Whole Exome Sequencing and Variant Analysis
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Corresponding Organization : Agency for Science, Technology and Research
Other organizations : Singapore General Hospital
Variable analysis
- Hybrid selection using the Human All Exon kit SureSelect Target Enrichment System (Agilent Technologies) version 6
- Sequencing on the Illumina HiSeq X platform (Illumina) as paired‐end 150‐base pair reads
- Alignment to the human reference genome NCBI GRC Build 37 (hg19) using Burrows‐Wheeler Aligner (BWA MEM)
- Optical duplicate marking with Picard
- Base score recalibration using GATK version 4.1.4
- Variant screening for missense or splice site variants with mapping quality >Q20, sequencing depth >50, alternate allele depth >15, min alt fraction of 0.1
- Somatic variant identification using Mutect2
- Variant annotation and prioritization using VEP
- Mutational signature identification using SigProfiler Bioinformatics Tools
- Copy‐number segmentation processing with TitanCNA v1.17.1
- Identified germline and somatic variants
- Mutational signatures
- Copy‐number segmentations
- Normal tissue samples for comparison to tumor samples
Annotations
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