Cnv370v1

The salting-out method was used for the isolation of DNA from the peripheral blood [38 (link)]. In the 168 patients recruited at the University Hospital Center Zagreb, single nucleotide polymorphisms (SNPs) were determined by ABI Prism 7300 Real-Time PCR System apparatus (Applied Biosystems, Foster City, CA, USA), using the following TaqMan SNP Genotyping Assays (Applied Biosystems): 5HTR1B rs13212041, 5HTR2A rs6313 (T102C), 5HTR2C rs3813929 (−759C/T), 5HTR6 rs1805054 (C267T), APOE rs7412, and rs429358. APOE SNPs were measured to determine APOE haplotypes (APOE ε2, ε3, and ε4) (rs429358 C allele and rs7412 C allele for ε4 variant, rs429358 T allele and rs7412 C allele for ε3 variant, and rs429358 T allele and rs7412 T allele for ε2 variant). SNPs were determined using Illumina genotyping platforms (CNV370v1, CNV370-Quadv3, and OmniExpressExome-8v1-2_A, Illumina, San Diego, CA, USA) in 2701 participants recruited from the “10,001 Dalmatians project”.

GoDARTS participants were genotyped using the Affymetrix 6.0 (n=927) and Illumina Human Omni Express (n=809) platforms. ORCADES samples were genotyped with either the Illumina HumanHap300 bead chip (n=890) or the Illumina Omni1M (n=304) or Illumina Omni Express bead chips (n=1073). Genotype data quality was assessed and imputed on the basis of 1000 Genome Projects reference panel. Imputed genotypes for 658, 1078, 1358 individuals from the GoDARTS data set 1, GoDARTS data set 2, and ORCADES cohorts, respectively, were used for the three independent GWAS analysis.
LBC1936 samples were genotyped using the Illumina Human 610Quad BeadChip. A total of 1398 participants from the 2 independent Croatian replication cohorts were available for the analysis, and subjects were genotyped on different genotyping platforms including Illumina CNV370v1 and CNV370-Quadv3 for Croatia-Korčula (n=378), and Illumina CNV370-Quadv3 and IlluminaOmniExpressExome-8v1_A for Croatia-Split (n=376). More details on QC, imputation, and processing can be found in the online-only Data Supplement.