Quantification of rare allelic variants from pooled genomic DNA

Rare germline variants are difficult to identify using traditional sequencing due to relatively high cost and low throughput. Using second-generation sequencing, we report a targeted, cost-effective method to quantify rare SNPs from pooled genomic DNA. We pooled DNA from 1,111 individuals and target...

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Detalles Bibliográficos
Autores principales: Druley, Todd E, Vallania, Francesco LM, 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
Formato: Texto
Lenguaje:English
Publicado: 2009
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776647/
https://www.ncbi.nlm.nih.gov/pubmed/19252504
http://dx.doi.org/10.1038/nmeth.1307
Descripción
Sumario:Rare germline variants are difficult to identify using traditional sequencing due to relatively high cost and low throughput. Using second-generation sequencing, we report a targeted, cost-effective method to quantify rare SNPs from pooled genomic DNA. We pooled DNA from 1,111 individuals and targeted four genes. Our novel base-calling algorithm, SNPSeeker, derived from Large Deviation theory, can detect SNPs present at frequencies below the raw error rate of the sequencing platform

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