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Nat Methods. 2009 Apr;6(4):263-5. doi: 10.1038/nmeth.1307. Epub 2009 Mar 1.

Quantification of rare allelic variants from pooled genomic DNA.

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1
Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.

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.

PMID:
19252504
PMCID:
PMC2776647
DOI:
10.1038/nmeth.1307
[Indexed for MEDLINE]
Free PMC Article
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