The genotyping was run using the Illumina Quad 610 chip and 660Wq at the “Centre National de Genotypage” (Paris, France). Only autosomal SNPs were kept for this study. SNPs with a minor allele frequency (MAF) of <5%, a missing SNP rate of 10%, or SNPs that did not respect Hardy Weinberg Equilibrium (HWE) (<1 × 10−6) were also removed from this study. All available SNPs in the genes of interest (CNR1, NAPE, FAAH, MGLL, DAGLA) within ±10 kb (to include promoter and flanker regions) were then selected. Gene length and location were obtained using the UCSC Genome Browser. The SNP coordinates were updated from hg18 to hg19 using Illumina information and the liftover tool from the genome browser (http://genome.ucsc.edu/cgi-bin/hgLiftOver ). Nevertheless, SNP information was scarce on the CNR2, and as such, the gene was not included in this study. A summary of the locations and details of each SNP (gene, chromosome, base pair, function, etc.) can be seen in Supplementary Table 2 .
Quad 610 chip
Manufactured by Illumina
Sourced in France
The Quad 610 chip is a laboratory equipment product designed for high-throughput data analysis. It is capable of processing multiple samples simultaneously, providing efficient and streamlined data processing capabilities. The core function of the Quad 610 chip is to enable rapid and accurate data analysis, supporting various research and scientific applications.
Automatically generated - may contain errors
6 protocols using quad 610 chip
1
Genetic Variation in Endocannabinoid Pathway
2
Genome-wide Genotyping and FKBP5 Imputation
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A precise description of genotyping and imputation procedures has been published elsewhere (Lett et al., 2020 ; Schumann et al., 2010 ). In brief, blood samples were collected during site visits and sent to the IMAGEN DNA biobank for processing. Analyses covered DNA, for which the Illumina Quad 610 chip and 660w chip (Illumina, San Diego, CA) were used to perform genome‐wide genotyping of about 600,000 SNPs. Genotype results for the FKBP5 gene SNP rs1360780 were derived from standard imputation procedures. The distribution of rs1360780 alleles did not deviate from the Hardy–Weinberg equilibrium (χ2 = 0.29, p = .59). As per Grabe et al. (2016 ) and other studies on rs1360780 genotype (Koopmann et al., 2016 ), we combined the CC and CT carriers into one group, thus comparing T‐homozygotes with C allele carriers.
3
Illumina Quad 610 Genotyping Protocol
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The genotyping was conducted using the Illumina Quad 610 chip and 660Wq at the ‘Centre National de Genotypage’ (Paris, France). Non-imputed autosomal SNPs are used for this study (498 892 SNPs). Following all quality control steps, genetic data (468 170 SNPs) remained for 1740 individuals. Baseline quality control steps and principal component analysis to control for ancestry are described in online Supplementary materials.
4
FKBP5 Gene Genotyping and Imputation
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A precise description of genotyping and imputation procedures has been published elsewhere (Lett et al., 2020; (link)Schumann et al., 2010) (link). In brief, blood samples were collected during site visits and sent to the IMAGEN DNA biobank for processing. Analyses covered DNA, for which the Illumina Quad 610 chip and 660w chip (Illumina, San Diego, CA, USA) were used to perform genome-wide genotyping of about 600mult.000 SNPs. Genotype results for the FKBP5 gene SNP rs1360780 were derived from standard imputation procedures. The distribution of rs1360780 alleles did not deviate from the Hardy-Weinberg equilibrium (χ2 = 0.29, p = .59). As per Grabe et al. (2016) (link) and other studies on rs1360780 genotype (Koopmann et al., 2016) (link), we combined the CC and CT carriers into one group, thus comparing T-homozygotes with C allele carriers.
5
Genotyping of Alzheimer's Disease Cohorts
6
Genome-Wide Genotyping and Imputation
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DNA was genotyped and imputed as previously described32 (link). Briefly: DNA samples from 880 Caucasian children were genotyped on an Illumina 610 quad chip. The Illumina genotypes were called using the Illumina GenCall application following the manufacturer’s instructions. Non-Caucasian samples were excluded to ensure there was no population stratification by reviewing a PCA plot of the genotypes (Supplementary Fig. S13 ). Quality control criteria for samples included: 97% call rate, exclusion of samples with an outlier autosomal heterozygosity (scree-plot visualisation) gender validation and sequenome genotype concordance. Quality control criteria for SNPs included a 95% call rate, Hardy–Weinberg equilibrium (HWE) > 5.9 × 10–7, minor allele frequency > 0.005.
Genotypes were subsequently prephased (SHAPEIT v2.r644) and imputed (IMPUTE V2.2.2). We used the “1000 Genomes Phase I integrated variant set” reference genotypes to impute 560 K genotypes to yield 37,985,335 genotypes per sample.
Genotypes were subsequently prephased (SHAPEIT v2.r644) and imputed (IMPUTE V2.2.2). We used the “1000 Genomes Phase I integrated variant set” reference genotypes to impute 560 K genotypes to yield 37,985,335 genotypes per sample.
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