ICGC WGS Assessment

[PMID:26647970] [Nature Communications]

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

“We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ~100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts.”

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