We first determined which SNPs were genotyped on both the 1M-Duo and the 550Kv3 illumina chip platforms. Given the small number of cases (n=56) genotyped using the 1M-Duo chip, we performed an independent association analysis of each matching SNP between the two chips using Fisher’s exact test on allele frequencies, using plink software [18]. Only one locus showed genome-wide significant associations. In Table 1 we show the nine SNPs with p-value p<10−7 that associated with disease. These were all located in and around the MYH9 locus on chromosome 22. We could not directly measure the association for haplotype E-1 defined in [14] which is mostly identified by the risk alleles for SNPs rs4821481 and rs3752462, since this last variant was genotyped only in cases. However, Hapmap data for the African Yoruba phopulation shows that SNP rs8141971 is a good proxy for rs3752462, with very high LD (r2>0.9). Therefore we also measured frequencies and associations for haplotype E-1p, which is defined by the risk alleles for SNP rs4821481 and rs8141971, and for haplotype T-1, defined by the risk alleles for SNP
