Humanomniexpressexome beadchip

Genotyping of the MDC-CC was made using the HumanOmniExpressExomeBeadChip and iScan system (Illumina, San Diego, CA, USA) analyzing 850,000 common, low frequency and rare SNPs. 5,451 individuals were successfully genotyped, i.e. passed our QC criteria. Criteria for excluding SNPs and study participants are presented in S2 Table.

To ensure the concordance of ancestry of study participants, in this study, we retrieved the GWAS summary data of BtC from Biobank Japan (BBJ) [17 ]. BBJ is a prospective genome biobank that collaboratively collected DNA and serum samples from 12 medical institutions in Japan, managed by the Institute of Medical Science, the University of Tokyo. BBJ has recruited approximately 260,000 participants, mainly of Japanese ancestry. All study participants had been diagnosed with one or more of 47 target diseases, among which the BtC was identified using ICD-10 codes of C22.1 and C23 and ICD-9 codes of 155 and 159.3. The BBJ participants were genotyped with the Illumina HumanOmniExpressExome BeadChip or a combination of the Illumina HumanOmniExpress and HumanExome BeadChips [18 ]. The genotype data were then imputed with 1000 Genome Project Phase 3 version 5 genotype and Japanese whole-genome sequencing data (n = 1037). Variants with an imputation quality < 0.7 were excluded, resulting in a total of 13,530,797 variants analyzed in the GWAS. For BtC, 418 cases and 159,201 controls that were East Asian ancestry were included (https://pheweb.jp/pheno/BtC). A generalized linear model that performed in SAIGE (version 0.37) was applied to conduct BtC GWAS, where age, age², sex, age × sex, age² × sex, and the top 20 principal components were adjusted.

We genotyped subjects using the Illumina HumanOmniExpressExome BeadChip or a combination of the Illumina HumanOmniExpress BeadChip and Illumina HumanExome BeadChip. We excluded individuals with a call rate <98%, closely related subjects estimated by identity-by-state analysis via visual inspection, and outliers in principal component analyses estimated using in-house software^{31 (link),32 (link)}.
We phased genotypes using MACH^{33 (link)} and imputed the variants using Minimac (v0.1.1). The phased genotype data of EAS samples from 1KG (phase1v3) were used as reference genotype information. We used the variants with a high imputation quality score (Rsq ≥ 0.7) in the association analysis. According to the heterozygosity of X-chromosomal variants, we excluded three males from the X-chromosomal analysis considering possible sex-errors.

A subset of 281 OE samples were genotyped using the Illumina HumanOmniExpressExome BeadChip (v1.2). We performed association analysis for each OE metabolite signal using this genetic dataset to identify exome SNPs associated with signal abundance. We restricted our analyses to 57,220 exome SNPs with minor allele count > = 3 and call rate > = 0.5 in OE, using the linear mixed model and kinship matrix calculation methods in EPACTS (v3.2.6) [27 ].

Genotyping was performed using the Illumina HumanExome and HumanOmniExpressExome BeadChip arrays. Our analyses were restricted to variants present on the HumanExome BeadChip, which in turn is a subset of those on the HumanOmniExpressExome BeadChip. The Illumina Exome BeadChip contains 247 870 genotyping probes, preferentially targeting rare coding variants. The design of the probes was based on over 12 000 sequenced genomes and exomes. Non-synonymous variants that have been observed at least three times (splice and start-stop mutations at least two times) and are observed in two or more data sets were considered for inclusion on the chip with additional custom content (see http://genome.sph.umich.edu/wiki/Exome_Chip_Design for full details).
All cases were typed at the Broad Institute (Cambridge, MA, USA) while the controls were genotyped by the Wellcome Trust Sanger Institute and The Broad Institute. Details of genotyping site and array are given in Supplementary Material, Table S5. The initial sample size was 6991 cases and 9070 controls.

A total of 2969 individuals were from BioBank Japan, which between 2003 and 2007 recruited ~200,000 patients with 47 common diseases from 12 Japanese medical institutes representing 67 hospitals (19 (link)). From the BioBank Japan database, we selected all the patients who were HCV-RNA positive at the time of recruitment and ascertained for primary HCC status (yes/no) based on histology, imaging, and laboratory tests. No information about HCV treatment and outcomes was available. The project was approved by the ethical committees of the University of Tokyo, and all participants provided written informed consent. Genomic DNA from peripheral blood was genotyped with an Illumina HumanOmniExpressExome BeadChip or a combination of the Illumina HumanOmniExpress and HumanExome BeadChips (20 (link)). The genotypes were prephased with MACH (21 (link)) and imputed with Minimac using the 1000 Genomes Project Phase 1 (version 3) East Asian reference panel (22 (link)). IFNL4-rs12979860 was imputed with high confidence, and association analysis was conducted using a logistic regression model using imputed gene dosage, adjusting for age, sex, and the top 2 principal components (PCs).