{"entity":{"id":"paper-nik-zainal-560-breast-cancer-genomes-nature-2016","kind":"paper","name":"Landscape of somatic mutations in 560 breast cancer whole-genome sequences","aka":[],"tldr":"The largest whole-genome study of breast cancer at the time read every part of 560 tumours' DNA and catalogued their mutations, the genes that drive them and the processes that cause them.","summary":"Nik-Zainal and colleagues sequenced the whole genomes of 560 breast cancers with matched normal tissue (556 women and four men). The full text reports 3,479,652 somatic base substitutions, 371,993 small insertions and deletions and 77,695 rearrangements, with substantial variation between individual cancers. The abstract reports 93 protein-coding cancer genes carrying probable driver mutations, twelve base-substitution and six rearrangement signatures, and three rearrangement signatures associated with defective homologous-recombination repair.","asOf":"2026-11-04","links":[{"label":"Nik-Zainal et al., Nature 2016","url":"https://doi.org/10.1038/nature17676"},{"label":"PubMed","url":"https://pubmed.ncbi.nlm.nih.gov/27135926/"}],"tags":[],"related":[],"cancers":["breast-cancer"],"sections":["diagnostics"],"technologies":["wes-wgs"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":[],"trials":[],"people":[],"bottlenecks":["b-subclone-attribution-residual-disease"],"keyPapers":[],"journals":["nature"],"dependsOn":[],"notes":[],"journal":"Nature","year":2016,"doi":"10.1038/nature17676","pmid":"27135926","authors":"Nik-Zainal S, Davies H, Staaf J, et al.","paperType":"translational","findings":["3,479,652 somatic base substitutions across 560 breast cancer genomes (full text); a mean of about 6,200 a cancer is OnCo arithmetic.","93 protein-coding cancer genes carried probable driver mutations.","Twelve base-substitution and six rearrangement signatures."],"whatItMeans":"A breast cancer genome carries thousands of mutations, most of them outside genes, so a residual disease test designed from the whole genome has far more to choose from than one designed from the exome.","caveats":["The per-cancer count varies widely; a mean says little about any one tumour.","Primary tumours sequenced at ordinary depth; low-fraction subclonal mutations are under-counted."],"participants":560},"route":"/key-papers/paper-nik-zainal-560-breast-cancer-genomes-nature-2016/","neighbours":{"cancer":[{"id":"breast-cancer","kind":"cancer","name":"Breast cancer (all types)","route":"/cancers/breast-cancer/"}],"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"}],"technology":[{"id":"wes-wgs","kind":"technology","name":"Whole-exome & whole-genome sequencing","route":"/technologies/wes-wgs/"}],"bottleneck":[{"id":"b-subclone-attribution-residual-disease","kind":"bottleneck","name":"Naming which clone or phenotype is left after treatment","route":"/bottlenecks/b-subclone-attribution-residual-disease/"}],"journal":[{"id":"nature","kind":"journal","name":"Nature","route":"/journals/nature/"}]}}