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Pipeline publication

[…] hese tumours that result from these mutations. We extended our splicing mutation analyses beyond molecular breast cancer subtypes and identified other clinical parameters associated with specific mutation pathways. We suggest that DNA sequencing analyses that incorporate in-depth splicing mutation studies reveal additional mutant genes and biochemical pathways, which may contribute to breast cancer etiology., Somatic mutations in 472 breast cancer tumours from 445 breast cancer patients were called using matched tumour-normal DNA exome sequencing data from TCGA (). There were 149,959 single-nucleotide variants (SNVs) and 10,000 insertion/deletions (indels) detected using the variant caller, Strelka (see for results from an alternative variant caller and reasons for our selection of Strelka). Protein coding mutations were annotated by ANNOVAR and splicing mutations with the Shannon Human Splicing Pipeline (, see for a list of all mutations). The Shannon Pipeline predicted significantly more splicing mutations than reported by TCGA, because the information-theoretic method employed enables analyses of variants beyond exon boundaries that alter mRNA splicing. 948 variants were found to affect both protein coding and splicing in 747 genes, among 319 tumours. DYNC2H1, TP53 and PASD were the most commonly mutated of this group, containing 21, 11, and 9 exonic variants, respectively. Alteration of mRNA splicing was predicted as a result of 213 substitutions at synonymous codons among 139 tumours. Reanalysis of coding changes confirmed high concordance with the validated TCGA SNVs, however indels were less reproducible (). Overall, 82.1% ( […]

Pipeline specifications

Software tools Strelka, ANNOVAR, Shannon pipeline
Diseases Breast Neoplasms, Breast Diseases, Neoplasm Metastasis, Neoplastic Processes, Neoplasms, Genetic Diseases, Inborn