American Association for Cancer Research
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

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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


Breast Cancer Research Foundation

Fondation Lombard-Odier


Operation Parrains Chercheurs

Dassault Foundation




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.

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