Paired-end alignment of sequencing data against the reference genome hg19 (GRCh 37) was performed using the Whole Genome Sequencing Application v2.0, based on the Isaac Alignment Tool (Raczy et al. 2013 (link)) within BaseSpace, a cloud-based analysis tool suit (Illumina).
Somatic single-nucleotide variant (SNV) and insertion/deletion (indel) variant calling analysis was performed using the Tumour-Normal Application v1.0, based on Strelka (Saunders et al. 2012 (link)), within BaseSpace. Calls were annotated using the Variant Effect Predictor v2.8 (McLaren et al. 2016 (link)), COSMIC v77 (Forbes et al. 2015 (link)), and 1000 Genomes v3 (The 1000 Genomes Project Consortium 2015 (link)). The SIFT (Kumar et al. 2009 (link)) and PolyPhen-2 (Adzhubei et al. 2010 (link)) algorithms were used to evaluate the impact of a mutation on protein structure or function as predicted by Ensembl (v84) (McLaren et al. 2016 (link)). All variants of interest were manually inspected using Integrative Genomics Viewer (IGV) (Robinson et al. 2011 (link)).
Somatic single-nucleotide variant (SNV) and insertion/deletion (indel) variant calling analysis was performed using the Tumour-Normal Application v1.0, based on Strelka (Saunders et al. 2012 (link)), within BaseSpace. Calls were annotated using the Variant Effect Predictor v2.8 (McLaren et al. 2016 (link)), COSMIC v77 (Forbes et al. 2015 (link)), and 1000 Genomes v3 (The 1000 Genomes Project Consortium 2015 (link)). The SIFT (Kumar et al. 2009 (link)) and PolyPhen-2 (Adzhubei et al. 2010 (link)) algorithms were used to evaluate the impact of a mutation on protein structure or function as predicted by Ensembl (v84) (McLaren et al. 2016 (link)). All variants of interest were manually inspected using Integrative Genomics Viewer (IGV) (Robinson et al. 2011 (link)).
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