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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
- 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