For the SSI replication cohort, genotyping of the selected SNPs was performed
using competitive allele-specific PCR (KASP) chemistry (LGC Genomics). In the
Australian cohort, genomic DNA was extracted from whole blood (Qiagen QIAamp DNA
Maxi Kit) and selected SNPs were genotyped by PCR amplification (Veriti Thermal
Cucler, Applied Biosystems) and bidirectional sanger sequencing
(BigDyeTM v.3.1 Terminator Cycle Sequencing Kit and 3730xl DNA
Analyzer, Applied Biosystems). The DBDS replication cohort had existing GWAS
data available from genotyping with Illumina Global Screening Array and
subsequent imputation, as described previously.27 Association testing was done by logistic
regression under an additive genetic model adjusting for sex. With the
availability of GWAS data, the replication results from DBDS were also adjusted
for the first four principal components. Combined analysis of the discovery and
replication stage data was done by fixed-effects inverse variance-weighted
meta-analysis. For the 1p31.1 locus, rs3001038 failed in genotyping of the
Australian cohort and rs998550 was used as a proxy instead. For the 15q22.31
locus, rs62023078 failed in the replication cohorts from SSI and Australia, and
rs13379670 was used as a proxy instead. We considered SNPs with
P < 0.05 in the replication stage and
P < 5 × 10−8 in the
combined analysis to indicate robust evidence of association.
using competitive allele-specific PCR (KASP) chemistry (LGC Genomics). In the
Australian cohort, genomic DNA was extracted from whole blood (Qiagen QIAamp DNA
Maxi Kit) and selected SNPs were genotyped by PCR amplification (Veriti Thermal
Cucler, Applied Biosystems) and bidirectional sanger sequencing
(BigDyeTM v.3.1 Terminator Cycle Sequencing Kit and 3730xl DNA
Analyzer, Applied Biosystems). The DBDS replication cohort had existing GWAS
data available from genotyping with Illumina Global Screening Array and
subsequent imputation, as described previously.27 Association testing was done by logistic
regression under an additive genetic model adjusting for sex. With the
availability of GWAS data, the replication results from DBDS were also adjusted
for the first four principal components. Combined analysis of the discovery and
replication stage data was done by fixed-effects inverse variance-weighted
meta-analysis. For the 1p31.1 locus, rs3001038 failed in genotyping of the
Australian cohort and rs998550 was used as a proxy instead. For the 15q22.31
locus, rs62023078 failed in the replication cohorts from SSI and Australia, and
rs13379670 was used as a proxy instead. We considered SNPs with
P < 0.05 in the replication stage and
P < 5 × 10−8 in the
combined analysis to indicate robust evidence of association.