title: 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.
authors.affiliation: Moores UCSD Cancer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. oharismendy@ucsd.edu
authors.forename: Olivier
authors.initials: O
authors.lastname: Harismendy
authors.forename: Richard B
authors.initials: RB
authors.lastname: Schwab
authors.forename: Lei
authors.initials: L
authors.lastname: Bao
authors.forename: Jeff
authors.initials: J
authors.lastname: Olson
authors.forename: Sophie
authors.initials: S
authors.lastname: Rozenzhak
authors.forename: Steve K
authors.initials: SK
authors.lastname: Kotsopoulos
authors.forename: Stephanie
authors.initials: S
authors.lastname: Pond
authors.forename: Brian
authors.initials: B
authors.lastname: Crain
authors.forename: Mark S
authors.initials: MS
authors.lastname: Chee
authors.forename: Karen
authors.initials: K
authors.lastname: Messer
authors.forename: Darren R
authors.initials: DR
authors.lastname: Link
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
mesh_terms: D000368:Aged; D000818:Animals; D057205:Automation, Laboratory; D002277:Carcinoma / Q000175:diagnosis* / Q000235:genetics; D030541:Databases, Genetic; D052138:Genes, Neoplasm / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D008875:Middle Aged; D009154:Mutation; D059645:Mutation Rate; D012509:Sarcoma / Q000175:diagnosis* / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D023041:Xenograft Model Antitumor Assays