Research Papers:

A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine

Eliezer M. Van Allen, Dan Robinson, Colm Morrissey, Colin Pritchard, Alma Imamovic, Scott Carter, Mara Rosenberg, Aaron McKenna, Yi-Mi Wu, Xuhong Cao, Arul Chinnaiyan, Levi Garraway and Peter S. Nelson _

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Oncotarget. 2016; 7:52888-52899. https://doi.org/10.18632/oncotarget.9184

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Eliezer M. Van Allen1,*, Dan Robinson2,*, Colm Morrissey3, Colin Pritchard5, Alma Imamovic1, Scott Carter1, Mara Rosenberg1, Aaron McKenna1, Yi-Mi Wu2, Xuhong Cao2, Arul Chinnaiyan2, Levi Garraway1, Peter S. Nelson3,4,6

1Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA

2Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA

3Department of Urology, University of Washington, Seattle, 98195, WA, USA

4Department of Medicine, University of Washington, Seattle, 98195, WA, USA

5Department of Laboratory Medicine, University of Washington, Seattle, 98195, WA, USA

6Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA

*These authors contributed equally to this work

Correspondence to:

Peter S. Nelson, e-mail: pnelson@fhcrc.org

Keywords: precision oncology, genomics, sequencing, prostate cancer

Received: October 31, 2015     Accepted: March 29, 2016     Published: May 05, 2016


Advances in next generation sequencing technologies provide approaches to comprehensively determine genomic alterations within a tumor that occur as a cause or consequence of neoplastic growth. Though providers offering various cancer genomics assays have multiplied, the level of reproducibility in terms of the technical sensitivity and the conclusions resulting from the data analyses have not been assessed.

We sought to determine the reproducibility of ascertaining tumor genome aberrations using whole exome sequencing (WES) and RNAseq. Samples of the same metastatic tumors were independently processed and subjected to WES of tumor and constitutional DNA, and RNAseq of RNA, at two sequencing centers. Overall, the sequencing results were highly comparable. Concordant mutation calls ranged from 88% to 93% of all variants including 100% agreement across 154 cancer-associated genes. Regions of copy losses and gains were uniformly identified and called by each sequencing center and chromosomal plots showed nearly identical patterns. Transcript abundance levels also exhibited a high degree of concordance (r2 ≥ 0.78;Pearson). Biologically-relevant gene fusion events were concordantly called. Exome sequencing of germline DNA samples provided a minimum of 30X coverage depth across 56 genes where incidental findings are recommended to be reported. One possible pathogenic variant in the APC gene was identified by both sequencing centers.

The findings from this study demonstrate that results of somatic and germline sequencing are highly concordant across sequencing centers that have substantial experience in the technological requirements for preparing, sequencing and annotating DNA and RNA from human biospecimens.

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