Genetic risk, incident gastric cancer, and healthy lifestyle: a meta-analysis of genome-wide association studies and prospective cohort study

Abstract

We newly genotyped 6,483 cases and 5,488 controls using the Illumina Global Screening Array (GSA), which included two studies (East-GWAS: 4,872 cases and 3,397 controls from Jiangsu province and Shanghai; North-GWAS: 1,611 cases and 2,091 controls from Shandong province, Hebei province and Tianjin). We consecutively recruited histopathologically confirmed gastric cancer cases from hospitals. Cancer-free controls were selected from individuals receiving routine physical examination at hospitals or those participating in community screening for non-communicable diseases. Demographic characteristics of all participants were displayed in Table S1. Onco-GWAS:Histopathologically confirmed gastric cancer cases were consecutively recruited from hospitals in Jiangsu province, China. The cancer-free control subjects were selected from individuals receiving routine physical examination at hospitals or those participating in community screening for non-communicable diseases in Jiangsu province. A total of 1,140 cases and 345 controls were genotyped using the Illumina OncoArray, and 708 controls were genotyped using the Illumina OmniZhongHua chips (Table S1). Detailed study design and genotype calling was provided previously. 1 NJ-GWAS and BJ-GWAS:For the NJ-GWAS and BJ-GWAS, individuals were derived from separate casecontrol studies conducted in Nanjing (565 cases and 1,162 controls) and Beijing (468 cases and 1,123 controls) (Table S1). Individuals were genotyped using the Affymetrix Genome-Wide Human SNP Array (V.6.0), which consisting ~ 900,000 markers. The details of study design and relevant data were reported previously. 2 1.4 SX-GWAS: A total of 1625 gastric cancer cases and 2100 controls were from the Shanxi Upper Gastrointestinal Cancer Genetics Project and the Linxian Nutrition Intervention Trial (Table S1). All participants were genotyped using the Illumina 660W Quad chip. The study was reported elsewhere 3 and the genotype data was downloaded from dbGap (study accession: phs00361.v1.p1). Quality control.The same protocol of quality control procedures on genotyping data was applied for all six GWAS datasets. The genotyped variants were excluded if they had a call rate of <95%, a P value for Hardy-Weinberg Equilibrium (HWE) in controls ≤1.0×10 −6 or a minor allele frequency (MAF) of <1% in controls; and samples were removed if they were with call rates of <95%, outliers (>6 s.d. from the mean) in population stratification analysis and heterozygosity analysis, or duplicated or related individuals (PI_HAT > 0.25).A total of 100,641 samples in the CKB cohort were genotyped with a customized Affymetrix Axiom® CKB array. Samples with call rate < 98% or gender discrepancy, or samples with extreme heterozygosity (F statistic S.D. score <5) were excluded. Variants with call rate <95% were excluded. Variants with call rate ≥ 95% and < 98%, or deviation from the expected frequency as observed in the 1000 Genomes project (the Phase III integrated variant set release, 504 East Asians), or deviation from Hardy-Weinberg disequil...

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“…Compared with the data from the National Cancer Database (NCDB) Research Unit of the American College of Surgeons, GC patents in eastern Asia are diagnosed at a relatively early stage and enjoy better survival. However, there is much room for improvement in treatment outcomes (3). The heterogeneity of GC is reflected in the complexity of its classification.…”