Genetic Cancer Susceptibility Panels Using Next .The objective of this evidence review is to...

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  • Genetic Cancer Susceptibility Panels Using Next Generation Sequencing Page 1 of 35

    Current Procedural Terminology American Medical Association. All Rights Reserved.

    Contains Public Information

    Medical Policy An independent licensee of the Blue Cross Blue Shield Association

    Title: Genetic Cancer Susceptibility Panels Using Next

    Generation Sequencing Professional Institutional Original Effective Date: February 7, 2014 Original Effective Date: February 7, 2014 Revision Date(s): February 7, 2014; October 28, 2014; August 5, 2015; January 1, 2016; July 7, 2016; November 8, 2017; January 1, 2018

    Revision Date(s): February 7, 2014; October 28, 2014; August 5, 2015; January 1, 2016; July 7, 2016; November 8, 2017; January 1, 2018

    Current Effective Date: February 7, 2014 Current Effective Date: February 7, 2014 State and Federal mandates and health plan member contract language, including specific provisions/exclusions, take precedence over Medical Policy and must be considered first in determining eligibility for coverage. To verify a member's benefits, contact Blue Cross and Blue Shield of Kansas Customer Service. The BCBSKS Medical Policies contained herein are for informational purposes and apply only to members who have health insurance through BCBSKS or who are covered by a self-insured group plan administered by BCBSKS. Medical Policy for FEP members is subject to FEP medical policy which may differ from BCBSKS Medical Policy. The medical policies do not constitute medical advice or medical care. Treating health care providers are independent contractors and are neither employees nor agents of Blue Cross and Blue Shield of Kansas and are solely responsible for diagnosis, treatment and medical advice. If your patient is covered under a different Blue Cross and Blue Shield plan, please refer to the Medical Policies of that plan.

    Populations Interventions Comparators Outcomes Individuals: With a personal and/or

    family history suggesting an inherited cancer syndrome

    Interventions of interest are: Next generation

    sequencing panels

    Comparators of interest are: Individual variant

    testing

    Relevant outcomes include: Overall survival Disease-specific survival Test accuracy Test validity

    DESCRIPTION Commercially available cancer susceptibility gene panels can test for multiple variants associated with a specific type of cancer or can include variants associated with a wide variety of cancers. While some patients may have a personal and/or family history of cancer that suggests the cancer is syndrome-related, numerous genetic variants are

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  • Genetic Cancer Susceptibility Panels Using Next Generation Sequencing Page 2 of 35

    Current Procedural Terminology American Medical Association. All Rights Reserved.

    Contains Public Information

    associated with inherited cancer syndromes. It has been proposed that variant testing using next generation sequencing technology to analyze multiple genes at one time (panel testing) can optimize genetic testing in these patients compared with sequencing single genes.

    OBJECTIVE The objective of this evidence review is to evaluate whether genetic testing with cancer susceptibility panels improves health outcomes.

    BACKGROUND Genetic Testing for Cancer Susceptibility Genetic testing for cancer susceptibility may be approached by a focused method that involves testing for well-characterized variants based on a clinical suspicion of which gene(s) may be the cause of the familial cancer. Panel testing involves testing for multiple variants in multiple genes at one time. Several companies, including Ambry Genetics and GeneDx, offer genetic testing panels that use NGS methods for hereditary cancers. NGS refers to 1 of several methods that use massively parallel platforms to allow the sequencing of large stretches of DNA. Panel testing is potentially associated with greater efficiencies in the evaluation of genetic diseases; however, it may provide information on genetic variants that are of unclear clinical significance or which would not lead to changes in patient management. Currently available panels do not include all genes associated with hereditary cancer syndromes. In addition, these panels do not test for variants (ie, single nucleotide polymorphisms [SNPs]), which may be associated with a low, but increased cancer risk. NGS Cancer Panels A list of the genes that are included in these panels is given in Tables 1 to 3. Table 4 provides a list of other hereditary cancer test panels. A brief description of each gene follows the tables. These panels are constantly evolving and the tables below may not represent what the test currently includes. Table 1. Ambry Genetics Hereditary Cancer Panel Tests

    Gene Tested CancerNext (34 gene)

    TumorNext (11 gene)

    ColoNext (17

    gene) ProstateNext

    (14 gene) BRCAplus (8 gene)

    OvaNext (25 gene)

    BreastNext (17 gene)

    ALK APC X AKT1 APC X ATM X X X X X X ATR AXIN2 BAP1 BARD1 X X X X BLM BMPR1A X X BRCA1 X X X X X X

  • Genetic Cancer Susceptibility Panels Using Next Generation Sequencing Page 3 of 35

    Current Procedural Terminology American Medical Association. All Rights Reserved.

    Contains Public Information

    Gene Tested CancerNext (34 gene)

    TumorNext (11 gene)

    ColoNext (17

    gene) ProstateNext

    (14 gene) BRCAplus (8 gene)

    OvaNext (25 gene)

    BreastNext (17 gene)

    BRCA2 X X X X X X BRIP1 X X X X CDH1 X X X X X CDK4 X CDKN2A X CHEK1 CHEK2 X X X X X X X CTNNA1 DICER1 X X EGFR EPCAM X X X X FAM175A FANCP FH FLCN GALNT12 GATA2 GEN1 GREM1 X X HOXB13 X X HRAS JAK2 KIT KRAS MAX MEN1 MET MITF MLH1 X X X X MLH2 MLH3 MRE11A X X X X MSH2 X X X X MSH6 X X X X MUTYH X X X X NBN X X X X X NF1 X X X NF2 NRAS PALB2 X X X X X X X PAX5 PDGFRA PHOX2B PIK3CA PMS2 X X X X POLD1 X X POLE X X PPM1D PRSS1 PTCH1 PTEN X X X X X RAD50 X X X RAD51 RAD51B RAD51C X X X X RAD51D X X X X X

  • Genetic Cancer Susceptibility Panels Using Next Generation Sequencing Page 4 of 35

    Current Procedural Terminology American Medical Association. All Rights Reserved.

    Contains Public Information

    Gene Tested CancerNext (34 gene)

    TumorNext (11 gene)

    ColoNext (17

    gene) ProstateNext

    (14 gene) BRCAplus (8 gene)

    OvaNext (25 gene)

    BreastNext (17 gene)

    RB1 RECQL4 RET RUNX1 SDHA SDHAF2 SDHB SDHC SDHD SMAD3 SMAD4 X X SMARCA4 X X SMARCB1 STK11 X X X SUFU TERT TGFBR1 TGFBR2 TMEM127 TP53 X X X X X X TP53BP1 TSC1 TSC2 VHL WT1 XRCC2

    Table 2. GeneDx Hereditary Cancer Panel Tests

    Gene Tested

    Comprehensive Cancer Panel (32 genes)

    High/Moderate Risk Panel (23

    genes)

    Lynch/Colorectal High Risk (7 genes)

    Colorectal Cancer

    (19 genes)

    Breast Cancer High/Moderate Risk (8 genes)

    Breast/Ovarian Cancer

    (20 genes) ALK APC AKT1 APC X X X X ATM X X X X X ATR AXIN2 X X BAP1 BARD1 X X BLM BMPR1A X X X BRCA1 X X X X BRCA2 X X X X BRIP1 X X X CDH1 X X X X X CDK4 X CDKN2A X X CHEK1 CHEK2 X X X X X CTNNA1 DICER1 EGFR EPCAM X X X X X

  • Genetic Cancer Susceptibility Panels Using Next Generation Sequencing Page 5 of 35

    Current Procedural Terminology American Medical Association. All Rights Reserved.

    Contains Public Information

    Gene Tested

    Comprehensive Cancer Panel (32 genes)

    High/Moderate Risk Panel (23

    genes)

    Lynch/Colorectal High Risk (7 genes)

    Colorectal Cancer

    (19 genes)

    Breast Cancer High/Moderate Risk (8 genes)

    Breast/Ovarian Cancer

    (20 genes) FAM175A FANCC X X FANCP FH FLCN GALNT12 GATA2 GEN1 GREM1 X X HOXB13 HRAS JAK2 KIT KRAS MAX MEN1 MET MITF MLH1 X X X X X MLH2 MLH3 MRE11A MSH2 X X X X X MSH6 X X X X X MUTYH X X X X NBN X X NF1 NF2 NRAS PALB2 X X X X PAX5 PDGFRA PHOX2B PIK3CA PMS2 X X X X X POLD1 X X POLE X X PPM1D PRSS1 PTCH1 PTEN X X X X X RAD50 RAD51 RAD51B RAD51C X X X RAD51D X X X RB1 RECQL4 RET RUNX1 SDHA SDHAF2 SDHB SDHC SDHD

  • Genetic Cancer Susceptibility Panels Using Next Generation Sequencing Page 6 of 35

    Current Procedural Terminology American Medical Association. All Rights Reserved.

    Contains Public Information

    Gene Tested

    Comprehensive Cancer Panel (32 genes)

    High/Moderate Risk Panel (23

    genes)

    Lynch/Colorectal High Risk (7 genes)

    Colorectal Cancer

    (19 genes)

    Breast Cancer High/Moderate Risk (8 genes)

    Breast/Ovarian Cancer

    (20 genes) SMAD3 SMAD4 X X SMARCA4 SMARCB1 STK11 X X SUFU TERT TGFBR1 TGFBR2 TMEM127 TP53 X X X X TP53BP1 TSC1 TSC2 VHL X WT1