Computational protocol: Establishing a patient-derived xenograft model of human myxoid and round-cell liposarcoma

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Protocol publication

[…] One microgram of each DNA sample, isolated from P5 xenograft tumors, was used for library construction using TruSeq DNA sample preparation kits (Illumina, San Diego, CA, USA). Five hundred nanogram-libraries of DNA from each sample were pooled for exome capturing using the TruSeq Exome Enrichment kit (Illumina). Sequencing was then performed with paired-end 2 × 100 base reads on the Illumina HiSeq 2000 platform (Illumina). Raw. fastq files were first processed by a proprietary algorithm to filter out mouse sequence contamination. We have previously shown that this filter step does not affect human SNP detection [, ]. After mouse sequences were removed, data were aligned to the human reference genome hg19/GRCh37 by BWA 0.6.1 and processed using variant calling by GATK 1.6. […]

Pipeline specifications

Software tools BWA, GATK
Application WES analysis
Organisms Homo sapiens
Diseases Immunologic Deficiency Syndromes, Liposarcoma, Neoplasms, Sarcoma, Desmoplastic Small Round Cell Tumor