Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.

ABSTRACT: Multi-region sequencing is used to detect intratumor genetic heterogeneity (ITGH) in tumors. To assess whether genuine ITGH can be distinguished from sequencing artifacts, we performed whole-exome sequencing (WES) on three anatomically distinct regions of the same tumor with technical replicates to estimate technical noise. Somatic variants were detected with three different WES pipelines and subsequently validated by high-depth amplicon sequencing. The cancer-only pipeline was unreliable, with about 69% of the identified somatic variants being false positive. Even with matched normal DNA for which 82% of the somatic variants were detected reliably, only 36%-78% were found consistently in technical replicate pairs. Overall, 34%-80% of the discordant somatic variants, which could be interpr

SUBMITTER: Shi W 

PROVIDER: S-EPMC6261536 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature