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Pipeline publication

[…] ght (kg) divided by height (m)2 and WHR was defined as waist circumference divided by hip circumference. Pack-years of smoking were calculated as the number of cigarettes smoked per day divided twenty and then multiplied by the number of years smoking., Genomic DNA was isolated from whole blood. Targeted sequencing of the exons in 68 genes within the 1 LOD unit down region on 7p (chr7:29.3Mb-42.8Mb) was performed using a customized Agilent SureSelect Enrichment kit. A detailed description of sequencing methods has been previously published[]. Briefly, DNA libraries were sequenced on an Illumina HiSeq2000 and the raw sequencing reads were aligned to the human reference sequence hg19 with the Burrows-Wheeler Aligner (BWA)[]. Variant calling was performed using the Genome Analysis ToolKit (GATK) and potential functions of variants were annotated using ANNOVAR (http://annovar.openbioinformatics.org/) and SeattleSeq (http://snp.gs.washington.edu/SeattleSeqAnnotation138/index.jsp)., Quality control was conducted in accordance with procedures we published previously[]. Briefly, variants with VQSLOD < -4 or call rate < 75% were removed and within each individual sample, variants with a depth < 4 or Phred-Like (PL) score < 100 were set as missing. Novel variants in genes with nominal evidence for replication were validated via Sanger sequencing. At the sample level, concordance between the sequencing data and genotypes from the previous peak-wide association study[] were assessed for each sample. Two samples with low concordance (<95%) were remo […]

Pipeline specifications

Software tools BWA, GATK, ANNOVAR