Aasheim, L. B. | bioRxiv Science

bioRxiv2017

Sample-Index Misassignment Impacts Tumor Exome Sequencing

Sample pooling enabled by dedicated indexes is a common and cost-effective strategy used in high-throughput DNA sequencing. Index misassignment leading to cross-sample contamination has however been described as a general problem of sequencing instruments which utilize exclusion amplification. Using real-life data from multiple tumor sequencing projects, we demonstrate that co-multiplexed samples can induce artifactual calls closely resembling high-quality somatic variant calls, and argue that dual indexing is the most reliable countermeasure.

genomics↗

bioRxiv2017

Personal Cancer Genome Reporter: Variant Interpretation Report For Precision Oncology

SummaryIndividual tumor genomes pose a major challenge for clinical interpretation due to their unique sets of acquired mutations. There is a general scarcity of tools that can i) systematically interrogate cancer genomes in the context of diagnostic, prognostic, and therapeutic biomarkers, ii) prioritize and highlight the most important findings, and iii) present the results in a format accessible to clinical experts. We have developed a stand-alone, open-source software package for somatic variant annotation that integrates a comprehensive set of knowledge resources related to tumor biology and therapeutic biomarkers, both at the gene and variant level. Our application generates a tiered report that will aid the interpretation of individual cancer genomes in a clinical setting.\n\nAvailability and ImplementationThe software is implemented in Python/R, and is freely available through Docker technology. Documentation, example reports, and installation instructions are accessible via the project GitHub page: https://github.com/sigven/pcgr)\n\nContactsigven@ifi.uio.no

bioinformatics↗