Design and validation of a next generation sequencing assay for hereditary breast and ovarian cancer
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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 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.
Cite this as
2015. Design and validation of a next generation sequencing assay for hereditary breast and ovarian cancer. PeerJ PrePrints 3:e1463v1 https://doi.org/10.7287/peerj.preprints.1463v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a submission to PeerJ for review.
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Competing Interests
All authors are employees and shareholders of Counsyl Inc.
Author Contributions
Hyunseok P. Kang conceived and designed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Jared R Maguire analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Clement S Chu conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Imran S. Haque analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Henry Lai performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Rebecca Mar-Heyming analyzed the data, reviewed drafts of the paper.
Kaylene Ready conceived and designed the experiments, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Valentina S. Vysotskaia wrote the paper, reviewed drafts of the paper.
Eric A. Evans conceived and designed the experiments, analyzed the data, reviewed drafts of the paper.
Human Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
Western Institutional Review Board (IRB number 1145639)
Data Deposition
The following information was supplied regarding data availability:
1) ClinVar
2) 320494
3) http://www.ncbi.nlm.nih.gov/clinvar/submitters/320494/
Funding
The authors received no funding for this work. No external funding was received. All authors are employed by Counsyl, and the manuscript describes the validation of a commercial genetic test.
