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从混合基因组DNA中对罕见等位基因变异进行定量分析。

Quantification of rare allelic variants from pooled genomic DNA.

作者信息

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

机构信息

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

出版信息

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

DOI:10.1038/nmeth.1307
PMID:19252504
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2776647/
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.

摘要

我们报告了一种使用第二代测序技术从混合的人类基因组DNA中定量罕见单核苷酸多态性的靶向、经济高效的方法。我们汇集了1111名个体的DNA，并靶向四个基因以识别罕见的种系变异。我们基于大偏差理论推导的碱基识别算法SNPSeeker检测到了频率低于测序平台原始错误率的单核苷酸多态性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dc9/2776647/596a5a4354b3/nihms92733f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dc9/2776647/284d10884faa/nihms92733f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dc9/2776647/596a5a4354b3/nihms92733f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dc9/2776647/284d10884faa/nihms92733f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dc9/2776647/596a5a4354b3/nihms92733f2.jpg

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