Genotype data pre-processing and imputations
Quality control of genotyped SNV data was carried out at both subject-
and SNV-level using Plink 1.9, an open-source whole-genome analysis
toolset.(23) Details are included in Supplemental Data 1 . In
brief, subjects who were missing more than 10% of genotypes were
omitted, as were those with sex discrepancies (i.e. reported sex did not
match sex as determined by genetic markers on the sex chromosomes), and
related subjects as determined using identity by descent measures. The
processed genotype data was then imputed using the Michigan imputation
server.(24) First, chromosomes were phased using ShapeIT (v2.r790), then
SNVs were imputed using the Minimac algorithm and the Haplotype
Reference Consortium reference panel (r1.1 2016).(25–27) SNVs that
passed the quality score R2>0.3 were
retained for further analysis.