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Pipeline publication

[…] he difficulty of collecting tumor samples [, ]., In this study, we analyzed seven different AYA cancers from patients with metastatic tumors using three different genomics platforms (whole-exome sequencing, whole-transcriptome sequencing, and OncoScan™). We identified single nucleotide variations (SNVs) and insertion and deletions (indels) by using whole-exome sequencing (WES) and detected fusions by using whole transcriptome sequencing (WTS). For copy number variations (CNVs), we used OncoScan™ that is the genomics platform for analysis of copy number variations which had high performance with samples from FFPE, especially []. We processed the WES data with well-known bioinformatics tools (bwa, Picard, GATK, MuTect, and Somatic Indel Detector), as other studies described and processed WTS data with fusion detection tools [–]. We then identified candidate genes and suggested potential drugs that are specific to the genetic alterations of each patient. We also compared candidate genes for AYA cancers with the same types of cancers from all age groups using published data., This study was approved by the Institutional Review Board (IRB) of Seoul National University Hospital (1206-086-414). We obtained written informed consent from the patients who participated to this study. All participants in this study gave us written informed consent for publication of their details. Written informed consent fo […]

Pipeline specifications

Software tools BWA, Picard, GATK, MuTect