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Int. J. Mol. Sci. 2016, 17(5), 651; doi:10.3390/ijms17050651

Data Interoperability of Whole Exome Sequencing (WES) Based Mutational Burden Estimates from Different Laboratories

1
Translational Molecular Biomarkers, Merck Research Laboratories, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
2
Companion Diagnostics, Translational Biomarkers, Merck Research Laboratories, Merck & Co., Inc., 126 E. Lincoln Avenue, Rahway, NJ 07065, USA
*
Author to whom correspondence should be addressed.
Academic Editor: William Chi-shing Cho
Received: 29 March 2016 / Revised: 21 April 2016 / Accepted: 25 April 2016 / Published: 29 April 2016
(This article belongs to the Special Issue Next-Generation Sequencing for Clinical Application)
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Abstract

Immune checkpoint inhibitors, which unleash a patient’s own T cells to kill tumors, are revolutionizing cancer treatment. Several independent studies suggest that higher non-synonymous mutational burden assessed by whole exome sequencing (WES) in tumors is associated with improved objective response, durable clinical benefit, and progression-free survival in immune checkpoint inhibitors treatment. Next-generation sequencing (NGS) is a promising technology being used in the clinic to direct patient treatment. Cancer genome WES poses a unique challenge due to tumor heterogeneity and sequencing artifacts introduced by formalin-fixed, paraffin-embedded (FFPE) tissue. In order to evaluate the data interoperability of WES data from different sources to survey tumor mutational landscape, we compared WES data of several tumor/normal matched samples from five commercial vendors. A large data discrepancy was observed from vendors’ self-reported data. Independent data analysis from vendors’ raw NGS data shows that whole exome sequencing data from qualified vendors can be combined and analyzed uniformly to derive comparable quantitative estimates of tumor mutational burden. View Full-Text
Keywords: next generation sequencing (NGS); whole exome sequencing (WES); mutational burden; immune checkpoint inhibitor; PD-1 next generation sequencing (NGS); whole exome sequencing (WES); mutational burden; immune checkpoint inhibitor; PD-1
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Qiu, P.; Pang, L.; Arreaza, G.; Maguire, M.; Chang, K.C.N.; Marton, M.J.; Levitan, D. Data Interoperability of Whole Exome Sequencing (WES) Based Mutational Burden Estimates from Different Laboratories. Int. J. Mol. Sci. 2016, 17, 651.

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