Assessment of tumor mutation burden from >60,000 clinical cancer patients using comprehensive genomic profiling.

Authors

null

Garrett Michael Frampton

Foundation Medicine, Inc., Cambridge, MA

Garrett Michael Frampton , David Fabrizio , Zachary Rockow Chalmers , Jeffrey S. Ross , Douglas Buckner Johnson , Christine Marie Lovly , Jeffrey Alan Sosman , Vincent A. Miller , Phil Stephens

Organizations

Foundation Medicine, Inc., Cambridge, MA, Foundation Medicine, Boston, MA, Albany Medical College, Albany, NY, Vanderbilt University, Nashville, TN, Vanderbilt-Ingram Cancer Center, Nashville, TN, Foundation Medicine, Cambridge, MA

Research Funding

Pharmaceutical/Biotech Company

Background: Tumor mutation burden (TMB), as measured by whole exome sequencing, has been shown to strongly correlate with objective responses to immune checkpoint inhibition (ICI), in several tumor types. Consequently, the ability to accurately measure TMB, in a clinical setting, may guide patient treatment decisions. We investigate whether TMB can be accurately measured using a comprehensize genomic profiling (CGP) assay targeting several hundred cancer genes (~1.25 Mb). We also describe the landscape of TMB observed from > 60,000 advanced clinical cancer specimens, across > 400 cancer types. Methods: CGP by hybridization capture and high-coverage sequencing (median > 500x) of the full coding regions from 236 or 315 cancer-related genes was performed. Base substitutions, indels, copy number alterations and gene fusion/rearrangements were assessed. TMB was calculated as the number of somatic, coding, base sub. and indel alterations, excluding known driver mutations, per megabase of genome examined. This metric correlates with response to anti-PD-1 in melanoma. Results: We validate that targeted sequencing of 1.25 Mb does provide an accurate measurement of genome-wide TMB. We describe the spectrum of TMB observed across a diversity of tumor types. Lower grade and pediatric malignancies tend to have the lowest TMB ( < 1 mut/MB), while epithelial cancers, associated with environmental DNA damage, were most highly mutated ( > 10 mut/MB). Mutations in mismatch-repair genes (MSH2, MSH6, MLH1, PMS2 and RAD50), DNA replication genes (POLD1, POLE) and TP53BP1 were associated with > 2x increases in TMB, though some specimens with high TMB lacked identifiable causative alterations. Several tumor types, in which ICI are not yet approved, had many cases with high TMB ( > 20 mut/MB), including intestinal type stomach adenocarcinoma (20%), and uterine endometrial adenocarcinoma (16%). Conclusions: These data demonstrate that TMB can be accurately assessed using a clinically available CGP assay, allowing assessment for current patients. Examining the landscape of TMB across a diversity of tumor types provides new data to expand the population that can potentially benefit from immunotherapy.

Disclaimer

This material on this page is ©2024 American Society of Clinical Oncology, all rights reserved. Licensing available upon request. For more information, please contact licensing@asco.org

Abstract Details

Meeting

2016 ASCO Annual Meeting

Session Type

Poster Session

Session Title

Tumor Biology

Track

Tumor Biology

Sub Track

Molecular Diagnostics and Imaging

Citation

J Clin Oncol 34, 2016 (suppl; abstr 11558)

DOI

10.1200/JCO.2016.34.15_suppl.11558

Abstract #

11558

Poster Bd #

255

Abstract Disclosures