Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity

Shi, Weiwei and Ng, Charlotte K. Y. and Lim, Raymond S. and Jiang, Tingting and Kumar, Sushant and Li, Xiaotong and Wali, Vikram B. and Piscuoglio, Salvatore and Gerstein, Mark B. and Chagpar, Anees B. and Weigelt, Britta and Pusztai, Lajos and Reis-Filho, Jorge S. and Hatzis, Christos. (2018) Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity. Cell reports, 25 (6). pp. 1446-1457.

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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 interpreted as ITGH, were found to constitute technical noise. Excluding mutations affecting low-mappability regions or occurring in certain mutational contexts was found to reduce artifacts, yet detection of subclonal mutations by WES in the absence of orthogonal validation remains unreliable.
Faculties and Departments:03 Faculty of Medicine
03 Faculty of Medicine > Bereich Querschnittsfächer (Klinik) > Pathologie USB
03 Faculty of Medicine > Departement Klinische Forschung > Bereich Querschnittsfächer (Klinik) > Pathologie USB
UniBasel Contributors:Piscuoglio, Salvatore
Item Type:Article, refereed
Article Subtype:Research Article
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:29 Jan 2019 13:08
Deposited On:29 Jan 2019 13:08

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