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*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

122 Scopus citations


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 (US)
Pages (from-to)263-265
Number of pages3
JournalNature Methods
Issue number4
StatePublished - 2009

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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