A peer-reviewed version of this preprint was published in PeerJ on 28 June 2016. View the peer-reviewed version (peerj.com/articles/2162), which is the preferred citable publication unless you specifically need to cite this preprint. Kang HP, Maguire JR, Chu CS, Haque IS, Lai H, Mar-Heyming R, Ready K, Vysotskaia VS, Evans EA. (2016) Design and validation of a next generation sequencing assay for hereditary BRCA1 and BRCA2 mutation testing. PeerJ 4:e2162 https://doi.org/10.7717/peerj.2162
Design and validation of a next generation sequencing assay for hereditary breast and ovarian cancer Hyunseok P. Kang, Jared Maguire, Clement Chu, Imran S. Haque, Henry Lai, Rebecca Mar-Heyming, Kaylene Ready, Valentina S. Vysotskaia, Eric A. Evans
Hereditary breast and ovarian cancer syndrome, caused by a germline deleterious variant in the BRCA1 or BRCA2 genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a next-generation-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 96-sample validation set consisting of samples from cell lines and deidentified patient samples, including the well-characterized NA12878 sample from HapMap/1000 Genomes.
PeerJ PrePrints | https://dx.doi.org/10.7287/peerj.preprints.1463v1 | CC-BY 4.0 Open Access | rec: 30 Oct 2015, publ: 30 Oct 2015
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Design and validation of a next generation sequencing assay for hereditary breast and ovarian cancer Hyunseok P. Kang*, Jared Maguire, Clement Chu, Imran S. Haque, Henry Lai, Rebecca MarHeyming, Kaylene Ready, Valentina S. Vysotskaia, Eric A. Evans Counsyl Inc., South San Francisco, CA, USA * Correspondence should be addressed to Hyunseok P. Kang (
[email protected]) ABSTRACT Hereditary breast and ovarian cancer syndrome, caused by a germline deleterious variant in the BRCA1 or BRCA2 genes, is characterized by an increased risk for breast, ovarian, pancreatic and other cancers. Identification of those who have a BRCA1/2 mutation is important so that they can take advantage of genetic counseling, screening, and potentially life-saving prevention strategies. We describe the design and analytic validation of the Counsyl Inherited Cancer Screen, a nextgeneration-sequencing-based test to detect pathogenic variation in the BRCA1 and BRCA2 genes. We demonstrate that the test is capable of detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy-number variants (CNVs, also known as large rearrangements) with zero errors over a 96-sample validation set consisting of samples from cell lines and deidentified patient samples, including the well-characterized NA12878 sample from HapMap/1000 Genomes. INTRODUCTION Clinical Scenario and Public Health Importance Hereditary breast and ovarian cancer syndrome (HBOC) is associated with mutations in tumor suppressor genes BRCA1 and BRCA2. Genetic analysis for individuals who are at risk for HBOC has become widely accepted. Several professional organizations and expert panels, including the National Comprehensive Cancer Network (NCCN) (National Comprehensive Cancer Network, 2014), the American Society of Clinical Oncology (ASCO) (Robson et al., 2010), the American Society of Human Genetics (ASHG) (Statement of the American Society of Human Genetics on genetic testing for breast and ovarian cancer predisposition, 1994), the American College of Medical Genetics and Genomics (ACMG) (Hampel et al., 2015), the National Society of Genetic Counselors (NSGC) (Hampel et al., 2015), the U.S. Preventive Services Task Force (USPSTF) (Nelson et al., 2014), the Society of Gynecologic Oncologists (SGO) (Lancaster et al., 2007), and the European Society for Medical Oncology (ESMO) (Balmaña et al., 2011) have developed clinical criteria and practice guidelines for identifying individuals who may benefit from BRCA1 or BRCA2 mutation testing. A selection of these is summarized below. According to the NCCN guidelines, personalized risk assessment, genetic counseling, and often BRCA1/2 testing and management are recommended for individuals with a significant personal
PeerJ PrePrints | https://dx.doi.org/10.7287/peerj.preprints.1463v1 | CC-BY 4.0 Open Access | rec: 30 Oct 2015, publ: 30 Oct 2015
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and/or family history of breast, ovarian, pancreatic and/or prostate cancer (National Comprehensive Cancer Network, 2014).
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The ESMO clinical practice guidelines indicate that BRCA testing criteria may differ between countries based on mutation prevalence (Balmaña et al., 2011). Widely accepted clinical criteria for referral include: three or more breast and/or ovarian cancer cases, at least one
