title: A comparative assessment of clinical whole exome and transcriptome profiling across sequencing centers: implications for precision cancer medicine.
abstract: 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.
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.
authors.forename: Eliezer M
authors.initials: EM
authors.lastname: Van Allen
authors.affiliation: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Robinson
authors.affiliation: Department of Urology, University of Washington, Seattle, 98195, WA, USA.
authors.forename: Colm
authors.initials: C
authors.lastname: Morrissey
authors.affiliation: Department of Laboratory Medicine, University of Washington, Seattle, 98195, WA, USA.
authors.forename: Colin
authors.initials: C
authors.lastname: Pritchard
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.
authors.forename: Alma
authors.initials: A
authors.lastname: Imamovic
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Carter
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.
authors.forename: Mara
authors.initials: M
authors.lastname: Rosenberg
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: McKenna
authors.affiliation: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA.
authors.forename: Yi-Mi
authors.initials: YM
authors.lastname: Wu
authors.affiliation: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA.
authors.forename: Xuhong
authors.initials: X
authors.lastname: Cao
authors.affiliation: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA.
authors.forename: Arul
authors.initials: A
authors.lastname: Chinnaiyan
authors.affiliation: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA.
authors.forename: Levi
authors.initials: L
authors.lastname: Garraway
authors.affiliation: Department of Urology, University of Washington, Seattle, 98195, WA, USA.|Department of Medicine, University of Washington, Seattle, 98195, WA, USA.|Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA.
authors.forename: Peter S
authors.initials: PS
authors.lastname: Nelson
mesh_terms: D059472:Exome / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D015894:Genome, Human / Q000235:genetics; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D057285:Precision Medicine / Q000379:methods*; D015203:Reproducibility of Results
keywords: genomics; precision oncology; prostate cancer; sequencing