Brief Communication abstract
Nature Methods 6, 263 - 265 (2009)
Published online: 1 March 2009 | doi:10.1038/nmeth.1307
Quantification of rare allelic variants from pooled genomic DNA
Todd E Druley1,2, Francesco L M Vallania2, Daniel J Wegner3, Katherine E Varley2, Olivia L Knowles2, Jacqueline A Bonds2, Sarah W Robison3, Scott W Doniger2, Aaron Hamvas3, F Sessions Cole3, Justin C Fay2 & Robi D Mitra2
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.
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA.
- Center for Genome Sciences, Washington University School of Medicine, St. Louis, Missouri, USA.
- Division of Newborn Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.
Correspondence to: Robi D Mitra2 e-mail: rmitra@genetics.wustl.edu
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