SuperFreq: Integrated mutation detection and clonal tracking in cancer

• DOI: 10.1371/journal.pcbi.1007603
• Publication Date: 2020-02-13T13:49:25Z
• Authors: Christoffer Flens...; Tobias Sargeant; Alicia Oshlack; Ian J. Majewski
• Keywords: Exome

Analysing multiple cancer samples from an individual patient can provide insight into the way disease evolves. Monitoring expansion and contraction of distinct clones helps to reveal mutations that initiate those drive progression. Existing approaches for clonal tracking sequencing data typically require user combine tools are not purpose-built this task. Furthermore, most methods a matched normal (non-tumour) sample, which limits scope application. We developed SuperFreq, exome analysis pipeline integrates identification somatic single nucleotide variants (SNVs) copy number alterations (CNAs) both. SuperFreq does instead relies on unrelated controls. When analysing patient, cross checks variant calls improve tracking, separate germline variants, resolve overlapping CNA calls. To demonstrate our software we analysed 304 cancer-normal across 33 types in The Cancer Genome Atlas (TCGA) evaluated quality SNV simulated evolution through silico mixing known proportion. found identified 93% with cellular fraction at least 50% were assigned correct clone high recall precision. In addition, maintained similar level performance aspects when run without normal. is highly versatile be applied many different experimental settings exomes other capture libraries. application leukaemia patients diagnosis relapse samples.