Supplemental Data s7

Supplemental Data

Imputation across Genotyping Arrays for Genome-wide Association Studies:

Assessment of Bias and a Correction Strategy

Eric O. Johnson, Dana B. Hancock, Joshua L. Levy, Nathan C. Gaddis, Nancy L. Saccone, Laura

J. Bierut, and Grier P. Page Figure S1. Quantile-quantile plots of SNP association results when combining studies genotyped on different Illumina BeadChip arrays (Human1M or HumanHap550 version 3). The plots compare the observed versus expected P values in (A) European American subjects from SAGE versus PanScan and (B) African American subjects from SAGE versus iControl. SNPs were imputed based on the union of genotyped SNPs available on either array. The number of imputed

SNPs with MAF>1% and the overall λgc are shown in each plot.

34,483 SNPs

Overall λgc=1.075 B.

42,894 SNPs

Overall λgc=1.102 Figure S2. Genomic inflation factors (grey lines) (λgc) and percentages of SNPs having spurious association (black lines) (P<1x10-6), by minor allele frequency (MAF), when combining studies genotyped on different Illumina BeadChip arrays (Human1M or HumanHap550 version 3) and conducting imputation using the IMPUTE2 program. (A, B) African American subjects from

SAGE were compared to iControl subjects. Two different imputed SNP sets were assessed: (A) imputed SNPs based on the union of genotyped SNPs available on either array, and (B) imputed

SNPs based on the intersection of genotyped SNPs available on both arrays. The number of imputed SNPs with MAF>1% and the overall λgc are shown in each plot.

42,826 SNPs

42,812 SNPs

Overall λgc=0.997 Figure S3. Genomic inflation factors (λgc) and percentages of SNPs having spurious association

(P<1x10-6), by minor allele frequency (MAF), when combining studies genotyped on slightly different Illumina BeadChips (HumanHap550 version 1 or version 3). Imputed SNPs, based on the union of genotyped SNPs available on either array, are shown for (A) European American subjects from PanScan versus CGEMS study subjects and (D) African American subjects from iControl subsets genotyped on different BeadChips. The number of imputed SNPs with

MAF>1% and the overall λgc are shown in each plot.

34,435 SNPs

42,853 SNPs

(P<1x10-6), by minor allele frequency (MAF), when combining studies genotyped on either the

Illumina Human1M or Affymetrix 6.0 array. SNPs were imputed based on the union of genotyped SNPs available on either array in (A) European American and (B) African American subjects from SAGE (genotyped on Illumina 1M) versus the GAIN GWAS of Schizophrenia

(genotyped on Affymetrix 6.0). The number of imputed SNPs with MAF>1% and the overall λgc are shown in each plot.

34,503 SNPs

Overall λgc=1.270

43,035 SNPs

(P<1x10-6), by minor allele frequency (MAF), when combining studies genotyped on different

Illumina BeadChip arrays (Human 1M or HumanHap550K version 3). (A) European American subjects from the SAGE study were compared to PanScan study subjects, and (B) African

American control subjects from the SAGE study were compared to iControl subjects. Imputed

SNPs, based on the union of genotyped SNPs available on either array, are shown, following the removal of imputed SNPs with R2<0.3. The remaining number of imputed SNPs with MAF>1%

2 2 and R >0.3 are shown, along with the overall λgc after the R filtering.

33,928 SNPs

42,064 SNPs

Overall λgc=1.080