Coreexom psychchip

Participants provided buccal mucosa cells collected by a cytology brush (Cytobrush plus C0012, Durbin PLC). Genomic DNA was extracted according to the protocol of Freeman et al. (33 (link)). Genotyping was performed by Illumina's CoreExom PsychChip. All laboratory work was performed under the ISO 9001:2000 quality management requirements and was blinded with regard to phenotype. Variants were positioned on the genome based on GRCh37/hg19. SHAPEIT was used to determine haplotype information, then missing genotypes were imputed using IMPUTE2 on the CLOCK gene with boundaries extended by 10 kilobase pairs on both sides. Imputation and subsequent filtering were carried out in line with multiple quality control steps (34 (link)), except that missingness rate (MR), Hardy-Weinberg equilibrium (HWE) and minor allele frequency (MAF) steps were limited to SNPs within the CLOCK gene. Variants with an imputation score certainty <0.7 or info <0.5 were excluded.

Participants provided buccal mucosa cells collected by a cytology brush (Cytobrush plus C0012, Durbin PLC) to detect DNA. Genomic DNA extraction was carried out according to the protocol described by Freeman et al.^{81 (link)}. Genotyping was performed by Illumina's CoreExom PsychChip. All laboratory work was performed under the ISO 9001:2000 quality management requirements, and was blinded regarding phenotype. Variant annotation was carried out based on the GRCh37/hg19 human assembly. For the purpose of phasing SHAPEIT was used to estimate additional haplotypes, followed by imputation of missing genotypes via IMPUTE2.

Participants provided DNA by a genetic saliva sampling kit. Genomic DNA was extracted from buccal mucosa cells according to established protocols^{19 (link)}. Genotyping was performed using Illumina’s CoreExom PsychChip, yielding a total of 573,141 variants, the genomic positions of which were defined according to the build GRCh37/hg19. Quality control and imputation was based on refs. ^{20 (link),21 (link)} (see Supplementary File 1).

In order to detect DNA, buccal mucosa cells were provided by participants using a cytology brush (Cytobrush plus C0012, Durbin PLC, Hayes, UK). Extraction of the genomic DNA was carried out according to the previously described protocol of Freeman et al. [114 (link)]. P2RX7 genotype characterization was performed using Illumina’s CoreExom PsychChip. All laboratory work was performed under the ISO 9001:2000 quality management requirements and was blinded regarding phenotype.

Participants provided buccal mucosa cells via a genetic sampling kit including a cytology brush (Cytobrush plus C0012, Durbin PLC) sent by mail to detect DNA. Extraction of genomic DNA was carried out according to the protocol of Freeman et al. (29 (link)). Genotyping was performed using Illumina CoreExom PsychChip. Genotyping was carried out in accordance with ISO 9001:2000 quality management requirements, and was blinded regarding phenotype.
Variant annotation was carried out based on the GRCh37/hg19 human assembly. For the purpose of phasing SHAPEIT was used to estimate additional haplotypes, followed by imputation of missing genotypes via IMPUTE2. This process yielded 186 SNPs on the IL6 gene with boundaries extended by 10 kilobase (kb) pairs at both sides.