotype and carriers may be potential candidates for treatment with PARP inhibitors.

Golan T, Raitses-Gurevich M, Kelley RK, et al. Overall Survival and Clinical Characteristics of BRCA-Associated Cholangiocarcinoma: A Multicenter Retrospective Study. Oncologist. 2017 Jul;22(7):804-810.

The aim of this study was to define the clinical characteristics of germline and somatic BRCA1/2 variants in cholangiocarcinoma (CCA) patients.  The authors performed a multicenter retrospective analysis of a historical cohort from clinical databases of 18 CCA patients with mean age 60 (range 36-75 years) years old diagnosed between January 2000 and December 2013.  Study demographics included males (n=11, 61.2%) and females (n=7. 38.8%), majority Caucasian, with 61% being Stage III or IV cancer.  Stage at diagnosis was I (n=4), II (n=3), III (n=3), and IV (n=8).  The analysis included detection of mutations by tumor tissue NGS according to each institution’s laboratory practice or at Foundation Medicine.  Results of the study identified five carriers of germline BRCA1/2 mutations and 13 somatic variations (7 BRCA1, 6 BRCA2).  Thirteen (72.2%) patients received platinum based therapy and four (22.2%) were treated with PARP inhibitors.  Median overall survival from diagnosis for patients at stages I/II was 40.3 months (95% confidence interval [CI], 6.73–108.15) and at stages III/IV was 25 months (95% CI, 15.23–40.57; no hazard ratio or p value shown).  Treatment resulted in a favorable response, with one patient’s overall survival censored at 64.76 months and a progression free survival (PFS) of 42.6 months.

Patients bearing either known pathogenic mutations or unknown variants and who were treated demonstrated more favorable OS, ranging from 11.01 to 64.78 months.  The authors acknowledged that the limitations of this study, including small sample size, retrospective study design, and the nondifferentiation between clearly pathogenic and VUS, made conclusions tentative.  The authors concluded that BRCA-associated CCA is uncommon, but suggests somatic and/or germline BRCA genotyping in all patients diagnosed with CCA.

Hjortkjær M, Malik Aagaard Jørgensen M, Waldström M, et al. The clinical importance of BRCAness in a population-based cohort of Danish epithelial ovarian cancer. Int J Gynecol Cancer. 2019 Jan;29(1):166-173.

The aim of the study was to analyze the distribution of homologous recombination deficiency in epithelial ovarian carcinoma caused by mutations in a panel of homologous recombination genes, including BRCA1/2.  The authors assessed 380 women with ovarian cancer for germline and somatic mutations in 18 different homologous recombination genes, including BRCA1 and BRCA2, using NGS by the MiSeq Illumina platform on tumor tissue specimens, as part of a historical cohort from a population based Danish registry.  The Danish Gynecologic Cancer Database is a nationwide registry, which files all diagnoses and related clinicopathology of gynecologic cancer cases.

Overall, 62.9% of the patients were >60 years of age at the time of diagnosis with median age 64 years (range 20 – 94 years) with serous adenocarcinomas (74.5%) and FIGO stage II (52.8%).  The cohort consisted of 24.8% International Federation of Gynecology and Obstetrics (FIGO) stage I, 9.0% stage II, 52.8% stage III, and 13.4% stage IV.  Patients were treated with standard surgical tumor debulking and chemotherapy.  Results of the study revealed that 17% of all patients with epithelial ovarian carcinoma carried a germline (9.8%, 37 patients) and/or somatic (6.3%) homologous recombination mutation in 12 (BRCA1, BRCA2, CHEK2, ATM, RAD51D, EMSY, PALB2, BRIP1, ERCC1, RAD50, ATR, RAD51C) of 18 sequenced homologous recombination genes. Germline BRCA1/2 mutation was associated with better overall survival (median 7.4 years, 95% confidence interval [CI] 4.0 to 10.0) compared with 3.0 years (95% CI 1.8 to 5.0, p=0.047) for those with other homologous recombination mutations, including somatic BRCA1/2 mutations, but this was not confirmed in multivariate analysis.  Ninety one of 380 patients (23.9%) were considered homologous recombination deficient and expressed the BRCAness phenotype.

The BRCAness phenotype was associated with improved overall survival in the high-grade serous carcinoma subgroup with a median overall survival of 4.4 years (95% CI 3.0 to 5.3) compared to 2.2 years (95% CI 1.9 to 2.4, p=0.0002) for the BRCAness wild type.  Multivariate analysis confirmed an independent prognostic value of the BRCAness phenotype compared to the wild type negative BRCAness phenotype among the high-grade serous carcinoma subgroup, hazard ratio 0.65 (95% CI 0.47 to 0.92, p=0.014).

As a limitation, the authors acknowledged that the subjects in their study were not selected for familial predisposition to epithelial ovarian cancer or hereditary breast cancer.  The authors concluded that the treated germline BRCA1/2 mutation group had the largest improvement in overall survival compared with subjects without or with other homologous recombination mutations. The BRCAness phenotype was associated with a significantly better overall survival in the treated high-grade serous carcinoma subgroup compared with wild type patients.  This suggests that homologous recombination deficiency is a favorable prognostic marker in addition to a potential indicator of possible sensitivity to PARP inhibitors.

Kotoula V, Fostira F, Papadopoulou K, et al. The fate of BRCA1-related germline mutations in triple-negative breast tumors. Am J Cancer Res. 2017 Jan 1;7(1):98-114.

The aim of the study was to compare germline and tumor genotypes in operable triple-negative breast cancer (TNBC) and evaluate their combined effects on prognosis upon anthracyclines-taxanes-based adjuvant chemotherapy.  The study used data from 196 TNBC women with breast cancer who had been treated during 1997-2012 in adjuvant clinical trials by the Hellenic Cooperative Oncology Group (HeCOG), i.e., HE 10/97, HE 10/00, HE 10/04A, HE 10/04B, HE 10/05, HE 10/08, HE 10/10, or had been treated with taxanes-based adjuvant chemotherapy in HeCOG affiliated clinical centers.  The adjuvant trials consisted of three Phase III trials, two feasibility studies, and two observational studies with each patient study arm receiving different drug treatment schedules without randomization.  The patients had a mean age 51.4 ± 12.6 years and majority were histological grade III (85.6%).  Patients were treated from 1997 to 2012 in adjuvant clinical trials. Patients also were histological grade I or II (14.4%) or III (85.6%).  The authors analyzed baseline germline and primary tumor genotype data obtained by Sanger and next generation sequencing on tissue blocks and peripheral blood from 194 TNBC patients.  Results of the study identified 50 (26%) germline mutation carriers (78% in BRCA1 and 8% in BRCA2) and 136 (71%) tumors with somatic mutations (83% in TP53).  Germline mutation status statistically significantly interacted with TP53 mutations for patient disease-free survival since in germline carriers, relapses were noticed in 9/25 (36%) patients with TP53 mutated tumors but in only 2/22 (9%) patients with TP53 wild-type tumors, with the interaction being statistically significant (interaction P=0.0266).  The authors acknowledged the limitation of small sample sizes within patient subgroups, and concluded that standard adjuvant treatment benefits germline carriers with TP53 wild-type tumors, while germline carriers with TP53 mutated tumors may need a different type of treatment.

Lang GT, Shi JX, Hu X, et al. The spectrum of BRCA mutations and characteristics of BRCA-associated breast cancers in China: Screening of 2,991 patients and 1,043 controls by next-generation sequencing. Int J Cancer. 2017 Jul 1;141(1):129-142.

The aim of the study was to characterize the prevalence of BRCA1 and BRCA2 mutations and update the clinical recommendations for BRCA testing.  Breast cancer patients with any one of the five following risk criteria were assigned to risk groups in the present study: (i) pathological diagnosis of triple-negative breast cancer (TNBC),(ii) male breast cancer (n=46), (iii) primary bilateral breast cancers in one individual, regardless of synchrony or asynchrony, (iv) early-age onset breast cancer (less than or equal to 40 years of age at diagnosis), and (v) patients with a family history of breast and/or ovarian cancer (at least one first- and/or second-degree relative with breast cancer or ovarian cancer).  For the prospective cohort study, all the cases were collected from three medical centers in China.  All 4,034 ethnic Chinese cases were collected from a wide screen for BRCA mutations using an NGS-based approach that they developed to perform BRCA1/2 screening on samples.  The BRCA1/2 mutation carriers were significantly younger than noncarriers (mean age, carriers vs. non-carriers, 45.4 vs. 47.3 years, p = 0.029).

Results of the study revealed that BRCA mutations were identified in 9.1% (232/2,560) of cases with at least one risk factor, in 3.5% (15/431) of sporadic patients and in 0.38% (4/1,043) of community-based healthy Chinese controls.  The prevalence of BRCA1 and BRCA2 mutations in the entire breast cancer cohort were 3.7 and 4.5%, respectively.  Clinical characteristics such as family history, invasive carcinoma, negative HER2, high Ki67 index, lymph node status, and high tumor grade were closely related to presence of BRCA mutations (p < 0.05).  Compared to non-carriers, germline BRCA1/2 carriers was statistically significantly associated with higher stage (p = 0.022) and presence of family history of breast cancer (p < 0.001).  There were no significant differences in disease-free survival (DFS) between the BRCA carriers and non-carriers (hazard ratio [HR] = 1.220, 95% confidence interval [CI]: 0.820–1.815, p = 0.324).  The authors acknowledged that the median follow-up and the observed events in their study were both low, and concluded that BRCA mutation carriers could be frequently identified among Chinese breast cancer patients with multiple risk factors.  They failed to demonstrate distinct disease free survival between BRCA associated and non-BRCA-associated breast cancer patients in both univariable and multivariable analyses.

Lin KK, Harrell MI, Oza AM, et al. BRCA Reversion Mutations in Circulating Tumor DNA Predict Primary and Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma. Cancer Discov. 2019 Feb;9(2):210-219.

The aim of the study was to estimate the prevalence of BRCA reversion mutations in germline BRCA mutation carriers with high-grade ovarian carcinoma (HGOC).  The authors performed NGS using the Illumina HiSeq platform on circulating cell-free DNA (cfDNA) from blood plasma samples.  Women with HGOC were enrolled in the open-label, single group assignment, drug treatment phase II study of rucaparib in relapsed high-grade ovarian carcinoma (HGOC) in the ARIEL2 trial (NCT01891344).  ARIEL2 is an international, multicenter, single group assignment, two-part, phase 2, open-label study done at 49 hospitals and cancer centers in Australia, Canada, France, Spain, the United Kingdom, and the United States to assess rucaparib sensitivity. The patients (n=112) had a median age of 60.5 years (range, 33 – 82 years), while 63.4% had a germline BRCA mutation and a median of three prior chemotherapy regimens (range, 1–4 regimens).  Results of the study revealed BRCA-mutant patients without BRCA reversion mutations detected in pretreatment cfDNA had statistically significantly longer median progression-free survival after rucaparib than those with reversion mutations (median, 9.0 vs. 1.8 months; hazard ratio [HR], 0.12; 95% confidence interval [CI], 0.05–0.26; P < 0.0001).  The authors concluded that this type of minimally invasive assay can efficiently detect BRCA reversion mutations that predict resistance to PARP inhibitors and may provide information on tumor heterogeneity.

Mitchell G, Ballinger ML, Wong S, et al. High frequency of germline TP53 mutations in a prospective adult-onset sarcoma cohort. PLoS One. 2013 Jul 22;8(7):e69026.

The aim of the study was to determine the incidence and clinical spectrum of germline TP53 mutations in adult-onset sarcoma populations.  This study used data from the International Sarcoma Kindred Study (ISKS), a clinic-based, prospective cohort of 559 consecutively recruited adult-onset sarcoma cases and families, 84% Caucasian, 47% women and median age 36 years (range 16 to 68 years) without regard to family history.  The analysis method of TP53 used high-resolution melting analysis, Sanger sequencing, and multiplex ligation-dependent probe amplification with targeted massively parallel sequencing for copy number changes.  Results of the study revealed pathogenic TP53 mutations were detected in blood DNA in 20/559 sarcoma probands (3.6%); 17 were germline and 3 appeared to be somatically acquired.  Germline mutation carriers were more likely to have multiple cancers (47% vs 15% for non-carriers, P = 0.003), and earlier cancer onset (33 vs 48 years, P = 0.00119).  The overall survival of carriers was not statistically significantly different from non-carriers (HR 1.02, 95% CI 0.36–2.89, Mantel-Cox P = 0.97).  Only 10/17 (59%) of the germline carriers met classical or Chompret criteria for Li-Fraumeni Syndrome (LFS).  No limitations were reported by the authors. The authors concluded that germline TP53 mutations are not rare in adult patients with sarcoma, which has implications for cancer treatment in carriers.

Norquist BM, Pennington KP, Agnew KJ, et al. Characteristics of women with ovarian carcinoma who have BRCA1 and BRCA2 mutations not identified by clinical testing. Gynecol Oncol. 2013 Mar;128(3):483-7.

The aim of the study was to compare clinical characteristics and outcomes of women with ovarian cancer whose BRCA1/2 mutations were identified through routine clinical care to those who were identified only though the research protocol.  This historical cohort study used data from women with ovarian, tubal or peritoneal carcinoma who were retrospectively identified from an IRB-approved gynecologic oncology tissue bank clinical database at one institution in the State of Washington.  The analysis method included the BROCA assay using targeted capture and massively parallel sequencing to identify mutations in BRCA1/2 and 19 other tumor suppressor genes.

Subjects were divided into three groups: 1) "known": those with known BRCA1/2 mutations identified through standard commercial testing at any time during their clinical care, 2) "BROCA": those with BRCA1/2 mutations identified by BROCA testing and not previously identified clinically, and 3) "wildtype": ovarian carcinoma patients without inherited loss of function mutations on BROCA testing including BRCA1/2 and 19 other tumor suppressor genes.

Among the BROCA BRCA1/2 group (n = 37), the median age was 58 years (range 41 – 77 years), 24.3% had neooadjuvant chemotherapy, and 0% were FIGO (The International Federation of Gynecology and Obstetrics) stage I, 2.8% stage II, 62.2% stage III, and 35.1% stage IV.  Among the known BRCA1/2 group (n = 70), the median age was 51 years (range 33 – 76 years), 15.2% had neooadjuvant chemotherapy, and 5.7% were FIGO (The International Federation of Gynecology and Obstetrics) stage I, 5.7% stage II, 72.9% stage III, and 15.7% stage IV.  The wild type group consisted of 291 individuals with a median age of 62 years (range: 29-91 years).

Results of the study revealed 107 BRCA1/2 mutation carriers with ovarian carcinoma and an additional 37 patients with BRCA1/2 mutations were identified through BROCA sequencing in patients that had not undergone commercial testing during their clinical care.  Median overall survival was statistically significantly worse for BROCA mutation carriers compared to known mutation carriers, (45 vs. 93 months, p<0.0001; hazard ratio [HR] 3.47 95% CI 1.79–6.72, Log-rank test).  Using Cox proportional hazards modeling in mutation carriers including the covariates age at diagnosis, platinum resistance, stage, debulking status, presence of high-grade serous histology, and genetic testing status (known vs. BROCA); only platinum resistance (relative risk [RR] 3.06, 95% CI=1.41–6.21, p=0.006) and stage IV disease (RR 2.85, 95% CI=1.31–6.18, p=0.009) were independent predictors of worse survival.  Overall survival was similar between BROCA mutation carriers and wildtype women.  For limitations, the authors acknowledged that their study did not assess cost, access to genetic counseling, lack of physician referral, or patient refusal of referral or testing.  The authors concluded that older age, absence of a strong family history, and poor survival are all associated with decreased clinical identification of inherited BRCA1/2 mutations in women with ovarian cancer.

Pastorino S, Yoshikawa Y, Pass HI, et al. A Subset of Mesotheliomas with Improved Survival Occurring in Carriers of BAP1 and Other Germline Mutations. J Clin Oncol. 2018 Oct 30:JCO2018790352.

The aim of the study was to test the hypothesis that germline BAP1-inactivating mutations (BAP1+/-) or other genes could help identify malignant mesotheliomas (MMs).  This study used data from 79 MM patients.  In this cohort study, the authors offered free testing to patients in three university medical centers, two in the US and one in Japan.  Study demographics included mean age of 51.7 years, 58% women, and 95% white.  The analysis method sought BAP1 mutations by targeted next-generation sequencing (tNGS) using an Illumina Truseq workflow on saliva or peripheral blood, and germline mutations in 55 additional cancer linked genes.  Deleterious mutations detected by tNGS were validated by Sanger sequencing.  This study found that of the 79 patients, 43 had deleterious germline BAP1 mutations.  Among those with BAP +/- the median age at diagnosis was 54 years and median survival was 5 years compared to BAP +/+ with median age at diagnosis was 45 years and median survival 9 years. Patients with MMs in the Surveillance, Epidemiology, and End Results (SEER) cohort having median age at diagnosis 72 years, median survival 8 months, and stage I were significantly different from the 79 patients with MM in the current study (P < 0.0001).

The authors acknowledged several limitations, including recall bias and the low statistical power.  The authors concluded that patients with BAP1 mutations had a worse survival than those with no BAP1 mutations.  Most of these patients were not aware of asbestos exposure and carried either pathogenic germline mutations of BAP1 or of additional genes linked to cancer, some of which may have targeted-therapy options.

Perdomo-Pantoja A, Mejía-Pérez SI, Reynoso-Noverón N, et al. Angiotensinogen rs5050 germline genetic variant as potential biomarker of poor prognosis in astrocytoma. PLoS One. 2018 Nov 1;13(11):e0206590.

The aim of the study was to determine the relationship between the human angiotensinogen (AGT) rs5050 genetic germline variant in blood and prognosis in astrocytoma.  This study used data from 48 adult newly diagnosed astrocytoma patients.  The prospective cohort study enrolled astrocytoma patients who received the standard-of-care treatment in a single tertiary referral center in Mexico.  Study demographics included mean age 49.1 (range 22–79) years, 58.3% WHO Grade IV, and 50% females.  For World Health Organization (WHO) Grade, 31.3% were Grade II, 10.4% Grade III, and 58.3% Grade IV.  The analysis method included next-generation sequencing using Ion Torrent platform and reporter software.

Results of the study revealed mean survival 14.8 (range 1–50) months and median follow-up of 41 (range 1–48) months.  Bivariate analysis showed a statistically significant difference between the survival status comparing genotypes (hazard ratio [HR] 0.130, 95% confidence interval [CI] 0.03-0.62, p = .011 and HR 0.152, 95% CI 0.03-0.70, p = .016, respectively).  In multivariate analyses, GG-genotype was negatively associated with survival.  After adjustment, AGT rs5050 genotype remained an independent risk factor for survival with an adjusted HR of 1.000 (95% CI not reported), 0.009 (95% CI 0.00–0.09, p<.001) and 0.02 (95% C.I. 0.00–0.17, p <.001), for GG-, TG- and TT-genotypes, respectively.  For limitations, the authors acknowledged the relatively small sample size, that the study was performed in a single tertiary referral center which is entirely dedicated to diseases of the nervous system, that the population of the study was composed of Mexicans, and that the patient had to cover the cost of their drug treatment.  The authors concluded that in patients with astrocytoma, AGT rs5050 GG-genotype was associated with poor prognosis, giving the clinician an additional tool for the pursuit of a personalized prognosis for these patients.

Swisher EM, Lin KK, Oza AM, et al. Rucaparib in relapsed, platinum-sensitive high-grade ovarian carcinoma (ARIEL2 Part 1): an international, multicentre, open-label, phase 2 trial. Lancet Oncol. 2017 Jan;18(1):75-87.

The aim of the study was to assess the ability of tumor genomic loss of heterozygosity (LOH), quantified with a next-generation sequencing assay, to predict response to rucaparib.  This study used data from ARIEL2, an international, multicenter, single group assignment, two-part, phase 2, open-label drug treatment study done at 49 hospitals and cancer centers to assess rucaparib sensitivity.  Women with recurrent, platinum-sensitive, high-grade ovarian carcinoma were classified on the basis of tumor mutational analysis.  The Foundation Medicine T5 next-generation sequencing assay was used to calculate the percentage of genomic LOH in archival and pretreatment tumor tissue biopsies.  Median age of the individuals with BRCA mutants was 58.5 years (interquartile range 53.5-67.5 years).  Results of the study revealed that 204 patients had received rucaparib with median duration of treatment 5.7 months (interquartile range [IQR] 2.8–10.1 months).  Median progression-free survival after rucaparib treatment was 12.8 months (95% confidence interval [CI] 9.0–14.7) in the BRCA mutant subgroup, 5.7 months (5.3–7.6) in the LOH high subgroup, and 5.2 months (3.6–5.5) in the LOH low subgroup.  Progression-free survival was significantly longer in the BRCA mutant (hazard ratio [HR] 0.27, 95% CI 0.16–0.44, p<0.0001) and BRCA wildtype LOH high (HR 0.62, 0.42–0.90, p=0.011) subgroups compared with the BRCA wildtype LOH low subgroup. The authors acknowledged the limitation that the homologous recombination deficiency assay was only prognostic; therefore, the predictive ability of the biomarker will need to be confirmed in the setting of a larger randomized study.

The authors concluded that the proportions of rucaparib-treated patients who achieved responses were similar between patients with a somatic or germline BRCA mutation and with a BRCA1 or BRCA2 mutation.  The results suggest that assessment of tumor LOH can be used to identify patients with BRCA wildtype platinum-sensitive ovarian cancers who might benefit from rucaparib, extending the potential usefulness of PARP inhibitors in the treatment setting.

Toomey S, Madden SF, Furney SJ, et al. The impact of ERBB-family germline single nucleotide polymorphisms on survival response to adjuvant trastuzumab treatment in HER2-positive breast cancer. Oncotarget. 2016 Nov 15;7(46):75518-75525.

The aim of the study was to determine the frequency of germline ERBB-family single nucleotide polymorphisms (SNPs) in women with HER-2+ breast cancer by NGS and correlate their genotype with the progression of HER2+ breast cancer and trastuzumab response.  This study used data from 122 patients with operable primary breast cancer and 72 patients from the TCHL study (NCT01485926) which was conducted in Ireland.  The cohort study TCHL (NCT01485926) was a single group Phase II neo- adjuvant study assessing TCH (docetaxel, carboplatin and trastuzumab) and TCHL (TCH and lapatinib) in early-stage HER-2 positive BC.

The study demographics included mean age 51 years, and majority Grade III (34%) or unknown (43%) with 2% Grade I, 21% Grade II, and 34% Grade III.  The analysis method included NGS using an Illumina MiSeq Sequencer, and mass spectrometry-based genotyping using an Agena MassArray to screen 10 ERBB-family single nucleotide polymorphisms (SNPs) in tumor samples.  Results identified 10 individual common ERBB-family SNPs present in at least two samples among 194 HER2+ patients.  SNPs in EGFR genes had a significant association with relapse free survival (RFS) and overall survival (OS).  Patients with the minor allele of EGFR N158N had significantly worse OS (adjusted hazard ratio [HR] = 4.01, (confidence interval [CI]) = 1.53– 10.69, p = 0.05; % for confidence interval not shown), after correcting for multiple testing, relative to those with either the heterozygous or wild-type (WT) allele.  Multivariate analysis of the impact of adjuvant trastuzumab on RFS in the EGFR SNP T903T was still significant when adjusted for ER status, tumor grade and age (HR = 6.51, CI = 1.98– 21.36, p = 0.01; % for CI not shown). The impact of EGFR- T903T on RFS survival did not extend to a significant benefit in OS.

The authors concluded that specific germline ERBB-family SNPs may play an important role in how a patient responds to adjuvant trastuzumab.

Wang YA, Jian JW, Hung CF, et al. Germline breast cancer susceptibility gene mutations and breast cancer outcomes. BMC Cancer. 2018 Mar 22;18(1):315.

The aim of the study was to clarify the prognostic value of BRCA and other breast cancer susceptibility germline gene mutations on hereditary breast cancer specific outcomes after conventional cancer treatment.  This study used data from a prospective cohort of 480 ethnic Chinese individuals in a Taiwanese cancer center with at least one of the six clinical risk factors for hereditary breast cancer, with the majority (44.1%) at Stage II. The six risk factors were family history of breast or ovarian cancer at any age (2 or more individuals on the same lineage of the family), personal history of breast cancer with age of diagnosis less than or equal to 40, bilateral breast cancer diagnosed at the same time or sequentially, triple negative (ER/PR/HER2 negative) breast cancer, breast and ovarian cancer in the same individual, and male breast cancer (n=6). The mean age of onset for breast cancer was 41.8 (range 17–82).

The analysis method included germline mutations in 20 breast cancer susceptibility genes, including BRCA1, BRCA2, PTEN, TP53, CDH1, STK11, NF1, NBN, MLH1, MSH2, MSH6, PMS2, ATM, BRIP1, CHEK2, PALB2, RAD50, BARD1, RAD51C, and RAD51D, using NGS-based techniques on an Illumina MiSeq platform from whole blood or frozen buffy coat samples.  Among those with BRCA mutation, 23.5% were Stage 1, 44.1% Stage 2, 23.5% Stage 3, and none were Stage 4. The study found a 13.5% carrier rate of pathogenic germline mutations, with BRCA2 being the most prevalent (52.3%) and the non-BRCA genes accounting for 38.5% of the mutation carriers.

The five-year disease-free survival was 73.3% for BRCA mutation carriers and 91.1% for non-carriers (hazard ratio for recurrence or death 2.42, 95% confidence interval [CI] 1.29–4.53; p = 0.013). After adjusting for clinical prognostic factors, BRCA mutation remained an independent poor prognostic factor for cancer recurrence or death (adjusted hazard ratio 3.04, 95% CI 1.40–6.58; p= 0.005). Overall survival at five years was 96.4% among BRCA mutation carriers, as compared with 100% among non- carriers (hazard ratio for death 1.84, 95% CI 0.52–6.54; p = 0.35).  The authors acknowledged that they did not conduct experiments to detect large genome rearrangement (LGR) in all study participants, and were conservative in classifying variants as pathogenic and limited those to protein truncating variants, which were without ambiguity in assignment of pathogenicity.

The authors concluded that BRCA mutation carriers had breast cancer specific outcomes that were significantly worse after adjusting for clinical prognostic factors, suggesting BRCA mutation to be an independent factor for poor prognosis.

Wong A, Kuick CH, Wong W, et al. Mutation spectrum of POLE and POLD1 mutations in South East Asian women presenting with grade 3 endometrioid endometrial carcinomas. Gynecol Oncol. 2016 Apr;141(1):113-20.

The aim of this study was to determine the mutation spectrum of somatic and germline POLE and POLD1 gene mutations.  This retrospective cohort study used data from 47 women diagnosed with The International Federation of Gynecology and Obstetrics (FIGO) grade 3 endometrioid endometrial carcinomas (ECs) at a single Singapore hospital were identified from a tissue repository database.  The analysis method included NGS using Ion Torrent PGM to sequence tumor and matched normal tissue.  Among the 45 patients with pathogenic POLE mutation, the median age was 57 years (interquartile range: 52 – 62 years), and 20% were FIGO stage 1A, 33.3% stage 1B, 13.3% stage II, 22.2% stage III, and 11.1% stage IV.

The study found that pathogenic POLE (somatic or germline) and POLD1 (germline) mutations were detected in 29.7% (14/47) and 4.3% (2/47) of patients, respectively.  Nine patients (19%) experienced disease recurrence or had died of the disease at the time of analysis did not harbor pathogenic POLE or POLD1 gene mutation.  All the patients with POLE and/or POLD1 pathogenic mutations were still alive at the time of analysis with no evidence of recurrence.  The three-year relapse free survival (RFS) for wild-type POLE and POLD1 patients was 72% (95% confidence interval [CI]: 52.9% to 84.3%; median follow-up: 53 months; range: 37 to 69 months) compared to 100% (median follow-up: 46 months, range: 9 to 78) for the group of patients with POLE and/or POLD1 mutation (p=0.03).

The authors acknowledge the limitation of having a small sample size and concluded that mutations in pathogenic POLE and POLD1 in South East Asian women with grade 3 endometrioid ECs are associated with improved recurrence free survival than their wild-type counterparts.

Yap YS, Munusamy P, Lim C, et al. Breast cancer in women with neurofibromatosis type 1 (NF1): a comprehensive case series with molecular insights into its aggressive phenotype. Breast Cancer Res Treat. 2018 Oct;171(3):719-735.

The aim of the study was to further characterize the molecular profile of neurofibromatosis type 1 (NF1, or von Recklinghausen disease)-associated breast cancers.  This study used data from 18 women with NF1 and breast cancer, the majority (38.9%) with stage 3 or 4 at diagnosis identified retrospectively from hospital records and prospectively when managed at National Cancer Centre Singapore (NCCS) and Singapore General Hospital (SGH) as part of a retrospective historical cohort study.  The analysis method included NGS performed on an Illumina Miseq or an Illumina Hiseq 4000 on blood and breast cancer specimens.  Seven of the patients (38.9%) had stage 3 or 4 breast cancer at diagnosis.

This study found that a higher frequency of grade 3 (83.3% vs 45.4%, p = 0.005), estrogen receptor (ER) negative (66.7% vs 26.3%, p < 0.001) and HER2+ (66.7% vs 23.4%, p < 0.001) tumors among NF1 patients compared to non-NF1 breast cancers.  To date, six out of 16 patients with stage 1–3 breast cancer (37.5%) had relapsed, all of whom also had HER2+ tumors.  Five-year overall survival (OS) was 69.6% (95% confidence interval [CI] 41.0–86.4%) in the NF1 group, and 84.5% (95% CI 83.4–85.5%) in the control group of non-NF1 breast cancers (p = 0.017).  Overall survival was inferior in NF1 patients in multivariable analysis (hazard ratio 2.25, 95% confidence [CI] 1.11–4.60; p = 0.025).

One of the limitations reported by the study authors was the inability to evaluate copy number aberrations.  The authors concluded that their comprehensive series of NF1- associated breast cancers suggested that their aggressive features were related to germline NF1 mutations in cooperation with other somatic mutations.

Yoshihama T, Fukunaga K, Hirasawa A, et al. GSTP1 rs1695 is associated with both hematological toxicity and prognosis of ovarian cancer treated with paclitaxel plus carboplatin combination chemotherapy: a comprehensive analysis using targeted resequencing of 100 pharmacogenes. Oncotarget. 2018 Jul 3;9(51):29789-29800.

The aim of this study was to find genetic variants that predicted toxicity and/or efficacy of paclitaxel plus carboplatin combination therapy (TC therapy).  This retrospective case-control study used data from 320 Japanese women who had received TC therapy for gynecological cancers.  The analysis method included a comprehensive pharmacogenomic analysis using a targeted resequencing panel of 100 pharmacogenes, using NGS with variants being called according to the Genome Analysis Toolkit in peripheral blood samples.

Among the 320 patients who received TC therapy for gynecological cancers, the median age was 54.5 years (range: 35-80) in the adverse drug reaction (ADR) group and 54 years (range: 27-80) in the control group.  Comparing the ADR group to the control group, most had ovarian cancer (54% versus 61%), were Stage III (Stage I: 36% versus 36%, Stage II: 12% versus 7%, Stage III: 42% versus 42%, and Stage IV: 10% versus 15%, comparing the ADR group to the control group, respectively), and a tri- weekly regiment (76% versus 80%, respectively).  Similarly, among 56 advanced ovarian cancer patient, median age was between 51 and 53 years, and most were Stage III, with tumor stage assessed according to the International Federation of Gynecology and Obstetrics (FIGO) classification.

This study found that GSTP1 rs1695 showed the smallest p value for an association with severe hematotoxicity, and the 105Ile wild type allele had a significantly higher risk of severe hematotoxicity than the 105Val allele (p=0.00034, odds ratio 5.71, 95% confidence interval:1.77-18.44).  In 56 advanced ovarian cancer patients who received tri-weekly TC as a first-line chemotherapy, patients with the 105Ile/105Ile genotype showed significantly better 5-year progression-free survival (PFS) (p=0.00070) and overall survival (OS) (p=0.0012) than those with the 105Ile/105Val or 105Val/105Val genotype.

The authors acknowledged the limitations of retrospective study design and small sample size and concluded that the GSTP1 rs1695 105Ile/105Ile genotype was associated with both severe hematotoxicity and high efficacy of paclitaxel plus carboplatin combination therapy in terms of improved survival, identifying a possible prognostic indicator for ovarian cancer patients with TC therapy.

Yurgelun MB, Chittenden AB, Morales-Oyarvide V, et al. Germline cancer susceptibility gene variants, somatic second hits, and survival outcomes in patients with resected pancreatic cancer. Genet Med. 2019 Jan;21(1):213-223.

The aim of the study was to determine the prevalence and significance of germline cancer susceptibility gene variants in double-strand DNA damage repair (dsDDR) genes linked to inherited risks of pancreatic adenocarcinoma (PDAC).  The analysis included a customized NGS panel that the authors built of 24 cancer susceptibility genes on tumor samples and multivariable-adjusted Cox proportional hazards regression.

This retrospective historical cohort study across three academic institutions used data from 289 patients with median age at diagnosis 67 years, 76% Caucasian, 48% women, 83% T3 – T4 resected PDAC ascertained without preselection for high-risk features (e.g., young age, personal/family history). Overall, 16% were stage T1 – T2 and 83% were stage T3 – T4.

This study found that 28/289 (9.7%; 95% confidence interval [CI] 6.5–13.7%) patients carried pathogenic/likely pathogenic (P/LP) germline variants, including 21 (7.3%) participants that carried germline variants in dsDDR genes, and 3 with Lynch syndrome genes.  Compared with noncarriers, patients with any germline gene variants had superior overall survival (adjusted hazard ratio [HR] 0.54; 95% CI 0.32–0.91; P=0.02) with a median overall survival of 34.4 months for germline variant carriers versus 19.1 months for noncarriers.

The authors acknowledged the limitations of heterogeneity of therapeutic regimens received by patients, and targeted recruited through academic medical centers, therefore findings may not be fully generalizable.  The authors concluded that nearly 10% of PDAC patients harbor germline variants, although the majority lack somatic second hits, the therapeutic significance of which warrants further study as many PDAC patients with germline BRCA1/2 variants have not had tumor responses to PARP inhibitors in other early-phase studies.

Zhao Q, Yang J, Li L, et al. Germline and somatic mutations in homologous recombination genes among Chinese ovarian cancer patients detected using next-generation sequencing. Gynecol Oncol. 2017 Jul;28(4):e39.

The aim of the study was to define genetic profiling of homologous recombination (HR) deficiency in ovarian cancer patients in China and analyze the relationship between genetic alterations and clinical parameters.

This prospective cohort study used data from paired whole blood and frozen tumor samples from 50 ethnic Chinese women (median age 53 years) diagnosed with epithelial ovarian carcinomas (EOC), which were primarily FIGO stage III (33%), prospectively enrolled and consecutively included who underwent surgical resection at a Beijing hospital.

The analysis method included genomic DNA (gDNA) for high throughput NGS to detect deleterious mutations through all exons in 31 core HR genes by using the Complete Genomics (CG) Black Bird platform (BGI group).  For International Federation of Gynecology and Obstetrics (FIGO) staging, 7% were stage I, 3% Stage II, 33% Stage III, and 7% Stage IV.  Eighty percent of the cases were in the advanced phase when diagnosed.

This study found that 21 deleterious germline HR-mutations (i.e., ATR, BRCA1/2, CHEK2, RAD50, RAD52, and RAD54B) were identified in 36% of the ovarian cancer patients.  BRCA1/2-mutation carriers had favorable platinum sensitivity (relative risk, 1.57, 95% confidence interval [CI], 1.22-2.00, p<0.05), resulting in a 100% remission probability and 100% survival rate (no hazard ratio shown) and were all alive during the study.  In contrast, mutations in other HR genes predicted poor prognosis.  The estimated five-year overall survival (OS) was 83.6% using Kaplan-Meier method, with a median survival period of 61.7 months.  The presence of a pathogenic mutation in non-BRCA1/2 HR genes was associated with poorer OS (p<0.05, no hazard ratio shown).  However, multivariate analysis demonstrated that platinum sensitivity and optimal cytoreduction were the independent impact factors influencing survival (hazard ratio [HR], 0.053; 95% CI, 0.004–0.774) and relapse (HR, 0.247; 95% CI, 0.083–0.739), respectively.

The authors acknowledge small sample size as a limitation and concluded that loss-of-function BRCA1/2 mutations were strongly associated with hereditary breast and ovarian cancer (HBOC).

Zhong X, Dong Z, Dong H, et al. Prevalence and Prognostic Role of BRCA1/2 Variants in Unselected Chinese Breast Cancer Patients. PLoS One. 2016 Jun 3;11 (6):e0156789.

The aim of this study was to investigate the distribution of both somatic and germline BRCA1/2 variants in unselected breast cancer patients in China, and explore their roles in tumor phenotype and disease prognosis.

This prospective cohort study used data from 507 ethnic Chinese women (median age at diagnosis 48 years) pathologically diagnosed with breast cancer, which were primarily (59%) stage II, unselected for family history of breast cancer or age at diagnosis prospectively enrolled from a Chinese hospital.  The analysis method included NGS and confirmed by Sanger sequencing in paired blood/normal tissue.  Tumor DNA samples were screened for variants in all coding exons and the splice boundaries (-20/+10 bp) of BRCA1 and BRCA2 genes on a MiSeq system.

This study found that BRCA1/2 pathogenic or likely pathogenic (P/LP) variants were detected in 50 patients (9.9%), including 40 (7.9%) germline carriers with a BRCA1/2 P/LP variant (18 in BRCA1, 22 in BRCA2), 9 (1.8%) patients with somatic BRCA1/2 pathogenic variants (3 in BRCA1, 6 in BRCA2), and 1 (1.8%) patient with concurrent germline and somatic pathogenic variants in BRCA2.  Of the 507 patients, 4% were clinical stage 0, 15% stage I, 59% stage II, 23.5% stage III, and 4 (0.8%) patients had an unspecified stage, and 72 patients had variants of uncertain significance (VUS).  The median age at diagnosis was 48 years (range 27 -84) and 99% were of Han ethnicity.  In this study, 426 patients of stage 0-III, excluding five patients with stage IV, 4 patients with unspecified stage, and 72 patients with the variants of uncertain significance (VUS), were followed for up to seven years (median, 39.3 months).  In this subgroup, the three-year disease free survival (DFS) rate of the 15 BRCA1 carriers (germline or somatic) was significantly worse than 287 non-carriers (76.6%±12.1% vs. 94.1%±1.6%; log-rank P = 0.03), and also worse than 21 BRCA2 carriers (germline or somatic) (76.6%±12.1% vs. 100%; log-rank P = 0.04).  In the subgroup analysis for stage 0~II, patients with a germline BRCA1 variant had a significantly worse 3-year DFS rate of 71.9%±14.3%, compared with 94.1%±1.6% for non-carriers (P = 0.009), and 100% for ones compared with a germline BRCA2 variant (P = 0.05).  There was no statistically significant associations between BRCA1 or BRCA2 carriers with overall survival, regardless of their germline or somatic status (all p values > 0.05).  The presence of a germline BRCA1 P/LP variant, which were associated with aggressive tumor phenotypes, particularly predicted an increased risk of relapse as compared to non-carriers in the subgroup of stage 0-II (unadjusted HR = 4.52; 95% CI = 1.31–15.61; p = 0.02), but the adjusted HR failed to show statistical significance (adjusted HR= 2.72; 95% CI = 0.65–11.44; p = 0.17).

The authors acknowledged the small sample size and the low frequency of BRCA1/2 P/LP variants (9.9%) as limitations in their study.  The authors stated that the sample size (n = 507) was relatively small when considering the large diversity of documented variants (for example, over 1500 recorded in genetic database) and the scattered distribution of these variants in the whole coding regions.

The authors concluded that a high frequency of germline and somatic BRCA1/2 P/LP variants was detected in unselected Chinese breast cancer patients and BRCA1 status was associated with a more aggressive tumor phenotype including triple-negative, higher tumor grade and advanced disease stage, which was not observed in germline BRCA2 carriers.  The presence of a germline or somatic BRCA1 P/LP variant, especially the germline one, was associated with worse disease progression, but not overall survival, in the patients diagnosed at an early stage (Stage 0~II, or N0) with breast cancer.                            

4.  Medicare Evidence Development & Coverage Advisory Committee (MEDCAC)

A MEDCAC meeting was not convened on this issue.

5.  Evidence-Based Guidelines

The pertinent evidence-based guidelines are summarized below.

We searched PubMed for evidence-based guidelines on the clinical utility of NGS used as a diagnostic test to identify germline mutation or a hereditary cancer for Medicare beneficiaries. The pertinent evidence-based guideline is summarized below.

Stoffel EM, McKernin SE, Brand R, et al. Evaluating Susceptibility to Pancreatic Cancer: ASCO Provisional Clinical Opinion. J Clin Oncol. 2019 Jan 10;37(2):153-164.

The purpose of an American Society of Clinical Oncology (ASCO) provisional clinical opinion (PCO) is to offer timely clinical direction to ASCO’s oncology membership and other health care providers including primary care physicians, which in this case, addresses identification and management of patients and family members with possible predisposition to pancreatic adenocarcinoma.  This PCO should be read with the understanding that results from randomized clinical trials were not available for the statements made in the guidance, but it is the opinion of the Expert Panel that the statements made represent the state of the data available.

ASCO convened an Expert Panel and conducted a systematic review of the literature published from January 1998 to June 2018, combined hereditary pancreatic neoplasm terms and screening and intervention-related terms and MeSH headings.  Results of the PubMed and the Cochrane Collaboration Library databases searched were supplemented with hand searching of the bibliographies of systematic reviews and selected seminal articles and contributions from Expert Panel members’ curated files.  A total of 40 papers met eligibility criteria and form the evidentiary basis for the PCO recommendations.  The papers informed the panel members but, ultimately, did not establish a strong evidence base to craft the recommendations.

All patients diagnosed with pancreatic adenocarcinoma should undergo assessment of risk for hereditary syndromes known to be associated with an increased risk for pancreatic adenocarcinoma.  Assessment of risk should include a comprehensive review of family history of cancer.

Research Question 2

Which individuals should undergo genetic testing for predisposition to pancreatic cancer?

PCO 2.1 All patients diagnosed with pancreatic adenocarcinoma should undergo assessment of risk for hereditary syndromes known to be associated with an increased risk for pancreatic adenocarcinoma.  Assessment of risk includes obtaining a personal cancer history and family history of cancers in first- and second-degree relatives.  However, recent data demonstrate that many individuals who develop pancreatic cancer in the setting of genetic predisposition lack clinical features or family cancer history typically associated with the corresponding hereditary syndrome.  Therefore, germline genetic testing may be discussed with patients with personal history of pancreatic cancer, even if family history is unremarkable (Type: informal consensus; benefits outweigh harms; Strength of statement: strong).

PCO 2.2 An individual with a cancer diagnosis is often the best candidate in whom to initiate genetic testing and has the highest likelihood of an informative test result; however, if a cancer-affected individual is not available, testing may be performed in a pancreatic cancer–unaffected individual following genetic risk assessment, with the understanding that a negative test result is considered clinically uninformative.

The following cancer-unaffected individuals should be offered genetic risk evaluation:

  • Members of families with an identified pathogenic cancer susceptibility gene variant
  • Pancreatic cancer–unaffected individuals from families that meet criteria for genetic evaluation for known hereditary syndromes that are linked to pancreatic cancer
  • Pancreatic cancer–unaffected individuals from families that meet criteria for familial pancreatic cancer, as outlined in PCO 1.2 (Type: informal consensus; benefits outweigh harms; Strength of statement: strong).

PCO 2.3 Genetic testing in a patient with pancreatic cancer may confirm the diagnosis of a hereditary cancer syndrome and inform management of at-risk family members.  Given the possibility that certain germline variants could potentially be used to guide therapeutic decision making and the limited prognosis of many patients with pancreatic cancer, the Expert Panel recommends that consideration of germline testing for inherited cancer susceptibility should be performed early in the disease course for patients with pancreatic cancer.

(Type: informal consensus; relative balance of benefits and harms; Strength of statement: moderate).

PCO 2.4 Several genes have been linked to risk for pancreatic cancer (Table 1 in PCO).  Unless a genetic diagnosis has previously been confirmed in a family member, germline genetic testing should be performed using a multigene panel that includes the genes listed in Table 1.  A finding of a pathogenic or likely pathogenic germline variant can confer increased risks of cancers beyond the pancreas for the probands and their families; finding a germline variant of uncertain significance is not considered to be causative of increased cancer susceptibility.

(Type: informal consensus; benefits outweigh harms; Strength of statement: strong).

Guidelines Submitted During Initial Public Comment Period

We also investigated the guidelines that were submitted to us during the comment period.  These included NCCN guidelines, as well as guidelines that were developed by other professional organizations (e.g., U.S. Multi-society Task Force on Colorectal Cancer).  Published guidelines provide relevant clinical context to diagnostic testing and treatment.  We recognize the importance of professional society recommendations and consensus statements as part of the evidence to support coverage policies and clinical practice.

As noted in the evidence/analysis section of this NCA, there were no meta-analyses or randomized controlled studies that specifically addressed NGS testing, and the observational studies varied in quality for a number of reasons.  The limited number of studies found in the medical literature was also a drawback.  Of all of the different types of cancers associated with germline mutations, only studies of breast and ovarian cancer had high quality evidence, and were able to demonstrate clinical utility through the use of NGS.  Some guidelines submitted to us during the comment period did not identify NGS as a viable tool to detect mutations, or listed only other testing methods such as IHC or PCR as a means of identifying germline mutations (AIM Specialty Health.  American Society of Clinical Oncology Policy Statement Update: Genetic Testing for Cancer Susceptibility-(ASCO), Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the U.S. Multi-society Task Force on colorectal cancer, American College of Medical Genetics and Genomics and the National Society of Genetic Counselors.  Society for Gynecologic Oncology-(SGO) Clinical Practice Statement: Next Generation Cancer Gene Panels Versus Gene by Gene Testing, SGO Clinical Practice Statement: Screening for Lynch Syndrome in Endometrial Cancer).  For this reason, only guidelines that specifically mentioned NGS as part of breast and ovarian cancer guidelines are discussed here.

Here we have listed guidelines by organization name, the type of cancer they addressed, as well as their position in reference to the use of NGS.  Only guidelines that list specific cancers for which evidence of clinical utility was found will be listed.  Guidelines that failed to mention the direct use of NGS were excluded.

NCCN Guidelines

Breast cancers The NCCN guideline listed five different types of breast cancers: ductal carcinoma in situ, invasive breast cancer, inflammatory breast cancer, phylloides tumor, as well as Paget’s disease. For patients with ductal carcinoma in situ, invasive breast cancer, or inflammatory breast cancer, the NCCN guidelines specifically mentions following its genetic/familial high risk assessment: breast and ovarian guidelines. In the document it notes that since its introduction, multi-gene testing for hereditary forms of cancer has rapidly altered the clinical approach testing at-risk patients and their families. It also notes that based on next generation sequencing technology, these simultaneously analyzes a set of genes that are associated with specific family cancer phenotypes or multiple phenotypes. Multigene testing can include "intermediate" penetrant (moderate-risk) genes. For many of these genes, there are limited data on the degree of cancer risk and there are no clear guidelines on risk management for carriers of pathologic/likely pathogenic variants. Not all genes included on multi-gene test are necessarily clinically actionable. For phylloides tumors as well as Paget’s disease, the guideline made no reference germline mutations, nor any mention of Genetic/Familial High Assessment.
Ovarian cancers The NCCN guideline listed eight different types of ovarian cancers: carcinosarcoma, clear cell carcinoma of the ovary, mucinous carcinoma of the ovary, Grade 1 endometrioid carcinoma of the ovary, low-grade serous carcinoma, low-grade serous carcinoma, ovarian borderline epithelial tumors, malignant sex cord stromal tumors, and malignant germ cell tumors. They note that tumor molecular analysis as clinically indicated: Next Generation Sequencing (NGS) for BRCA 1/2 somatic mutations, Immunohistochemical (IHC) for Polymerase Chain Reaction (PCR). They also suggest considering evaluation of homologous recombination deficiency. The guideline made no specific recommendations on type of test based on tumor type. As with breast cancer, the guideline mentions following its Genetic/Familial High Risk Assessment: Breast and Ovarian guidelines, and the use of multi-gene testing for hereditary forms of cancer.

Submitted Guidelines (other than NCCN) during the comment period and their use of NGS

There were other guidelines submitted during the comment period that were not NCCN guidelines.  As was noted earlier, through the use of NGS, treatment of breast and ovarian cancers were the only cancers to demonstrate clinical utility. For that reason, only guidelines that addressed breast and ovarian cancers will be discussed.

American Society of Breast Surgeons, Consensus Guidelines on Genetic Testing for Hereditary Breast Cancer (2019).

This consensus guideline notes that genetic testing is increasingly provided through multi-gene panels.  It also noted that there are a wide variety of panels available, with different genes on different panels.  There is a lack of consensus among experts regarding which genes should be tested in different clinical scenarios.  The guideline mentions a number of genetic mutations (e.g., BRCA 1/2, PALB2).  It also notes that improvements in technology, like next-generation sequencing, has made testing for more than one gene at a time a reality.  While BRCA1 and BRCA2 remain the most likely genes to be mutated in a family with high breast and ovarian cancer risk, panel testing can allow for more comprehensive coverage of less common syndromes that can also confer hereditary cancer risk.

For patients with potentially actionable genes, this guideline refers the readers to the NCCN guidelines, (e.g., Familial High-Risk Assessment: Breast and Ovarian Cancer), which does mention NGS as a possible option for multi-gene testing.

6.  Professional Society Recommendations / Consensus Statements / Other Expert Opinion

We searched PubMed for professional society recommendations or consensus statements exclusively concerning the clinical utility of NGS used as a diagnostic test to identify germline mutation or a hereditary cancer for Medicare beneficiaries.  Additional professional society recommendations, consensus statements and other expert opinions included those submitting comments during the public comment period. The pertinent professional society recommendation is summarized below.

Mandelker D, Donoghue MTA, Talukdar S, et al. Germline-Focused Analysis of Tumour-Only Sequencing: Recommendations from the ESMO Precision Medicine Working Group. Ann Oncol. 2019 May 3.

The aim of the study by the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup was to generate (i) recommendations regarding germline-focused analyses of tumor-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.  The recommendations were based on analyses of paired somatic/germline sequencing data from 17,152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. The European Society of Medical Oncology (ESMO) Precision Medicine Working Group (PMWG) convened a subgroup tasked with addressing germline management of tumor-detected pathogenic variants, specifically: (i) to identify the key issues relevant to laboratory and clinical management, (ii) to undertake analyses of relevant tumor and germline data, (iii) to generate consensus recommendations applicable in routine clinical-laboratory services regarding: a. extent of germline-focused analyses to be performed as routine, b. when follow-up testing in a germline sample should be undertaken, and c. patient information and consent.

The Subgroup utilized the largest available dataset of paired tumor-normal sequencing, comprising 17,152 unselected cancer patients who presented to Memorial Sloan Kettering Cancer Center between 2014 and 2017 in whom clinical sequencing of both germline (blood) and tumor samples had been successfully performed using the MSK-IMPACT assay, which formed "the MSK Dataset".

Results of the study revealed that across the 65 genes analyzed in 16,322 tumors, in total 1,997,499 tumor variants were identified, of which 1,959,587 were of true germline origin.  For the 27 standard actionability cancer susceptibility genes (CSGs) analyzed, a >10% on-tumor germline conversion rate was attained for genes BAP1, FLN, POLE and FH and a near 10% rate for CDKN2A (8.9%, 8 of 90) and NF1 (9 of 107, 8.4%).  In the tumor-focused germline analysis of the MSK dataset, restricting firstly by variant allele frequency (VAF) and secondly to the 27 genes yielding germline conversion rate >10% as per specified gene/context/age, the number of tumor- detected pathogenic variants requiring ‘germline follow-up’ could be reduced by 94% from 17,075 to 1,042 such that germline follow-up would only be required in 6.4% of tumors  (1,042/16,322).

The authors concluded that through their large-scale analysis of paired somatic/germline data, the ESMO PMWG Germline Subgroup was able to develop recommendations regarding germline-focused analysis of tumor-only sequencing in order to optimize detection of true germline variants in genes of clinical utility, while avoiding excessive diversion of effort and resources towards ‘germline follow-up testing’ of vast numbers of variants.  Pragmatic, strategic germline-focused tumor analysis can offer a high yield of true germline findings, i.e., 63% true germline yield from follow-up of 6.4% of tumors from the MSK dataset.

The authors made the following recommendations:
  • Germline-focused tumor analysis should be performed in all laboratories as part of routine analysis of a large tumor panel.
  • Germline-focused tumor analysis can be delivered via an automated pipeline so as not to add substantial additional manual work, cost or delay to tumor analysis.
  • Variants in should be flagged which are (i) predicted to result in protein truncation in genes acting through loss-of-function and/or (ii) classified as Pathogenic/Likely Pathogenic via a well-maintained, comprehensive and curated clinical resource (ClinVar is recommended).
  • Germline-focused tumor analysis can be restricted to variants of VAF >30% (SNVs) or >20% (small insertions/deletions). Local validation will be required to confirm the accuracy of tumor VAF estimates, especially for PCR-based NGS methodologies.
  • Samples known or suspected to be hypermutated should be included for germline-focused tumor analysis
  • Germline-focused tumor analysis in the off-tumor context should be restricted to ‘High Actionability-CSGs’.
  • Recessively acting ‘High Actionability-CSGs’ (currently MUTYH alone) should be included for germline-focused tumor analysis but reporting and germline follow-up testing should be undertaken only on detection of two pathogenic variants.
  • Germline-focused tumor analysis of ‘standard actionability’-CSGs should be restricted to the on tumor setting.
  • ‘Standard actionability’-CSGs included for germline-focused tumor analysis can be restricted genes of high penetrance.
  • Germline-focused tumor analysis can be restricted to gene-scenarios for which the germline conversion rate is >10%. For selected genes, it may therefore be appropriate to restrict germline-focused tumor analysis to just those tumors arising age <30 years.
  • Formal variant review and classification should be undertaken by an experienced clinical scientist prior to initiation of patient re-contact and/or germline testing.
  • Prior to analysis of their germline sample for the pathogenic variant, adequate information should be provided to the patient regarding the implications of germline testing, along with documentation of their consent.
  • The tumor-observed pathogenic variant should be analyzed in an appropriate germline sample (lymphocytes, saliva/buccal swab, normal tissue) in a laboratory accredited for germline analysis.
  • A patient in whom a germline pathogenic variant is detected should be referred to a specialist genetics service for long term follow-up and management of the family.
  • A normal/negative tumor sequencing result should not be taken as equivalent to a normal/negative germline result unless robust analysis of dosage has been performed. This distinction is particularly important for genes such as BRCA1 and MSH2, for which whole exon deletion/duplications constitute a substantial proportion of pathogenic variants.
  • Re-evaluation of this workflow, revised analyses and update of these recommendations should be undertaken at least two-yearly. Reanalysis should include updated data regarding pathogenicity of variants and penetrance of cancer susceptibility genes, along with review of thresholds for ‘germline conversion rates’ and VAF cut-offs.
  • 7.  Public Comment

    Public comments sometimes cite the published clinical evidence and give CMS useful information.  Public comments that give information on unpublished evidence such as the results of individual practitioners or patients are less rigorous and therefore less useful for making a coverage determination.

    CMS uses the initial public comments to inform its proposed decision.  CMS responds in detail to the public comments on a proposed decision when issuing the final decision memorandum.  All comments that were submitted without personal health information may be viewed in their entirety by using the following link https://www.cms.gov/medicare-coverage-database/details/nca-view-public-comments.aspx?NCAId=296.

    Initial Comment Period: 04/29/2019 – 05/29/2019

    During the initial 30-day public comment period, CMS received 82 comments from academic medical centers, hospitals, laboratories, providers, patient-advocates, manufacturers and professional organizations.  The comments were supportive of CMS’ decision to reconsider the current NCD and recognized this as an opportunity to refine the policy.  Some comments questioned why only advanced stage cancer while many others stressed the need for repeat testing.  Many comments specifically addressed brain cancer and clarified that brain tumors are classified by grades and not stages.  Forty-five of the comments were from patient-advocates or caregivers who provided their personal experiences.

    Second Comment Period:  10/29/2019 – 11/28/2019

    During the 30-day public comment period following the release of the proposed NCD and decision memorandum, CMS received 43 comments.  The majority of comments were supportive of CMS’ decision to reconsider this NCD and applauded CMS for being responsive to concerns from the stakeholder community.  All comments were in support of expanding access to NGS testing while many comments point out areas that they believe were inadvertently misrepresented by CMS.  The majority of comments point out a potential coverage gap for patients with germline (inherited) breast or ovarian cancer, the need to remove the lifetime testing limit, restructuring of the NCD Manual, and the need for clarification of the distinction between clinical indications and risk factors for germline (inherited) cancer.  Of the 43 comments, 17 included mark-ups with suggested revisions to the NCD language.  Detailed summaries of all submitted comments with CMS responses are included below.

    The majority of comments were provided by professional organizations and associations including one joint comment submitted by various patient and provider organizations.  The remaining comments were submitted by developers/manufacturers of NGS tools, academic medical center/hospitals, providers, laboratories, a consultant and a data analytics company. 

    A number of commenters submitted references for us to review.  Of the numerous references submitted during the comment period on colorectal cancer, male breast cancer, lung cancer, prostate cancer, and pancreatic cancer, none of these references fulfilled the search criteria used in our internal technology assessment.  The references either did not use NGS, test for germline mutations, or assess a clinical health outcome, such as mortality or survival.  But we still carefully subjected these references to the same critical review of the evidence that we used in our internal technology assessment.  The references failed to show clinical utility for using NGS to identify germline mutations.  The submitted evidence was insufficient to show that using NGS to identify germline mutations improved health outcomes in patients with an inherited cancer of the colon or rectum, lung, prostate, or pancreas, or male patients with inherited breast cancer. 

    Coverage under Section 1862(a)(1)(A) of the Social Security Act

    Comment:  Many commenters commended CMS on the proposed expansion of coverage for breast and ovarian cancer but suggested other cancers including male breast cancer, colorectal cancer, lung cancer, pancreatic cancer and prostate cancer should also be nationally covered.  One commenter specifically pointed out that the NCCN guidelines for colorectal cancer and Lynch syndrome were not included in CMS’ evidence review because the studies did not evaluate mortality.  One commenter requested CMS expand ovarian cancer to include epithelial ovarian, fallopian tube or primary peritoneal cancer.

    Response:  The evidence for ovarian and breast cancer suggests that using NGS to identify germline mutations can lead to better stratification of patients in the physician management of inherited cancers of the breast and ovary.  At this time, there is insufficient evidence of clinical utility for other cancer types including male breast cancer, colorectal, lung, pancreatic and prostate cancer and we acknowledge the evidence in this field is rapidly developing.  Therefore, the final NCD will nationally cover FDA approved or cleared NGS as a diagnostic laboratory test for patients with breast or ovarian cancer if the required criteria are met.  Medicare Administrative Contractors (MACs) will act on behalf of CMS to make reasonable and necessary determinations under 1862(a)(1)(A) of the Act for other NGS diagnostic tests for patients with other germline cancer diagnoses.  Moreover, Medicare contractors will also make the § 1862(a)(1)(A determination for NGS germline tests that are not FDA approved as long as required patient criteria are met.  MACs may also determine coverage of NGS for RNA sequencing and protein analysis testing. 

    Comment: Some commenters suggested NGS be used for indications other than cancer (e.g. used as a diagnostic tool in infectious diseases).  Some commenters wanted CMS to allow MACs to use their discretion to cover non-oncologic use of NGS.

    Response: The final NCD clarifies that Medicare contractors have discretion to make the § 1862(a)(1)(A) determination for all non-cancer diagnostic uses of NGS.

    Comment: Several commenters requested clarification as to whether somatic testing using NGS for patients with recurrent, relapsed, refractory, metastatic, or advanced stage III or IV cancer would continue to be covered.

    Response: This NCD reconsideration addresses the use of NGS in patients at risk for germline (inherited) mutations and does not negate coverage of somatic testing using NGS for beneficiaries with recurrent, relapsed, refractory, metastatic, and/or advanced stage III or IV cancer.

    Comment: One commenter requested clarification regarding assessing breast and ovarian cancer simultaneously.

    Response:  CMS is not requiring that germline testing for breast and ovarian cancer be performed together.  CMS acknowledges these are two distinct cancer types.  The managing physician has discretion to determine which test is appropriate, but if both tests are ordered at the same time based on the clinical situation (because of similar genetic makeup or etiologies), they would be covered.

    Comment:  One commenter requested testing adult children of cancer patients who are diagnosed with a positive germline mutation.  Two commenters requested people with significant family history of cancers should have access to germline genetic testing in their 30s or 40s before any diagnostic cancer is determined.

    Response: We appreciate the comment.  In general, the Medicare population are adults 65 years and older, disabled, or those who have end stage renal disease.  We would not cover diagnostic testing for relatives of Medicare patients who are not independently entitled to Medicare under part B. 

    Comment: One commenter pointed out that the decision language was missing the phrase, “reasonable and necessary.”

    Response:  We appreciate the comment and included it in the final NCD.

    Access

    Comment:  Many commenters pointed out that while CMS expanded coverage of NGS testing for germline (inherited) breast and ovarian cancer it inadvertently created a coverage gap.  The commenters believe that although it was CMS’ intent to increase access for these patients, it actually restricted coverage.  The proposed decision memorandum (PDM) proposed to only cover NGS testing for ovarian and breast cancer, on the condition that the test is either approved or cleared by the Food and Drug Administration.  Many commenters brought to our attention that there are currently no FDA-approved or FDA-cleared NGS tests for germline (inherited) cancer on the market.  Furthermore, the proposal for MAC discretion excludes breast and ovarian cancer diagnoses.  Several commenters pointed out that NGS testing for breast and ovarian cancers are currently covered through MAC discretion.

    Response:  It was not CMS’ intent to restrict or remove coverage.  CMS’ intent was to expand coverage. In the final NCD, we have clarified language to allow MAC discretion for any cancer diagnosis including tests that are not FDA approved or cleared for breast and ovarian cancer provided all the criteria is met.  The final NCD also removed the diagnostic laboratory test criteria of the indication for NGS to be used for breast and ovarian cancer only.

    Comment: Many commenters expressed their support for MAC discretion for germline (inherited) testing for patients with cancer.  Many commenters referenced the MolDX program as a working model for CMS to model its NCD after.  One commenter specifically supported MAC discretion for germline (inherited) testing for patients with lung cancer.  Many commenters expressed support for MAC discretion stating it offers a degree of flexibility as new evidence is collected without having to reconsider each time.

    Response: We appreciate the supportive comments.  The final NCD permits MAC discretion for any cancer diagnosis including breast and ovarian cancer provided all NCD criteria are met.

    Patient Criteria

    Comment: Many commenters requested that CMS distinguish between risk factors and clinical indications to avoid confusion and eliminate redundancy.  Several commenters requested the criteria for risk factors for germline (inherited) breast or ovarian cancer be deleted altogether.  Another commenter assumed that CMS intentionally left the distinction between clinical indications and risk factors vague so that the Medicare Administrative Contractors (MACs) could interpret these coverage criteria.

    Response: We appreciate the comments.  Clinical indications are different from risk factors.  In clinical medicine, a clinical indication, unlike a risk factor, is a sign, symptom, laboratory test result, or medical condition, or a combination of these factors, that leads to the recommendation of a treatment, test, or procedure.  A risk factor is a variable associated with an increased risk of a disease, such as age, gender, or family history of disease but does not have signs or symptoms of the disease.  We have included a paragraph within the Background section of the final decision memorandum that distinguishes risk factors from clinical indications for germline (hereditary) breast and ovarian cancer.

    Repeat Testing

    Comment:  Many commenters requested that the final NCD not limit coverage to a single diagnostic laboratory test using NGS in a patient’s lifetime. Commenters suggest this limits testing in anyone who has had prior NGS testing for any reason including somatic testing, and requested the final NCD allow NGS testing for somatic and germline (inherited) cancers separately.  Many commenters provided scenarios where repeat testing using NGS testing is appropriate.  One commenter requested modification of repeat NGS testing for somatic cancer.

    Response:  We recognize that specific clinical scenarios may necessitate repeat testing for those patients with germline (inherited) cancers.  We also acknowledge this is a rapidly evolving field.  In response to public comments and to support further innovation and patient access, we have clarified our decision to include coverage for appropriate repeat NGS testing for germline (inherited) cancer and somatic cancers when criteria are met.  The principle is identical to both inherited and acquired mutations so the NCD Manual has been revised with corresponding language for clarity and consistency purposes.

    Staging of Cancer

    Comment: Many commenters commended CMS for considering coverage of NGS tests for germline cancers of all stages.  One commenter requested CMS clarify early and late stage breast and ovarian cancer.

    Response: We appreciate the supportive comment.  A review of the medical literature revealed that the use of NGS demonstrated clinical utility in patients with germline (inherited) breast and ovarian cancer.  This final NCD provides coverage for all stages of breast and ovarian cancer.

    Comment: Several commenters suggested CMS remove the staging criteria in the current NCD.

    Response:  This reconsideration is limited to diagnostic laboratory tests using NGS of germline (inherited) mutations to identify those with hereditary cancer who may benefit from targeted treatments based on the results of the tests.  All stages of cancer are coverable for germline (inherited) cancers.  If there is new evidence available showing patients with somatic cancers other than advanced stages benefit from NGS, CMS would be interested in reviewing those studies in a separate reconsideration.

    Comment: Some commenters specifically addressed hematologic cancers pointing out that they are not staged and therefore may not meet CMS’ definition of advanced cancer.  Some commenters felt that because of the hematogenous spread, hematologic malignancies should be considered advanced cancers.

    Response: The original NCD which covers advanced somatic cancers (either stage III or IV) addressed the use of NGS specifically for patients with advanced cancer to determine if they had somatic mutations.  Based upon our review of the medical literature it is unclear as to whether hematologic malignancies have germline or somatic mutations.  Because of the nature of hematologic malignancies, they could potentially be considered advanced cancer.  As such, this NCD reconsideration permits coverage decisions regarding coverage of NGS for hematologic malignancies to be made by the MACs.  

    The National Comprehensive Cancer Network® (NCCN) Guidelines

    Comment: Several commenters suggest that the NCCN guidelines are evidence-based and provide information on the guideline development process and the evidence base for the guideline recommendations.  One commenter requested CMS remove the content from the treatment guidelines that are currently cited within the PDM.

    Response:  We appreciate the comment.  We agree and have revised our description of the NCCN guidelines. The NCCN is an alliance of leading academic cancer centers in the US and develops evidence-based recommendations regarding cancer prevention, screening, diagnosis, treatment and supportive care.  The NCCN guidelines are reviewed and updated on a continual basis to ensure that the recommendations take into account the most current evidence.  We recognize the importance of professional society recommendations and guidelines such as NCCN in coverage policies and clinical practice.  These publications provide relevant clinical context on testing and treatment.  While conducting this assessment, published NCCN guidelines on cancer diagnosis and treatment were reviewed and considered as part of the evidence to support our coverage determination.  

    Non-Coverage

    Comment:  Many commenters expressed that the non-coverage section as written in Appendix B (Draft NCD Manual) was confusing and potentially restricted coverage for the reconsideration language, specifically the reference to ‘Section B.1 noted above.”  Several commenters recommended that the non-coverage language be removed.

    Response:  We agree that the draft manual language as included in the proposed NCD could potentially cause confusion.  As such, we revised the structure of the NCD in the NCD Manual for clarity.

    Comment: One commenter specifically suggested CMS consider the Genetic/Familial High-Risk Assessment:  colorectal cancer guidelines.

    Response: This guideline was reviewed, but based on the internal technology assessment we found no clinical utility for colorectal cancer.

    Comment: One commenter notes that the United States Preventive Services Task Force (USPSTF) recommends that women who have family members with breast, ovarian, fallopian tube, or peritoneal cancer be evaluated to see if they have a family history that is associated with an increased risk of a harmful mutation in one of these genes.

    Response: We appreciate the comment.  Cancer screening in patients who do not have signs or symptoms of cancer and USPSTF screening recommendations are beyond the scope of the NCD.

    Scope of NCD

    Comment: Several commenters suggested changing the approach of this NCD. One commenter recommended specifying germline cancer risk testing using NGS technology as the focus of the proposed decision, or just specifying germline cancer risk testing without specifying the method.

    Another commenter suggested addressing cancer type, genetics, alterations, and target therapy rather than specific methodology.

    Response: We appreciate the comment and agree it is an innovative approach to NCDs, however the function of CMS is to evaluate the diagnostic capacity of the test.  NCDs assess the medical literature to determine whether an item or service improves health outcomes in the Medicare population.  NCDs do not assess risk determination.  

    Comment: One commenter stressed the importance of 'diagnostic tools-using artificial/augmented intelligence (AI), powered by streams of data and algorithms-can and should serve as a vital means of realizing the benefits of therapeutics.

    Response: We appreciate the comment.

    Comment:  Several commenters expressed that NGS is a platform, not a single type of test.  They acknowledge that there are other technologies beside NGS that are able to determine somatic genetic profiling and detection of germline (inherited) mutations that could lead to cancer risk (e.g. PCR, Sanger sequencing).  One comment requested a more flexible coverage framework since NGS testing includes innovative technologies and suggested an appropriate use criteria (AUC)-like framework.

    Response: We appreciate the comments and acknowledge that NGS is not a single type of test.  CMS acknowledges that polymerase chain reaction (PCR), immunohistochemistry (IHC), Sanger Sequencing, or Fluorescence in situ hybridization (FISH) testing could potentially be used to assess mutations as a potential cause of cancer.

    Comment:  One commenter sought clarification on whether other uses of NGS testing in patients with cancer were included in this NCD.

    Response:  We appreciate the comment.  This NCD only considered NGS for DNA sequencing to detect genomic mutations.  RNA sequencing and protein sequencing were not considered, therefore, coverage determinations for those diagnostic tests will be made by the MACs.

    NCD Title Change

    Comment: Some commenters suggested the title be changed to more appropriately reflect the expansion of the NCD to include germline (inherited) cancer.  One commenter suggested we remove the phrase, “for Medicare beneficiaries” from the title citing that all NCDs are for Medicare beneficiaries and CMS does not usually include this in the NCD title.

    Response: We appreciate the comments. We have revised the structure of the NCD in the NCD Manual and have included a new title to address these comments.  

    Report of Test Results

    Comment:  One commenter suggested the report template listed within the diagnostic laboratory test using NGS criteria would benefit from specifying treatment options (i.e. pharmacotherapy) known to improve quality of life or survival.  The commenter also recommended that the NCD explicitly state that an FDA-approved companion diagnostic exists for the qualitative detection and classification of variants in the protein coding regions and intron/exon boundaries of the BRCA1 and BRCA2 genes used in the management of ovarian and metastatic breast cancer patients.  One commenter requested that we remove the requirement for companion in vitro diagnostic designation for somatic testing.

    Response: The reporting criteria is consistent with the criteria in the original NCD with the exception of requiring companion diagnostic testing for treatment management.  It allows laboratories and diagnostic laboratory test developers to determine what is included in the test report. The requirement of an FDA-approved companion diagnostic test that uses qualitative detection and classification of variants is not part of the process when evaluating the use of NGS for the detection of germline (inherited) mutations.  This NCD only requires the identification of germline (inherited) mutations.

    Laboratory-Developed Tests (LDTs)

    Comment: Several commenters suggested that CLIA regulatory standards for laboratory-developed tests are sufficient to allow access to this testing.

    Response: Tests that are FDA approved or cleared are able to demonstrate analytic and clinical validity.  LDTs are not FDA approved or cleared, and may not be able to demonstrate analytic and clinical validity.  CMS believes that a lab developed test, even with CLIA certification, may not have sufficient evidence to demonstrate clinical utility.

    Comment: One commenter pointed out that the risk factors section within the Background Section of the proposed decision memorandum did not address germline testing in men with breast cancer.

    Response:  We acknowledge that germline testing in men with breast cancer was not included in the background section.  We reviewed an article submitted during the second public comment period regarding men with breast cancer and we found no clinical utility in the use of NGS.

    Miscellaneous

    Comment: One commenter recommended including a shared decision making (SDM) requirement for the treating physician to obtain the explicit consent of the beneficiary to be treated in the NCD.

    Response: While we did not include a SDM requirement in this final NCD, we require that NGS testing be ordered by the patient’s treating physician and we strongly encourage open communication between patients and their treating physician to inform and aid them in treatment recommendations that are tailored to their individual circumstances.

    Comment: One commenter asked for CMS to work with stakeholders and Congress to address genetic counseling and coverage for unaffected beneficiaries or those beneficiaries with no personal history of cancer.  Another commenter supported the proposed change to designate certified genetic counselors as CMS health providers who can bill under Medicare.  Their organization supports the current house bill, the Access to Genetic Counselor Services Act of 2019. HR 3235.

    Response: While we appreciate the comment, these requests for support in seeking legislative changes are beyond the scope of a National Coverage Determination (NCD).

    Comment: One commenter acknowledged and supported that liquid biopsies (also referred to as circulating tumor DNA (ctDNA) or plasma cell-free DNA (cfDNA) tests) are left to contractor discretion.  They requested CMS continue to engage with stakeholders to ensure that beneficiaries have consistent access to liquid biopsies.

    Response: We appreciate the comment and we agree that continued stakeholder engagement is important.

    VIII. CMS Analysis

    National coverage determinations are determinations by the Secretary with respect to whether or not a particular item or service is covered nationally by Medicare (§1869 (f)(1)(B) of the Act).  In general, in order to be covered by Medicare, an item or service must fall within one or more benefit categories contained within Part A or Part B, and must not be otherwise excluded from coverage.  Moreover, with limited exceptions, the expenses incurred for items or services must be reasonable and necessary for the diagnosis or treatment of illness or injury or to improve the functioning of a malformed body member.  (§1862(a)(1)(A) of the Act).  When making national coverage determinations, we evaluate the evidence related to our analytic questions based on the quality, strength and totality of evidence presented in the reviewed literature.  As part of this evaluation, it is important to consider whether the evidence is relevant to the Medicare beneficiary population.

    Well-designed and implemented randomized controlled trials form the highest quality of evidence.  In the case of NGS, there is no randomized controlled trial demonstrating that use of NGS as a diagnostic test significantly improves health outcomes such as mortality.  Moreover, there is no published randomized clinical trial or observational study that directly compared the use of NGS as a diagnostic test to the current standard of diagnostic testing for identifying a germline mutation or diagnosing an inherited cancer, nor were there any meta-analyses that analyzed the effectiveness of NGS testing.

    The body of evidence from observational population-based and retrospective cohort studies indicate that the diagnosis of germline mutations in patients with certain inherited cancers changes clinical management (including use of medications) that in turn improves health outcomes including survival.  The evidence does not include the use of NGS as a screening test in asymptomatic patients without cancer, since we limited our review to the use of NGS as a diagnostic test in symptomatic patients with certain inherited cancers.

    Evidence from observational studies is subject to bias.  Bias, or systematic error, is an issue in the design or conduct of a study that can introduce distortions in observed relationships between an exposure and an outcome; in this case, use of NGS as a diagnostic test, and an outcome measure such as mortality.  Inferences drawn from biased studies can lead to flawed conclusions about the effect of using NGS as a diagnostic test to identify germline mutations or inherited cancers on health outcomes, which has lesser quality in the hierarchy of evidence.  It is important to identify well-designed and implemented studies that are highest in the hierarchy of evidence to assure that we are making valid inferences from the data generated by such studies.

    In the evidence reviewed, none of the observational studies were specifically designed to compare the effect on health outcomes for Medicare beneficiaries of using NGS as a diagnostic test to find inherited cancers to another diagnostic test.  Moreover, even if there were observational studies that could answer such a question, they would likely not be able to minimize bias or incorporate adjustments for possible confounders, which could lead to invalid inferences that could overestimate or underestimate the effect of NGS as a diagnostic test.  We chose to answer the specific assessment question with the highest quality evidence from published clinical research that has results from well-designed and implemented studies about the effectiveness of NGS as a diagnostic test on health outcomes among patients with certain inherited cancers that can be generalized to Medicare beneficiaries.

    Our analysis includes peer-reviewed, published clinical studies, and guidelines pertaining to using NGS as a diagnostic test to identify germline mutations in the diagnosis of inhertied cancers.  All of the evidence comes from observational studies that assessed the effect of identifying germline mutation carriers compared to non-carriers on health outcomes, such as mortality among patients with inherited cancers.  In the majority of these clinical studies, the spectrum of interventions included chemotherapy, radiotherapy, adjuvant therapy, or surgery, but there was no randomization of the cancer intervention nor randomization of the NGS test.  Some well-designed and implemented studies that minimize bias demonstrate the clinical utility of NGS as a diagnostic test in identifying germline mutations in the diagnosis of certain inherited cancer and its effect on the clinical management of the patients and pertinent health outcomes.

    In our internal technology assessment, we searched for studies that examined the effect of using NGS as a diagnostic test to identify germline mutations or to diagnose inherited cancers on health outcomes.  We focused our review on health outcomes such as mortality, disease-free survival and progression-free survival.  This approach limits the cancer types reviewed to those that are found in our internal technology assessment.

    In determining the generalizability of the results of the body of evidence to the Medicare population, we consider, at minimum, the age, race and gender of the study participants.  There are a number of structured methods for evaluating diagnostic tests.  In past diagnostic imaging NCDs, we considered the evidence in the hierarchical framework of Fryback and Thornbury (1991) where Level 1 concerns technical quality of the images; Level 2 addresses diagnostic accuracy, sensitivity, and specificity of the test; Level 3 focuses on whether the information produces change in the physician's diagnostic thinking; Level 4 concerns the effect on the patient management plan; Level 5 measures the effect of the diagnostic information on patient outcomes; and Level 6 examines societal costs and benefits of a the diagnostic imaging technology. In our analysis, we generally look for sound evidence that shows the test is analytically and clinically valid (Levels 1-2) and that use of the test to guide treatment is reasonable and necessary for improved health outcomes (clinical utility, Levels 3-5).

    While a number of the clinical research studies were conducted in the United States (7 studies), many studies were completed in Europe (10), Australia (3), Canada (2), China (5), other Asian countries (5), South America (2), or Central America (1).  The conclusions of the studies conducted outside of the United States are congruent with those conducted inside the United States.  The study populations had a mean age between 42 and 60 years or a median age between 48 and 67 years.  The lower age limit ranged from 18 to 41 years, while the upper age limit ranged from 75 to 98 years.  Thus, these studies are relevant in generalizations of the results to the Medicare population.

    Medicare’s current coverage of NGS is restricted to patients with a metastatic, or recurrent, or relapsed, or refractory, or a stage III or stage IV advanced cancer.  As a result of new evidence and our present analysis, we now believe that the use of NGS has additional benefits.  It is an important tool in treating certain types of inherited cancer to improve health outcomes for Medicare beneficiaries.

    Question: Does NGS as a diagnostic test, either to detect germline mutations or identify inherited cancers, improve health outcomes for Medicare beneficiaries with certain inherited cancers?

    Yes, for some inherited cancers.  For NGS, we have focused on evidence for clinical utility, i.e., use of the test improves health outcomes (equivalent to Level 5 above) (Fryback and Thornbury, 1991).  For diagnosis of inherited cancer by NGS, numerous observational studies support the conclusion that use of NGS as a diagnostic test to identify germline mutations improves cancer treatment in patients diagnosed with inherited cancer and leads to improved health outcomes such as survival, which includes overall survival, progression free survival, and relapse-free survival.  For some cancers, use of NGS as a diagnostic test can lead to the identification of the most effective treatment for the diagnosis of inherited cancer.(Norquist et al., 2013).  We believe an accurate diagnosis of some inherited cancers by NGS through the identification of germline mutations will directly guide physician treatment and improve patient health outcomes that are germane to Medicare beneficiaries with those inherited cancers. For validated tests, we find the benefits in health outcomes of NGS testing for germline mutations for certain cancers outweigh the harms associated with testing.

    In the reviewed studies, treatment modalities included chemotherapy, radiotherapy, or surgery, unless treatment modality was not reported (Lang et al., 2017; Pastorino et al., 2018; Yurgelun et al., 2019).  In prospective studies, such as the clinical trials by Lin et al. (2019) and Swisher et al. (2017), NGS diagnostic test results were used to guide medical decision making in the treatment of inherited cancer patients and revealed a beneficial impact on health outcomes.  In historical cohort studies by Golan et al. (2017) and Kotoula et al.(2017), the authors conducted a retrospective analysis showing benefits of NGS testing performed at the time of diagnosis and then treatment of the inherited cancer that was obtained from a clinical database.  But in other historical cohort studies (Brianese et al., 2018; Deng et al., 2019; Hjortkjær et al., 2019) and a retrospective case-control study (Yoshihama et al., 2018), the authors performed NGS testing on archived germline samples obtained from a biobank.  Even though NGS testing was performed after the diagnosis and treatment of cancer, the beneficial results from these four studies show that if the physician had used the NGS diagnostic test results in the clinical management of inherited cancer patients, it is likely that the beneficial effects on health outcomes still would have been found.  In certain inherited cancers, the reviewed studies demonstrate that physicians using NGS as a diagnostic test to guide medical decision making in the clinical treatment of inherited cancer patients is reasonable and necessary to improve health outcomes for Medicare beneficiaries.

    Ovarian Cancer

    Among the studies examining ovarian cancer, evidence of moderate quality comes from two studies (Lin et al., 2019; Swisher et al., 2017) of the ARIEL2 drug treatment trials.  The limitations include study design issues such as the study being unblinded with treatment not blinded to the patient or investigator, and having no control group, both of which are study methods typically used in studies of drug treatments.  Study strengths include that ARIEL2 was an international multicenter trial, some of which was conducted in the United States, permitting some generalizability of study results to the Medicare population. The median age was 60.5 years (range, 33 – 82 years) for the Lin et al (2019) study and 58.5 years (interquartile range 53.5 – 67.5 years) for the Swisher et al. (2017) study.  No data for race or gender were reported from either study.

    In the moderate quality retrospective study of the Danish Gynecologic Cancer Database registry by Hjortkjær et al. (2019), although this study was a population based study reflecting the positive impact of NGS diagnostic testing on overall survival in a large nationwide sample, the registry was not in the United States and thus could limit the generalizability of the findings to Medicare beneficiaries.  The majority (62.9%) of the individuals were > 60 years old at the time of diagnosis, and no data was presented for race or gender from the Danish registry. Given the retrospective nature of the registry study, bias was not entirely minimized a priori in the design of this registry study, though multivariate adjustment was in the analysis, which could affect any inferences drawn from this study.  A major strength of the Danish study by Hjortkjaer, et al. (2019) is that it is population-based.

    The evidence of all of the above studies is of moderate quality. However, we believe that the weight of the above evidence suggest that use of NGS as a diagnostic test to identify germline mutations, such as BRCA, to diagnose ovarian cancer improves survival and can impact clinical decision making in the clinical management of ovarian carcinoma.

    There are three relevant studies of ovarian cancer whose evidence is of low quality due to the small sample size of each of the studies.  A retrospective cohort study (Chen, et al., 2016) and a retrospective case-control study (Yoshihama et al., 2018) showed that NGS testing for germline mutations, such as P53 (Chen, et al., 2016) and GSTP1 (Yoshihama, et al., 2018), in the diagnosis of ovarian cancer or gynecological cancers improved overall survival.  A prospective cohort study (Zhao, et al., 2017) showed that NGS testing for other germline mutations besides BRCA1/2, such as RAD and ATR, were associated with poor overall survival, which could lead to better stratification in the individualized clinical management of ovarian cancer patients other than merely using BRCA1/2 to improve survival.  Small sample sizes in the ovarian cancer studies led to wide confidence intervals and a greater variability in the estimate of the effect of NGS testing.  Chance variability in the relationship between the use of NGS and a positive health outcome, such as survival, may have accounted for the results observed in any individual study.  Because of chance, the study results may have overestimated or underestimated the true effect of NGS diagnostic testing on overall survival.  This could lead to an imprecise effect estimate and an invalid conclusion being drawn from the results of these studies.  Although the above studies had major limitations, they all suggested that there was benefit in using NGS to diagnose and treat ovarian cancer.

    There was one study (Yoshihama, et al., 2018) examining the use of NGS to diagnose other gynecological cancers, in addition to ovarian cancer.  This study defined gynecological cancers as different types of cancers including ovarian, fallopian tube, peritoneal, uterine, and cervical cancers.  With one study, we do not have the evidence to include these others for national coverage at this time.  We recognize that evidence continues to rapidly accrue, like in somatic cancers, and believe these cancers may be addressed by the Medicare contractors.

    Breast Cancer

    For breast cancer, the quality of the evidence was moderate for two clinical trials (Kotoula et al., 2017; Toomey et al., 2016).  One of the studies by Kotoula et al. (2017) had a small sample size.  Both clinical trials showed that using NGS to identify germline mutations to diagnose breast cancer improves survival.  Three other lower quality studies were conducted at single institutions (Deng et al., 2019; Wang et al., 2018; Zhong et al., 2016).  All three were prospective cohort studies that showed that the BRCA1 germline mutation status found by NGS was associated with a worse disease progression, but not overall survival, in women with breast cancer.  With the median follow-up ranging from three to five years, it is less likely that these study results are affected by a short follow-up period.  Results from studies conducted at a single institution might not be generalizable to the Medicare population since the population at a single medical center might not be representative of the population of Medicare beneficiaries as a whole due to differences in sociodemographic factors, such as age, race, and gender, of beneficiaries at different medical centers.  In addition, differences in oncologic practice between medical centers might not reflect the overall oncologic practice experience of Medicare beneficiaries as a population.

    There were several studies that failed to show the effect of NGS on breast cancer outcomes.  Two studies were of low quality due to small sample size (Yap et al., 2018) or having a small number of events (Fan et al., 2018).  Both showed inferior survival when using NGS to identify germline mutations, such as NF1 or RAD50, respectively, in the diagnosis of breast cancer.  Two additional studies (Brianese et al., 2018; Lang et al., 2017) failed to show a statistically significant effect of using the NGS diagnostic test to identify germline mutations, such as BRCA, to diagnose breast cancer on survival.  While both studies had a small number of observed events, the Lang et al. (2017) study also had a short follow-up period whereas the Brianese et al (2018) study also had a small sample size.  The short follow up period means that the cancer patients have not been observed for a long enough time period to accrue outcomes of interest, such as death. The outcomes of interest may be missed and an incorrect inference might be made about the relationship between the use of NGS and mortality.  A small sample size or a small number of observed events, such as death, could result in a lack of statistical power to find a statistically significant effect on mortality of using the NGS diagnostic test to identify a germline mutation in the diagnosis of breast cancer.  A small sample size, or a small number of observed events might result in a study failing to have sufficient statistical power to conclude that chance was not a likely explanation of the relationship between the use of NGS test and mortality.  Thus, it is possible that both studies would fail to find the true effect on mortality of using NGS as a diagnostic test to identify a germline mutation to diagnose breast cancer.

    Despite the limitations in both, the findings of the moderate quality studies and the low quality studies are coherent.  They present sufficient evidence to warrant using NGS as a diagnostic test to identify germline mutations in the diagnosis of breast cancer to improve health outcomes of Medicare beneficiaries depending on the clinical management of breast cancer based on physician clinical decision-making.

    Pancreatic Cancer

    For pancreatic cancer, two studies (Blair et al., 2018; Yurgelun et al., 2019) demonstrated conflicting results on the use of the NGS diagnostic test to identify a germline mutation, such as BRCA1/2, in the diagnosis of pancreatic adenocarcinoma.  Among resected pancreatic ductal adenocarcinoma (PDAC) cases, Blair et al. (2018) concluded that carriers of a germline BRCA1/BRCA2 mutation had worse overall survival after pancreatectomy than their matched BRCA1/2 wild-type normal counterparts.  They concluded that platinum-based adjuvant chemotherapy regimens were associated with markedly improved survival in patients with BRCA1/BRCA2 mutations.  However, among patients with resection of pancreatic adenocarcinoma, Yurgelun et al. (2019) found that germline gene variant carriers of double-strand DNA damage repair (dsDDR) genes found by NGS, including BRCA1/2 and MSH2 and MSH6 in Lynch syndrome, had superior overall survival compared to noncarriers.

    Comparing analytic methods, Yurgelun et al. (2019) failed to account for the adjuvant treatment and palliative therapy regimens received by the patients with germline variants in the interpretation of the overall data analysis.  The Yurgelun et al. (2019) study shows superior overall survival in germline gene variant carriers likely because 20 of 28 (71.4%) of germline variant carriers had either or both adjuvant treatment or treatment for metastatic disease, but treatment effect was not accounted for in the analysis or discussed in the conclusions.  Further, Blair et al. (2018) only compared BRCA1/BRCA2 germline mutations, while Yurgelun et al. (2019) compared many germline gene variants beyond BRCA1/BRCA2.  The comparison group in the Yurgelun et al. (2019) study consisted of noncarriers of the germline variants, and not those patients with wild-type normal alleles, as in the Blair et al. (2018) study  We acknowledge that analytic differences can change the direction of effect on overall survival for patients who received treatment for germline variants.  Lack of consistency in findings across several studies suggests that results are more likely to represent chance fluctuations in the data rather than a true finding.   We do not have the evidence to include pancreatic cancer for national coverage at this time.  We recognize that evidence continues to rapidly accrue, like in somatic cancers, and believe these cancers may be addressed by the Medicare Administrative Contractors.

    Other Cancers

    Low quality evidence exists for three other cancers, cholangiocarcinoma (CCA), malignant mesothelioma, and astrocytoma because only one study was conducted for each of the cancers.  Among cholangiocarcinoma (CCA) patients diagnosed by NGS, Golan et al (2017) found that patients bearing BRCA1/2 variants mutations and treated with either platinum-based therapy or poly ADP ribose polymerase inhibitors (PARPi) demonstrated favorable overall survival.  In a malignant mesothelioma study, Pastorino et al. (2018) concluded that patients with BAP1 mutations identified by NGS had a worse survival than those with no BAP1 mutations.  A study of astrocytoma patients by Perdomo-Pantoja et al. (2018) showed that the human angiotensinogen (AGT) rs5050 GG-genotype identified by NGS was associated with lower survival from astrocytoma.  In an evidence-based approach, we believe it is important to have multiple studies report study findings that are consistent and provide coherence in the inferences drawn from the evidence.  Subsequent studies, if conducted by different investigators among various study populations using alternative study designs and analytic methodologies, should show similar results to previous studies with respect to the use of NGS.  The three single studies of a cancer had other severe limitations.  While all three studies had small sample sizes, the Golan et al. (2017) study also was a retrospective cohort study, the Perdomo-Pantoja et al. (2018) study was conducted at a single institution and the Pastorino et al. (2018) study also lacked an appropriate comparison group and statistical analysis.

    Guidelines

    The NCCN and American Society of Breast Surgeons guidelines for breast cancer and ovarian cancer mention the use of NGS, but the other guidelines made no specific recommendation on type of test, such as NGS, to be used for a specific cancer type.

    In our search of the literature for guidelines, Stoffel et al. (2019) conducted a systematic review of pancreatic cancer for the American Society of Clinical Oncology.  The expert panel made a statement that "unless a genetic diagnosis has previously been confirmed in a family member, germline genetic testing should be performed using a multigene panel".  Based on a dataset analysis unselected for cancer types (Mandelker et al., 2019), the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup made the recommendation that "local validation will be required to confirm the accuracy of tumor VAF (variant allele frequency) estimates, especially for PCR-based NGS methodologies".  However, the use of NGS to diagnose germline cancers was not specifically mentioned in the American Society of Clinical Oncology (ASCO) provisional clinical opinion (PCO) on pancreatic cancer or the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup recommendations.

    As noted before in our responses to the public comments, we critically reviewed numerous references submitted to us on colorectal cancer, male breast cancer, lung cancer, prostate cancer, and pancreatic cancer, using the same methodological approach that we used in our internal technology assessment.  The reviewed evidence was insufficient to show that using NGS to identify germline mutations improved health outcomes in patients with an inherited cancer of the colon or rectum, lung, prostate, or pancreas, or male patients with inherited breast cancer.  We recognize that evidence on clinical utility of NGS testing continues to rapidly accrue, like in somatic cancers, and believe these cancers may be addressed by the Medicare Administrative Contractors.

    Patient Criteria

    In addition to nationally covering breast and ovarian cancers based on the evidence reviewed, the published studies were consistent in identifying which cancer patients  most likely benefit from NGS germline testing.  Patients enrolled and included in published studies generally had at least one diagnosed cancer.  Further, clinical indications and risk factors were used to identify appropriate patients.  As part of the clinical pathway to evaluate patients suspected of having germline (inherited) mutations, guidelines such as NCCN Clinical Practice Guidelines in Oncology (for example breast, ovarian, and pancreatic cancers) are often used during their clinical management.  These published guidelines are important in the diagnostic pathway and specify diagnostic testing criteria for breast, ovarian, as well as other inherited cancers to identify susceptibility genes.  These criteria include specific patient characteristics such as the clinical indications of a personal history of breast or ovarian cancer, as well as risk factors such as family history of breast or ovarian cancer.  We did not find evidence on NGS germline testing for patients that did not have cancer, a clinical indication and a risk factor for inherited cancer.  NGS germline tests in patients who do not meet specific patient criteria are not reasonable and necessary.

    Repeat Testing

    Manufacturers have noted that germline tests, as well as somatic tests, are rapidly evolving and that new genetic markers are being developed and added to many existing tests.  As such, patients who have previously received NGS testing to detect somatic mutations may have a clinical indication to repeat NGS testing to detect new genetic mutations associated with the cancer.  Newer tests may be more comprehensive.  Also, patients who have received NGS testing to detect mutations in the diagnosed somatic cancer may require germline NGS testing if there criteria are met.  Likewise, patients who have received NGS testing to detect germline mutations may require somatic NGS testing of the somatic cancer if criteria are met.  To foster development of new NGS companion diagnostics and targeted therapies to improve health outcomes, we will cover a repeat germline test if it tests for a different genetic mutation(s) associated with inherited cancer, as we would cover a repeat somatic test if it tests for a different genetic mutation associated with the somatic cancer. 

    Health Disparities

    In the evidence reviewed, health disparities is not addressed in the clinical research study summaries as related to the clinical utility of using NGS as a diagnostic test for germline cancer.  Analyses stratified by race, ethnicity, religion, or socioeconomic status were not found in the clinical research studies.

    In order to provide data on health disparities in the Medicare population, the CMS Office of Minority Health provides a Mapping Medicare Disparities Tool to identify areas of disparities between sub-populations in health outcomes, service utilization, and health- related data geographically, which may be used to target populations for potential interventions.  Measuring the prevalence in a limited focus to breast, colorectal, lung, and prostate cancers identified disparities in the prevalence of these cancers in 36 states for Black and in 40 states for Hispanic relative to White males over 85 years old.

    Measuring the incidence and prevalence of cancer among different races/ethnicities identifies areas of health disparities among those with disproportionate burdens of cancer.  This information may be used to target populations for potential interventions.  However, the evidence presented here includes different populations.  The evidence for the breast cancer studies consisted almost entirely of women and the majority of the populations studied were Caucasian (Brianese, 2018; Kotoula, 2017; Toomey, 2016) or ethnic Chinese (Deng, 2019; Fan, 2018; Lang, 2017; Wang, 2018; Zhong, 2016).  Among the cited ovarian cancer studies, the study populations consisted of women and the majority populations were Caucasian (Chen, 2016; Hjortkjær, 2019; Lin, 2019; Norquist, 2013; Swisher, 2017), Japanese (Yoshihama, 2018) or ethnic Chinese (Zhao, 2017).  That the evidence includes different study populations suggests that those with identified health disparities also comprise a minority of study participants in the area of applying NGS as a diagnostic laboratory test for inherited cancer.  Further research to identify the barriers that are unique to accessing and increasing the inclusion of a diverse population of patients in cancer clinical trials is warranted.

    Summary

    The evidence for cancers of the breast and ovary suggests that the use of NGS can identify germline mutations which will lead to better treatment and health outcomes for patients with inherited cancers of the breast and ovary.  The evidence for cancer of the breast and ovary indicates that NGS as a diagnostic tool can identify the germline mutations most likely to be targeted by a treatment regimen tailored to certain germline mutation.  It is likely that the identification of such a tailored treatment regimens in the clinical management of inherited cancers of the breast and ovary diagnosed by NGS will improve health outcomes of Medicare beneficiaries.  Use of NGS as a diagnostic test has utility for patients in the discovery of new targeted therapies for inherited cancers and in the physician management of inherited cancers of the breast and ovary in Medicare beneficiaries.  We believe that, for other cancers, the evidence on clinical utility is rapidly developing and accumulating.  We are therefore maintaining the Medicare Administrative Contractors (MACs) discretion to determine clinical utility and make coverage decisions on diagnostic uses of NGS testing for inherited mutations in patients with inherited cancers based on new evidence that may arise.

    IX.      Conclusion

    A.   The Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a CLIA-certified laboratory, when ordered by a treating physician and when all of the following requirements are met:

    1. The patient has:
      • ovarian or breast cancer; and
      • a clinical indication for germline (inherited) testing for hereditary breast or ovarian cancer; and
      • a risk factor for germline (inherited) breast or ovarian cancer; and
      • not been previously tested with the same germline test using NGS for the same germline genetic content.
    2. The diagnostic laboratory test using NGS must have all of the following:
      • Food and Drug Administration (FDA) approval or clearance; and
      • results provided to the treating physician for management of the patient using a report template to specify treatment options.

    B.  Other

    Medicare Administrative Contractors (MACs) may determine coverage of Next Generation Sequencing (NGS) as a diagnostic laboratory test when performed in a CLIA-certified laboratory, when ordered by a treating physician, when results are provided to the treating physician for management of the patient and when the patient has:

    • any cancer diagnosis; and
    • a clinical indication for germline (inherited) testing of hereditary cancers; and
    • a risk factor for germline (inherited) cancer; and
    • not been previously tested with the same germline test using NGS for the same germline genetic content.

    We are making other technical, clarifying, and conforming changes in Section 90.2 of the National Coverage Determinations Manual.  We are clarifying the existing policy related to diagnostic tests for Somatic (Acquired) Cancer. 

    See Appendix B for the draft manual language.

    For ease of the reader, this National Coverage Determination (NCD) is only applicable to diagnostic lab tests using NGS for somatic (acquired) and germline (inherited) cancer.  Medicare Administrative Contractors (MACs) may determine coverage of diagnostic lab tests using NGS for RNA sequencing and protein analysis.  MACs also have discretion to determine coverage of diagnostic lab tests using NGS for any non-cancer (e.g., infectious disease and heart disease) use.  These uses are outside the scope of this NCD.



    APPENDIX A
    General Methodological Principles of Study Design

    (Section VI of the Decision Memorandum)

    When making national coverage determinations, CMS evaluates relevant clinical evidence to determine whether or not the evidence is of sufficient quality to support a finding that an item or service is reasonable and necessary. The overall objective for the critical appraisal of the evidence is to determine to what degree we are confident that: 1) the specific assessment questions can be answered conclusively; and 2) the intervention will improve health outcomes for patients.

    We divide the assessment of clinical evidence into three stages: 1) the quality of the individual studies; 2) the generalizability of findings from individual studies to the Medicare population; and 3) overarching conclusions that can be drawn from the body of the evidence on the direction and magnitude of the intervention’s potential risks and benefits.

    The methodological principles described below represent a broad discussion of the issues we consider when reviewing clinical evidence. However, it should be noted that each coverage determination has its unique methodological aspects.

    Assessing Individual Studies

    Methodologists have developed criteria to determine weaknesses and strengths of clinical research. Strength of evidence generally refers to: 1) the scientific validity underlying study findings regarding causal relationships between health care interventions and health outcomes; and 2) the reduction of bias. In general, some of the methodological attributes associated with stronger evidence include those listed below:

    • Use of randomization (allocation of patients to either intervention or control group) in order to minimize bias.
    • Use of contemporaneous control groups (rather than historical controls) in order to ensure comparability between the intervention and control groups.
    • Prospective (rather than retrospective) studies to ensure a more thorough and systematical assessment of factors related to outcomes.
    • Larger sample sizes in studies to demonstrate both statistically significant as well as clinically significant outcomes that can be extrapolated to the Medicare population. Sample size should be large enough to make chance an unlikely explanation for what was found.
    • Masking (blinding) to ensure patients and investigators do not know to that group patients were assigned (intervention or control). This is important especially in subjective outcomes, such as pain or quality of life, where enthusiasm and psychological factors may lead to an improved perceived outcome by either the patient or assessor.

    Regardless of whether the design of a study is a randomized controlled trial, a non-randomized controlled trial, a cohort study or a case-control study, the primary criterion for methodological strength or quality is to the extent that differences between intervention and control groups can be attributed to the intervention studied. This is known as internal validity. Various types of bias can undermine internal validity. These include:

    • Different characteristics between patients participating and those theoretically eligible for study but not participating (selection bias).
    • Co-interventions or provision of care apart from the intervention under evaluation (performance bias).
    • Differential assessment of outcome (detection bias).
    • Occurrence and reporting of patients who do not complete the study (attrition bias).

    In principle, rankings of research design have been based on the ability of each study design category to minimize these biases. A randomized controlled trial minimizes systematic bias (in theory) by selecting a sample of participants from a particular population and allocating them randomly to the intervention and control groups. Thus, in general, randomized controlled studies have been typically assigned the greatest strength, followed by non-randomized clinical trials and controlled observational studies. The design, conduct and analysis of trials are important factors as well. For example, a well-designed and conducted observational study with a large sample size may provide stronger evidence than a poorly designed and conducted randomized controlled trial with a small sample size. The following is a representative list of study designs (some of that have alternative names) ranked from most to least methodologically rigorous in their potential ability to minimize systematic bias:

    Randomized controlled trials
    Non-randomized controlled trials
    Prospective cohort studies
    Retrospective case control studies
    Cross-sectional studies
    Surveillance studies (e. g. , using registries or surveys)
    Consecutive case series
    Single case reports

    When there are merely associations but not causal relationships between a study’s variables and outcomes, it is important not to draw causal inferences. Confounding refers to independent variables that systematically vary with the causal variable. This distorts measurement of the outcome of interest because its effect size is mixed with the effects of other extraneous factors. For observational, and in some cases randomized controlled trials, the method in that confounding factors are handled (either through stratification or appropriate statistical modeling) are of particular concern. For example, in order to interpret and generalize conclusions to our population of Medicare patients, it may be necessary for studies to match or stratify their intervention and control groups by patient age or co-morbidities.

    Methodological strength is, therefore, a multidimensional concept that relates to the design, implementation and analysis of a clinical study. In addition, thorough documentation of the conduct of the research, particularly study selection criteria, rate of attrition and process for data collection, is essential for CMS to adequately assess and consider the evidence.

    Generalizability of Clinical Evidence to the Medicare Population

    The applicability of the results of a study to other populations, settings, treatment regimens and outcomes assessed is known as external validity. Even well-designed and well-conducted trials may not supply the evidence needed if the results of a study are not applicable to the Medicare population. Evidence that provides accurate information about a population or setting not well represented in the Medicare program would be considered but would suffer from limited generalizability.

    The extent to that the results of a trial are applicable to other circumstances is often a matter of judgment that depends on specific study characteristics, primarily the patient population studied (age, sex, severity of disease and presence of co-morbidities) and the care setting (primary to tertiary level of care, as well as the experience and specialization of the care provider). Additional relevant variables are treatment regimens (dosage, timing and route of administration), co-interventions or concomitant therapies, and type of outcome and length of follow-up.

    The level of care and the experience of the providers in the study are other crucial elements in assessing a study’s external validity. Trial participants in an academic medical center may receive more or different attention than is typically available in non-tertiary settings. For example, an investigator’s lengthy and detailed explanations of the potential benefits of the intervention and/or the use of new equipment provided to the academic center by the study sponsor may raise doubts about the applicability of study findings to community practice.

    Given the evidence available in the research literature, some degree of generalization about an intervention’s potential benefits and harms is invariably required in making coverage determinations for the Medicare population. Conditions that assist us in making reasonable generalizations are biologic plausibility, similarities between the populations studied and Medicare patients (age, sex, ethnicity and clinical presentation) and similarities of the intervention studied to those that would be routinely available in community practice.

    A study’s selected outcomes are an important consideration in generalizing available clinical evidence to Medicare coverage determinations. One of the goals of our determination process is to assess health outcomes. These outcomes include resultant risks and benefits such as increased or decreased morbidity and mortality. In order to make this determination, it is often necessary to evaluate whether the strength of the evidence is adequate to draw conclusions about the direction and magnitude of each individual outcome relevant to the intervention under study. In addition, it is important that an intervention’s benefits are clinically significant and durable, rather than marginal or short-lived. Generally, an intervention is not reasonable and necessary if its risks outweigh its benefits.

    If key health outcomes have not been studied or the direction of clinical effect is inconclusive, we may also evaluate the strength and adequacy of indirect evidence linking intermediate or surrogate outcomes to our outcomes of interest.

    Assessing the Relative Magnitude of Risks and Benefits

    Generally, an intervention is not reasonable and necessary if its risks outweigh its benefits. Health outcomes are one of several considerations in determining whether an item or service is reasonable and necessary. CMS places greater emphasis on health outcomes actually experienced by patients, such as quality of life, functional status, duration of disability, morbidity and mortality, and less emphasis on outcomes that patients do not directly experience, such as intermediate outcomes, surrogate outcomes, and laboratory or radiographic responses. The direction, magnitude, and consistency of the risks and benefits across studies are also important considerations. Based on the analysis of the strength of the evidence, CMS assesses the relative magnitude of an intervention or technology’s benefits and risk of harm to Medicare beneficiaries.



    APPENDIX B
    Medicare National Coverage Determinations Manual

    This draft NCD is subject to formal revisions and formatting changes prior to the release of the final NCD contractor instructions and publication in the Medicare National Coverage Determinations Manual.

    Table of Contents

    (Rev.)

    90.2 Next Generation Sequencing (NGS) for Patients with Somatic (Acquired) and Germline (Inherited) Cancer

    A.  General

    Clinical laboratory diagnostic tests can include tests that, for example, predict the risk associated with one or more genetic variations.  In addition, in vitro companion diagnostic laboratory tests provide a report of test results of genetic variations and are essential for the safe and effective use of a corresponding therapeutic product.  Next Generation Sequencing (NGS) is one technique that can measure one or more genetic variations as a laboratory diagnostic test, such as when used as a companion in vitro diagnostic test.

    This National Coverage Determination (NCD) is only applicable to diagnostic lab tests using NGS for somatic (acquired) and germline (inherited) cancer.  Medicare Administrative Contractors (MACs) may determine coverage of diagnostic lab tests using NGS for RNA sequencing and protein analysis.  MACs also have discretion to determine coverage of diagnostic lab tests using NGS for any non-cancer (e.g., infectious disease and heart disease) use.  These uses are outside the scope of this NCD.

    B. Nationally Covered Indications

    1. Somatic (Acquired) Cancer

    Effective for services performed on or after March 16, 2018, the Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, when ordered by a treating physician, and when all of the following requirements are met:

    1. Patient has:
      1. either recurrent, relapsed, refractory, metastatic, or advanced stage III or IV cancer; and
      2. not been previously tested with the same test using NGS for the same cancer genetic content, and
      3. decided to seek further cancer treatment (e.g., therapeutic chemotherapy).
    2. The diagnostic laboratory test using NGS must have:
      1. Food & Drug Administration (FDA) approval or clearance as a companion in vitro diagnostic; and,
      2. an FDA-approved or -cleared indication for use in that patient’s cancer; and,
      3. results provided to the treating physician for management of the patient using a report template to specify treatment options.
    1. Germline (Inherited) Cancer

    Effective for services performed on or after [DATE], CMS has determined that NGS as a diagnostic laboratory test is reasonable and necessary and covered nationally for patients with germline (inherited) cancer, when performed in a CLIA-certified laboratory, when ordered by a treating physician and when all of the following requirements are met:

    1. Patient has:
      1. ovarian or breast cancer; and,
      2. a clinical indication for germline (inherited) testing for hereditary breast or ovarian cancer; and,
      3. a risk factor for germline (inherited) breast or ovarian cancer; and
      4. not been previously tested with the same germline test using NGS for the same germline genetic content.
    2. The diagnostic laboratory test using NGS must have all of the following:
      1. FDA-approval or clearance; and,
      2. results provided to the treating physician for management of the patient using a report template to specify treatment options.

    C. Nationally Non-Covered Indications

    1. Somatic (Acquired) Cancer
    Effective for services performed on or after March 16, 2018, NGS as a diagnostic laboratory test for patients with acquired (somatic) cancer are non-covered if the cancer patient does not meet the criteria noted in section B.1. above.

    D. Other

    1. Somatic (Acquired) Cancer

    Effective for services performed on or after March 16, 2018, Medicare Administrative Contractors (MACs) may determine coverage of NGS as a diagnostic laboratory test for patients with advanced cancer only when the test is performed in a CLIA-certified laboratory, when ordered by a treating physician, and when the patient has:

    a. either recurrent, relapsed, refractory, metastatic, or advanced stages III or IV cancer; and,
    b. not been previously tested with the same test using NGS for the same cancer genetic content, and
    c. decided to seek further cancer treatment (e.g., therapeutic chemotherapy).

    1. Germline (Inherited) Cancer

    Effective for services performed on or after [DATE], MACs may determine coverage of NGS as a diagnostic laboratory test for patients with germline (inherited) cancer only when the test is performed in a CLIA-certified laboratory, when ordered by a treating physician, when results are provided to the treating physician for management of the patient and when the patient has:

    1. any cancer diagnosis; and,
    2. a clinical indication for germline (inherited) testing of hereditary cancers; and,
    3. a risk factor for germline (inherited) cancer; and,
    4. not been previously tested with the same germline test using NGS for the same germline genetic content.

    (This NCD last reviewed XX.)



    APPENDIX C
    Current Medicare National Coverage Determinations Manual

    90.2 Next Generation Sequencing (NGS) for Patients with Advanced Cancer (Rev. 215, Issued: 04-10-19, Effective: 03-16-18, Implementation: 04-08-19)

    A.   General

    Clinical laboratory diagnostic tests can include tests that, for example, predict the risk associated with one or more genetic variations. In addition, in vitro companion diagnostic laboratory tests provide a report of test results of genetic variations and are essential for the safe and effective use of a corresponding therapeutic product. Next Generation Sequencing (NGS) is one technique that can measure one or more genetic variations as a laboratory diagnostic test, such as when used as a companion in vitro diagnostic test.

    Patients with cancer can have recurrent, relapsed, refractory, metastatic, and/or advanced stages III or IV of cancer. Clinical studies show that genetic variations in a patient’s cancer can, in concert with clinical factors, predict how each individual responds to specific treatments.

    In application, a report of results of a diagnostic laboratory test using NGS (i.e., information on the cancer’s genetic variations) can contribute to predicting a patient’s response to a given drug: good, bad, or none at all. Applications of NGS to predict a patient’s response to treatment occurs ideally prior to initiation of such treatment.

    B.  Nationally Covered Indications

    Effective for services performed on or after March 16, 2018, the Centers for Medicare & Medicaid Services (CMS) has determined that Next Generation Sequencing (NGS) as a diagnostic laboratory test is reasonable and necessary and covered nationally, when performed in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, when ordered by a treating physician, and when all of the following requirements are met:

    1.  Patient has:

    • either recurrent, relapsed, refractory, metastatic, or advanced stage III or IV cancer; and,
    • either not been previously tested using the same NGS test for the same primary diagnosis of cancer, or repeat testing using the same NGS test only when a new primary cancer diagnosis is made by the treating physician; and,
    • decided to seek further cancer treatment (e.g., therapeutic chemotherapy).

    2.  The diagnostic laboratory test using NGS must have:

    • Food & Drug Administration (FDA) approval or clearance as a companion in vitro diagnostic; and,
    • an FDA-approved or -cleared indication for use in that patient’s cancer; and,
    • results provided to the treating physician for management of the patient using a report template to specify treatment options.

    C.  Nationally  Non-Covered

    Effective for services performed on or after March 16, 2018, NGS as a diagnostic laboratory test for patients with cancer are non-covered if the cancer patient does not meet the criteria noted in section B.1. above.

    D. Other

    Effective for services performed on or after March 16, 2018, Medicare Administrative Contractors (MACs) may determine coverage of other NGS as a diagnostic laboratory test for patients with cancer only when the test is performed in a CLIA-certified laboratory, ordered by a treating physician, and the patient has:

    • either recurrent, relapsed, refractory, metastatic, or advanced stages III or IV cancer; and,
    • either not been previously tested using the same NGS test for the same primary diagnosis of cancer or repeat testing using the same NGS test was performed only when a new primary cancer diagnosis is made by the treating physician; and,
    • decided to seek further cancer treatment (e.g., therapeutic chemotherapy).

    (This NCD last reviewed March 2018.)



    Appendix D-Supplemental Bibliography (Reviewed but not included in DM)

    Abida, W et al. Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making. (2017) Precis Oncol.

    AGS Choosing Wisely Workgroup. American Geriatrics Society Identifies Another Five Things That Healthcare Providers and Patients Should Question. Journal of the American Geriatrics Society, U.S. National Library of Medicine, May 2014, (www.ncbi.nlm.nih.gov/pubmed/24575770).

    Ahronian L and Corcoran R. Strategies for monitoring and combating resistance to combination kinase inhibitors for cancer therapy. Genome Medicine. 2017;9:37.

    AIM Specialty Health. Clinical Appropriateness Guidelines Genetic Testing for Hereditary Cancer Susceptibility. Effective March 31, 2019. (http://aimspecialtyhealth.com/PDF/Guidelines/2019/Mar31/HereditaryCancerSusceptibility.pdf).

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