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Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity

52 Pages Posted: 9 Apr 2018 Sneak Peek Status: Published

See all articles by Weiwei Shi

Weiwei Shi

Yale University - Department of Medicine

Charlotte K.Y. Ng

Memorial Sloan Kettering Cancer Center - Department of Pathology

Raymond S. Lim

Memorial Sloan Kettering Cancer Center - Department of Pathology

Tingting Jiang

Yale University - Department of Medicine

Sushant Kumar

Yale University - Molecular Biophysics and Biochemistry

Xiaotong Li

Yale University - Department of Medicine

Vikram B. Wali

Yale University - Department of Medicine

Salvatore Piscuoglio

Memorial Sloan Kettering Cancer Center - Department of Pathology

Mark B. Gerstein

Yale University - Molecular Biophysics and Biochemistry

Anees Chagpar

Yale University - School of Medicine

Britta Weigelt

Memorial Sloan Kettering Cancer Center - Department of Pathology

Lajos Pusztai

Yale University - Department of Medicine

Jorge S. Reis-Filho

Memorial Sloan Kettering Cancer Center - Department of Pathology

Christos Hatzis

Yale University - Department of Medicine

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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 whole-exome sequenced (WES) 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 where 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.

Suggested Citation

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 and Weigelt, Britta and Pusztai, Lajos and Reis-Filho, Jorge S. and Hatzis, Christos, Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity (2018). Available at SSRN: https://ssrn.com/abstract=3155634 or http://dx.doi.org/10.2139/ssrn.3155634
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Weiwei Shi

Yale University - Department of Medicine

New Haven, CT
United States

Charlotte K.Y. Ng

Memorial Sloan Kettering Cancer Center - Department of Pathology

New York, NY
United States

Raymond S. Lim

Memorial Sloan Kettering Cancer Center - Department of Pathology

New York, NY
United States

Tingting Jiang

Yale University - Department of Medicine

New Haven, CT
United States

Sushant Kumar

Yale University - Molecular Biophysics and Biochemistry

New Haven, CT
United States

Xiaotong Li

Yale University - Department of Medicine

New Haven, CT
United States

Vikram B. Wali

Yale University - Department of Medicine

New Haven, CT
United States

Salvatore Piscuoglio

Memorial Sloan Kettering Cancer Center - Department of Pathology

New York, NY
United States

Mark B. Gerstein

Yale University - Molecular Biophysics and Biochemistry

New Haven, CT
United States

Anees Chagpar

Yale University - School of Medicine ( email )

Department of Surgery
New Haven, CT 06520-8034
United States

Britta Weigelt

Memorial Sloan Kettering Cancer Center - Department of Pathology

New York, NY
United States

Lajos Pusztai

Yale University - Department of Medicine

New Haven, CT
United States

Jorge S. Reis-Filho

Memorial Sloan Kettering Cancer Center - Department of Pathology ( email )

New York, NY
United States

Christos Hatzis (Contact Author)

Yale University - Department of Medicine ( email )

New Haven, CT
United States

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