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Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.

ABSTRACT: Ultra-deep targeted sequencing (UDT-Seq) can identify subclonal somatic mutations in tumor samples. Early assays' limited breadth and depth restrict their clinical utility. Here, we target 71 kb of mutational hotspots in 42 cancer genes. We present novel methods enhancing both laboratory workflow and mutation detection. We evaluate UDT-Seq true sensitivity and specificity (> 94% and > 99%, respectively) for low prevalence mutations in a mixing experiment and demonstrate its utility using six tumor samples. With an improved performance when run on the Illumina Miseq, the UDT-Seq assay is well suited for clinical applications to guide therapy and study clonal selection in heterogeneous samples.

SUBMITTER: Harismendy O

PROVIDER: S-EPMC3334619 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature

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Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing.

Harismendy Olivier O Schwab Richard B RB Bao Lei L Olson Jeff J Rozenzhak Sophie S Kotsopoulos Steve K SK Pond Stephanie S Crain Brian B Chee Mark S MS Messer Karen K Link Darren R DR Frazer Kelly A KA

Genome biology 20111220 12

Ultra-deep targeted sequencing (UDT-Seq) can identify subclonal somatic mutations in tumor samples. Early assays' limited breadth and depth restrict their clinical utility. Here, we target 71 kb of mutational hotspots in 42 cancer genes. We present novel methods enhancing both laboratory workflow and mutation detection. We evaluate UDT-Seq true sensitivity and specificity (> 94% and > 99%, respectively) for low prevalence mutations in a mixing experiment and demonstrate its utility using six tum ...[more]

PMID: 22185227

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