Comprehensive variation discovery in single human genomes
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Author
Weisenfeld, Neil I.
Yin, Shuangye
Sharpe, Ted
Lau, Bayo
Hegarty, Ryan
Holmes, Laurie
Sogoloff, Brian
Tabbaa, Diana
Williams, Louise
Russ, Carsten
Nusbaum, Chad
MacCallum, Iain
Jaffe, David B.
Note: Order does not necessarily reflect citation order of authors.
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https://doi.org/10.1038/ng.3121Metadata
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Weisenfeld, N. I., S. Yin, T. Sharpe, B. Lau, R. Hegarty, L. Holmes, B. Sogoloff, et al. 2014. “Comprehensive variation discovery in single human genomes.” Nature genetics 46 (12): 1350-1355. doi:10.1038/ng.3121. http://dx.doi.org/10.1038/ng.3121.Abstract
Complete knowledge of the genetic variation in individual human genomes is a crucial foundation for understanding the etiology of disease. Genetic variation is typically characterized by sequencing individual genomes and comparing reads to a reference. Existing methods do an excellent job of detecting variants in approximately 90% of the human genome, however calling variants in the remaining 10% of the genome (largely low-complexity sequence and segmental duplications) is challenging. To improve variant calling, we developed a new algorithm, DISCOVAR, and examined its performance on improved, low-cost sequence data. Using a newly created reference set of variants from finished sequence of 103 randomly chosen Fosmids, we find that some standard variant call sets miss up to 25% of variants. We show that the combination of new methods and improved data increases sensitivity several-fold, with the greatest impact in challenging regions of the human genome.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244235/pdf/Terms of Use
This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAACitable link to this page
http://nrs.harvard.edu/urn-3:HUL.InstRepos:17295794
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