Somatic mutation analysis and interpretation is crucial for understanding cancer genomics and advancing cancer precision medicine. However, accurately detecting somatic events in cancer samples remain challenging due to the complexity of cancer genome, sequencing platform biases, sample preservation effects, imperfect assay protocols, lack of reference samples, and suboptimal bioinformatics analysis methods. To address these challenges and to advance the field, the Somatic Mutation Working Group of SEQC2 consortium, consisting of nearly 200 researchers from more than 60 organizations from government agencies, academia, and sequencing industries, has been established to systematically investigate factors affecting the accuracy and reproducibility of somatic mutation calling in paired breast cancer and normal cell lines. Six sequencing centers have performed whole exome sequencing (WES) and whole genome sequencing (WGS) in parallel to assess the reproducibility of NGS runs on these same biological samples. The Working Group not only characterized the paired cell lines as reference samples for benchmarking, but also evaluated factors affecting somatic mutation detection results, such as biosamples (fresh cells vs FFPE), tumor purity, amount of input DNA, library preparations, reads coverage and NGS machine models, as well as bioinformatics components, such as preprocessing, alignment, post-alignment processing, and mutation callers.
The ultimate goals of SEQC2 Somatic Mutation Working Group are: (1) to develop guidelines for somatic mutation detection using next generation sequencing technologies; (2) to establish wide-accepted paired tumor/normal reference samples/materials (HCC1395, HCC1395BL) for NGS testing; (3) to define golden-standard variant sets for each reference samples for NGS benchmarking. These data will become critical resources for regulatory agency like FDA, platform developers, method developers, and clinical sequencing labs. Less...