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Performance of genomic data strategies for cancer precision medicine across distinct contexts and ethnicities

Performance of genomic data strategies for cancer precision medicine across distinct contexts and ethnicities

Authors :
David Liu
Ali Amin-Mansour
Nelly Oliver
Eliezer M. Van Allen
Neal I. Lindeman
Brendan Reardon
Diana Miao
Stacy W. Gray
Nikhil Wagle
Judy Garber
Arezou A. Ghazani
Andrea Garofalo
Levi A. Garraway
Lynette M. Sholl
Steven Joffe
Pasi A. Jänne
Source :
Journal of Clinical Oncology. 34:1500-1500
Publication Year :
2016
Publisher :
American Society of Clinical Oncology (ASCO), 2016.

Abstract

1500Background: The expanding appeal of clinical tumor profiling has led to many sequencing strategies, ranging from small gene panels to exomes, with or without patient-matched germline data. This diversity of approaches may engender uncertainty about their benefits and liabilities, particularly in light of reported germline false positives in tumor-only profiling, and emerging immunotherapies that leverage genome-wide data. Methods: We modeled common tumor profiling modalities - large (n = 300 genes) and small (n= 15 or 48 genes) panels - onto clinical whole exomes (WES) from 157 patients with lung or colon adenocarcinoma. We created a tumor-only analysis algorithm to assess germline false positives (variants erroneously called as somatic), impact of patient ethnicity on results, and neoantigen detection. Results: The germline false positive rate with tumor-only large panel sequencing was 14% (144/1012 variants). For patients whose results underwent molecular pathologist review, 50/54 (93%) false positi...

Details

ISSN :
15277755 and 0732183X
Volume :
34
Database :
OpenAIRE
Journal :
Journal of Clinical Oncology
Accession number :
edsair.doi...........8d30d5201f16afe6906425f6179d0ed8
Full Text :
https://doi.org/10.1200/jco.2016.34.15_suppl.1500