Quantification of rare allelic variants from pooled genomic DNA

Todd E. Druley, Francesco L.M. Vallania, Daniel J. Wegner, Katherine E. Varley, Olivia L. Knowles, Jacqueline A. Bonds, Sarah W. Robison, Scott W. Doniger, Aaron Hamvas, F. Sessions Cole, Justin C. Fay, Robi D. Mitra

Research output: Contribution to journalArticlepeer-review

117 Scopus citations

Abstract

We report a targeted, cost-effective method to quantify rare single-nucleotide polymorphisms from pooled human genomic DNA using second-generation sequencing. We pooled DNA from 1,111 individuals and targeted four genes to identify rare germline variants. Our base-calling algorithm, SNPSeeker, derived from large deviation theory, detected single-nucleotide polymorphisms present at frequencies below the raw error rate of the sequencing platform.

Original languageEnglish
Pages (from-to)263-265
Number of pages3
JournalNature Methods
Volume6
Issue number4
DOIs
StatePublished - 2009

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