00085472can153457-sup-159846_2_supp_3548269_99k2t9.xlsx (11.81 kB)

Supplementary Table 2 from Improving the Performance of Somatic Mutation Identification by Recovering Circulating Tumor DNA Mutations

dataset

posted on 2023-03-31, 00:26 authored by Yu Fu, Cécile Jovelet, Thomas Filleron, Marion Pedrero, Nelly Motté, Yannick Boursin, Yufei Luo, Christophe Massard, Mario Campone, Christelle Levy, Véronique Diéras, Thomas Bachelot, Julie Garrabey, Jean-Charles Soria, Ludovic Lacroix, Fabrice André, Celine Lefebvre

Details of the 1000 Genomes samples used in data simulation

Funding

Breast Cancer Research Foundation

Fondation Lombard-Odier

Odyssea

Operation Parrains Chercheurs

Dassault Foundation

NCI

History

ARTICLE ABSTRACT

DNA extracted from cancer patients' whole blood may contain somatic mutations from circulating tumor DNA (ctDNA) fragments. In this study, we introduce cmDetect, a computational method for the systematic identification of ctDNA mutations using whole-exome sequencing of a cohort of tumor and corresponding peripheral whole-blood samples. Through the analysis of simulated data, we demonstrated an increase in sensitivity in calling somatic mutations by combining cmDetect to two widely used mutation callers. In a cohort of 93 breast cancer metastatic patients, cmDetect identified ctDNA mutations in 54% of the patients and recovered somatic mutations in cancer genes EGFR, PIK3CA, and TP53. We further showed that cmDetect detected ctDNA in 89% of patients with confirmed mutated cell–free tumor DNA by plasma analyses (n = 9) within 46 pan-cancer patients. Our results prompt immediate consideration of the use of this method as an additional step in somatic mutation calling using whole-exome sequencing data with blood samples as controls. Cancer Res; 76(20); 5954–61. ©2016 AACR.