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Tumour procurement, DNA extraction, coverage analysis and optimisation of mutation-detection algorithms for human melanoma genomes

Pathology Jan 28, 2018

Wilmott JS, et al. - Researchers designed this study to test sample preparation, sequencing specifications and bioinformatic algorithms for their effect on accuracy and cost-efficiency in a large Whole genome sequencing (WGS) analysis of human melanoma samples. Results suggested that 60X coverage for melanoma tissue and 40X for melanoma cell lines empowered the detection of 98–99% of informative single nucleotide variants (SNVs). Likewise, the number and quality of SNVs detected were strongly influenced by the bioinformatic mutation analysis methodology. Detecting mutations in the blood genomes separate to the tumour genomes generated 41% more SNVs than if the blood and melanoma tissue genomes were analysed simultaneously. Therefore, they recommended employing simultaneous analysis on matched melanoma tissue and blood genomes to reduce errors in mutation detection.
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