Oncopanel testing capture was carried out with Illumina’s TruSight Cancer Kit, which screens 94 genes and 284SNPs (Illumina, Inc). Sequencing was performed using MiSeq sequencer (Illumina) to produce 2 × 150 bp reads. Raw reads were mapped against reference genome hg19 using bwa-mem, de-duplicated using Picard tools and variant calling was performed using GATK best practices pipeline. Quality filtered variants (minimum of × 20 coverage and no more than 10% MAPQ0) were annotated using ANNOVAR with avSNP release of 142, 1000 genomes release of 2014 along with NIH-NHLBI 6500 exome database version 2. MAF filter (<0.01) was set based on ExAC, NIH 6500, gnomAD and 1000 genomes data. Pathogenicity evaluation was performed based on the inheritance mode, database entries (HGMD, ClinVar, CentoMD), in silico prediction tools (SIFT, Polyphen2, MutationTaster) and ACMG recommendations. All intronic variants located outside the boundaries of 10 bp from the exons and synonymous exonic ones were filtered out. Putative splicing variants were analyzed using Human Splicing Finder (HSF).
- Project data type: Other
- Scope:
- Monoisolate
- KOC UNIVERSITY