Genotype imputation of SNP genotype data
The genotype imputation was performed using the Michigan imputation
server (https://imputationserver.sph.umich.edu). We used Haplotype
Reference Consortium release v1.1 and considered only ‘non-European’ or
‘mixed’ population16. Pre-phasing and imputation were
performed using Eagle V 2.417 and
Minimac418, respectively. After the imputation
processes, imputed SNPs were removed if the Rsq was less than 0.3, or
there were duplicated SNPs, missing genotype rates were larger than
0.05, P values in HWE tests were less than
1×10-5, or MAFs were less than 0.05. In addition,
subjects whose identity-by-descent (IBS) > 0.9 and
principal component (PC) score was outside the 5×IQRPC were excluded.
Finally, 1,386 asthmatic patients and 5,205 controls and their 4,935,875
SNPs were used for our analyses. The detailed procedure is shown in
Figure E1.