Genomic sequence context differs between germline and somatic structural variants allowing for their differentiation in tumor samples without paired normals.

ABSTRACT: There is currently no method to distinguish between germline and somatic structural variants (SVs) in tumor samples that lack a matched normal sample. In this study, we analyzed several features of germline and somatic SVs from a cohort of 974 patients from The Cancer Genome Atlas (TCGA). We identified a total of 21 features that differed significantly between germline and somatic SVs. Several of the germline SV features were associated with each other, as were several of the somatic SV features. We also found that these associations differed between the germline and somatic classes, for example, we found that somatic inversions were more likely to be longer events than their germline counterparts. Using these features we trained a support vector machine (SVM) classifier on 555,849 TCGA SV

SUBMITTER: Chukwu W 

PROVIDER: S-EPMC10723258 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature