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Pipeline publication

[…] 130 samples have only WES data. The EA samples include those from the gastric-esophageal junction, not treated with chemotherapy or radiation before surgery. The tumor samples were examined by a board-certified pathologist and ensured that their carcinoma content >70 %. The samples were sequenced on multiple Illumina HiSeq flow cells to have the average target exome coverage of ~80× in WES data, and sequenced on the Illumina Genome Analyzer Iix or the Illumina HiSeq sequencer with an average of ~30× coverage depth in WGS data. The details of the sample collection, DNA extraction, and sequencing procedures can be found in []., The raw sequence data were extracted from dbGaP using the NCBI SRA Toolkit; the sequences were aligned to the NCBI build 37 (hg19) reference using BWA [] and processed following GATK best practices. The base score re-calibrated bam files were used for CNA detection., Control-FREEC was applied in this study on both WGS and WES data. It divided the genome into small contiguous regions using sliding windows. The read count profiles in each region for normal and tumor samples were computed and normalized accounting for GC-content and mappability. The read count ratios of tumors to matched normal samples were calculated and used as the proxy of the copy number ratios. A LASSO-based algorithm was used to segment the data. LASSO is a widely used generalized linear regression method that involves penalizing the absolute size of its regression coefficients []. Using LASSO, a piecewise constant smoothed step profile was used to model the copy number ratios, and th […]

Pipeline specifications

Software tools SRA Toolkit, BWA, GATK, Control-FREEC