Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 67,095 bioRxiv papers from 295,233 authors.
Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment
Valentina S. Vysotskaia,
Gregory J Hogan,
Genevieve M Gould,
Alex D. Robertson,
Kevin R Haas,
Mark R Theilmann,
Peter V Grauman,
Henry H. Lai,
Clement S Chu,
Jared R Maguire,
Eric A. Evans,
H. Peter Kang,
Imran S. Haque
Posted 17 Nov 2016
bioRxiv DOI: 10.1101/088252 (published DOI: 10.7717/peerj.3046)
Posted 17 Nov 2016
The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen′s high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers. Datasets for this article are available online (10.5281/zenodo.193264).
- Downloaded 903 times
- Download rankings, all-time:
- Site-wide: 9,067 out of 67,095
- In genetics: 672 out of 3,775
- Year to date:
- Site-wide: 48,814 out of 67,095
- Since beginning of last month:
- Site-wide: 58,055 out of 67,095
Downloads over time
Distribution of downloads per paper, site-wide
- Top preprints of 2018
- Paper search
- Author leaderboards
- Overall metrics
- The API
- Email newsletter
- 21 May 2019: PLOS Biology has published a community page about Rxivist.org and its design.
- 10 May 2019: The paper analyzing the Rxivist dataset has been published at eLife.
- 1 Mar 2019: We now have summary statistics about bioRxiv downloads and submissions.
- 8 Feb 2019: Data from Altmetric is now available on the Rxivist details page for every preprint. Look for the "donut" under the download metrics.
- 30 Jan 2019: preLights has featured the Rxivist preprint and written about our findings.
- 22 Jan 2019: Nature just published an article about Rxivist and our data.
- 13 Jan 2019: The Rxivist preprint is live!