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

被引：68

作者：

Harismendy, Olivier ^{[1
,2
,3
]}

Schwab, Richard B. ^{[1
]}

Bao, Lei ^{[1
]}

Olson, Jeff ^{[4
]}

Rozenzhak, Sophie ^{[1
,2
,3
]}

Kotsopoulos, Steve K. ^{[4
]}

Pond, Stephanie ^{[5
]}

Crain, Brian ^{[1
]}

Chee, Mark S. ^{[5
]}

Messer, Karen ^{[1
]}

Link, Darren R. ^{[4
]}

Frazer, Kelly A. ^{[1
,2
,3
,6
]}

机构：

[1] Univ Calif San Diego, Moores UCSD Canc Ctr, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Rady Childrens Hosp, La Jolla, CA 92093 USA

[4] RainDance Technol, Lexington, MA 02421 USA

[5] Prognosys Biosci, La Jolla, CA 92037 USA

[6] Univ Calif San Diego, Inst Genom Med, La Jolla, CA 92093 USA

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 12期

关键词：

CELL LUNG-CANCER; VARIANTS; QUANTIFICATION; CARCINOMA; SPECIMENS; THERAPY; SAMPLES; PCR; DNA;

D O I：

10.1186/gb-2011-12-12-r124

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：13