Computational protocol: The implication of FLT3 amplification for FLT targeted therapeutics in solid tumors

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Protocol publication

[…] Genomic DNA was extracted, and a SureSelect customized kit (Agilent Technologies, Santa Clara, CA, USA) was used for capturing 83 or 379 cancer-related genes depending on the version of sequencing panel. Illumina HiSeq 2500 was used for sequencing with 100 bp paired-end reads. The sequencing reads were aligned to the human genome reference sequence (hg19) using BWA-mem (v0.7.5), SAMTOOLS (v0.1.18), Picard (v1.93), and GATK (v3.1.1) for sorting SAM/BAM files, duplicate marking, and local realignment, respectively. Local realignment and base recalibration were carried out based on dbSNP137, Mills indels, HapMap, and Omni. SNVs and InDels were identified using Mutect (v1.1.4) and Pindel (v0.2.4), respectively. ANNOVAR was used to annotate the detected variants. Only variants with over 1% of allele frequency were included in the results. Copy number variations were calculated for targeted sequencing regions by dividing read-depth per exon by the normal reads per exon using an in-house reference. Translocations in the target region were identified using an in-house algorithm (in preparation). […]

Pipeline specifications

Software tools BWA, SAMtools, Picard, GATK, MuTect, Pindel, ANNOVAR
Application WES analysis
Organisms Homo sapiens, Danio rerio
Diseases Colonic Neoplasms, Neoplasms
Chemicals Tyrosine