Infinium global screening array v2

HLA types were imputed using HIBAG version 1.18.1 [69 (link)] and the multi-ethnic prediction model specific for Illumina Infinium Global Screening Array v2.0.

The genotyping of the samples was conducted with the Illumina Infinium Global Screening Array v2.0. The genotype calls were done using Illumina GenomeStudio 2.0. We filtered variants with minor allele frequency (MAF) less than 1%, genotype missingness greater than 2.5%, and Hardy-Weinberg equilibrium (HWE) p-value less than 1e-5. This resulted in 484886 variants which were imputed using the Michigan Imputation Server with the HRC (Version r1.1 2016) reference panel. Post-imputation filters, r² less than 0.3, MAF less than 1%, and HWE p-value less than 1e-6 were applied, resulting in 7924221 variants. Principle component analysis of the samples, together with 1000 genomes samples [48 (link)] revealed that 2 samples have non-European ancestry, thus were excluded from further analyses. The human reference genome build used was GRCh37.

Genotyping was conducted on the Infinium Global Screening Array v2.0 (Illumina, San Diego, California, US). Quality control of samples was carried out to filter extremely low-quality samples and variants (call rate <97.5%) using PLINK (version 1.9). A total of 729,526 SNPs were mapped to the GRCh37 (hg19) reference genome. To reduce heterogeneity in population structure, we conducted principal component analysis using PLINK on the whole genome SNP data and extracted the top five principal components for correcting genetic heterogeneity across different races/ethnic groups. We limited our analyses to SNPs with minor allele frequency > 0.05 and with a Hardy-Weinberg equilibrium P > 1^*10⁻⁶.

Assessment of copy number variation in the NTHL1 region was carried out using the Illumina Infinium Global Screening Array v2.0. Data on hybridization intensity for each probe were used to calculate the Log R ratio (LRR) and B allele frequency (BAF) values. These values were used to identify copy number regions and to segment the genome. Segmentation calculations were performed with genoCN software^{17 (link)} using the R package.

Additional information regarding genotyping on the Infinium Global Screening Array v2.0 (Illumina, San Diego, and Calif) and RNA-seq (Differential Gene Expression Analysis) performed at Admera Health (Plainfield NJ) on RNA extracted from human blood using PAXgene Blood RNA kit (Qiagen, Hilden, and Germany) at baseline and 6 weeks is available in the Supplementary Material.

DNA from the healthy individuals were genotyped on the Infinium Global Screening Array v2.0 (Illumina). The genetic structure of the study population was analysed using EIGENSOFT [65 (link)] after excluding long-range linkage disequilibrium (LD) regions [66 (link)], SNVs with MAF < 0.05 and SNVs in LD r² > 0.2 using the HapMap3 cohort as reference population. All individuals mapped to the CEU population (< 10 SD from the mean HapMAP CEU population for the first 5 principle components) and passed the exclusion criteria for heterozygosity (> 5 SD from population mean), call rate (< 98%) and discordance for reported sex. One individual was excluded due to relatedness (π-hat > 0.1875, PLINK software v1.90).
Variants with a call rate < 98%, a MAF < 1% or with deviation from Hardy-Weinberg equilibrium (p < 0.00001) were excluded. Imputation of additional variants was performed at the Sanger imputation service [67 (link)] using the Haplotype reference consortium r1.1 reference and the “pre-phase with EAGLE2 and impute” pipeline [68 (link)]. Imputed genotype calls with a genotype probability score below 0.9 were set to missing and variants with an info score below 0.8, a MAF < 0.01, deviation from Hardy-Weinberg equilibrium (p < 0.0001) or a call rate < 95% were excluded. The final dataset contained 303 individuals and 5,084,123 genetic variants.