Computational protocol: Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making

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Protocol publication

[…] An established analytical pipeline was used for identifying somatic nucleotide and copy-number aberrations throughout the genome from tumor DNA in comparison to normal DNA from the same patient, as previously described (). De novo assembly of genomic and transcriptomic data was carried out using ABySS () and Trans-ABySS (; ) to detect structural rearrangements and fusions. Copy number and LOH were visualized with Circos (). Gene fusions were evaluated and visualized using MAVIS (http://mavis.bcgsc.ca/). Visualization of gene alterations by sample was through OncoPrinter and MutationMapper, and recurrence of mutations across TCGA was determined through CBioPortal (http://www.cbioportal.org/) (; ). Mutation signatures were computed based on genome-wide single-nucleotide variant calls and trinucleotide contexts as previously described () and compared to COSMIC reference signatures (http://cancer.sanger.ac.uk/cosmic/signatures). Signature scores represent the fraction of mutations contributed by a particular signature. To examine the relationship between signatures, in particular signatures 5 and 16, we used a hierarchical Bayesian categorical mixture model to explore the posterior distribution of signature exposures (E Zhao, S Jones, in prep.). […]

Pipeline specifications

Software tools ABySS, Trans-ABySS, Circos, OncoPrinter, MutationMapper, cBioPortal
Databases TCGA Data Portal
Application Genome data visualization
Organisms Homo sapiens
Diseases Carcinoma, Adenoid Cystic, Neoplasms