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Genomic characterization of hepatocellular carcinoma in Hispanic patients

ABSTRACT: The genomic DNA was extracted from paired tumor and adjacent non-tumor samples of 27 Hispanic HCC patients. The TruSeq Rapid Exome Library Prep kit (Illumina, CA) was used to capture the coding regions of the human genome. The 100Ã¢Â€Â‰bp paired-end sequencing of every 6-plex whole exome library pool was performed on an Illumina HiSeq 3000 system according to the manufacturerÃ¢Â€Â™s recommended protocol to achieve an average coverage of ~100X. The paired-end reads were aligned to the human reference genome (hg19) with decoy sequences (as used in the 1000 Genomes Project) using BWA software. The duplicate reads were marked and removed using Picard and SAMtools, respectively. Local realignment around insertions/deletions (indels) and base quality recalibration were performed using GATK.

PROVIDER: EGAS00001007431 | EGA |

REPOSITORIES: EGA

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