Automated next-generation profiling of genomic alterations in human cancers

Laurel A. Keefer, James R. White, Derrick E. Wood, Kelly M. R. Gerding, Kenneth C. Valkenburg, David Riley, Christopher Gault, Eniko Papp, Christine M. Vollmer, Amy Greer, James Hernandez, Paul M. McGregor, Adriana Zingone, Bríd M. Ryan, Kristen Deak, Shannon J. McCall, Michael B. Datto, James L. Prescott, John F. Thompson, Gustavo C. Cerqueira, Siân Jones, John K. Simmons, Abigail McElhinny, Jennifer Dickey, Samuel V. Angiuoli, Luis A. Diaz, Victor E. Velculescu and Mark Sausen ()
Additional contact information
Laurel A. Keefer: Personal Genome Diagnostics Inc.
James R. White: Personal Genome Diagnostics Inc.
Derrick E. Wood: Personal Genome Diagnostics Inc.
Kelly M. R. Gerding: Personal Genome Diagnostics Inc.
Kenneth C. Valkenburg: Personal Genome Diagnostics Inc.
David Riley: Personal Genome Diagnostics Inc.
Christopher Gault: Personal Genome Diagnostics Inc.
Eniko Papp: Personal Genome Diagnostics Inc.
Christine M. Vollmer: Personal Genome Diagnostics Inc.
Amy Greer: Personal Genome Diagnostics Inc.
James Hernandez: Personal Genome Diagnostics Inc.
Paul M. McGregor: Personal Genome Diagnostics Inc.
Adriana Zingone: National Cancer Institute
Bríd M. Ryan: National Cancer Institute
Kristen Deak: Duke University School of Medicine
Shannon J. McCall: Duke University School of Medicine
Michael B. Datto: Duke University School of Medicine
James L. Prescott: PathGroup
John F. Thompson: Personal Genome Diagnostics Inc.
Gustavo C. Cerqueira: Personal Genome Diagnostics Inc.
Siân Jones: Personal Genome Diagnostics Inc.
John K. Simmons: Personal Genome Diagnostics Inc.
Abigail McElhinny: Personal Genome Diagnostics Inc.
Jennifer Dickey: Personal Genome Diagnostics Inc.
Samuel V. Angiuoli: Personal Genome Diagnostics Inc.
Luis A. Diaz: Memorial Sloan Kettering Cancer Center
Victor E. Velculescu: Johns Hopkins University School of Medicine
Mark Sausen: Personal Genome Diagnostics Inc.

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract The lack of validated, distributed comprehensive genomic profiling assays for patients with cancer inhibits access to precision oncology treatment. To address this, we describe elio tissue complete, which has been FDA-cleared for examination of 505 cancer-related genes. Independent analyses of clinically and biologically relevant sequence changes across 170 clinical tumor samples using MSK-IMPACT, FoundationOne, and PCR-based methods reveals a positive percent agreement of >97%. We observe high concordance with whole-exome sequencing for evaluation of tumor mutational burden for 307 solid tumors (Pearson r = 0.95) and comparison of the elio tissue complete microsatellite instability detection approach with an independent PCR assay for 223 samples displays a positive percent agreement of 99%. Finally, evaluation of amplifications and translocations against DNA- and RNA-based approaches exhibits >98% negative percent agreement and positive percent agreement of 86% and 82%, respectively. These methods provide an approach for pan-solid tumor comprehensive genomic profiling with high analytical performance.

Date: 2022
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DOI: 10.1038/s41467-022-30380-x

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