Figure 2
Comparison of SNPs between CEHs. A. Upper panel: Previously reported SNP distribution over the human MHC (NCBI dbSNP Build 126) indicating the higher density of SNPs in the HLA-A, Cw, B and HLA-DR/DQ regions. Across the indicated region (position 28,944,796 to 33,362,643; from ~1 Mb telomeric to HLA-A to ~0.2 Mb centromeric to HLA-DPB1), there is a mean frequency of ~790 SNP/50 kb genomic DNA. Lower panel: Distribution of SNPs incorporated into the Affymetrix GeneChip Human Mapping 500 K array. The horizontal line represents the mean distribution in the region (~5 SNP/50 kb) and the vertical bar to the left of the line indicates one standard deviation. Thus, the chip uses only 0.6% (428 SNPs) of the SNPs reported in the region to date. Note that gene chip SNP representation in the regions harboring defined HLA polymorphic alleles is even lower. B. Top panel: SNP variations were determined between two cell lines (EM10 and FS10) homozygous for the CEH [HLA-A*2601, E*010301, Cw*1203, B*3801, SC21, DRB1*0402, DQA1*0301, DQB1*0302] except for EM10, which is heterozygous for HLA-E*0101 and HLA-E*010301. For all panels in this figure, a value of 0 indicates homozygous identity between the two cell lines, a value of 1 indicates heterozygosity for the SNP in at least one of the cell lines, and a value of 2 indicates complete discordance between the two cell lines. Second panel: SNP variations between the B8HM1 and B8HM2 cell lines each homozygous for the CEH [HLA-A*0101, E*0101, Cw*0701, B*0801, SC01, DRB1*0301, DQB1*0201]. Third panel: A comparison of the homozygous SNP identities shared between EM10 and FS10 (the HLA-A*26, B*38 CEH) cell lines with the homozygous SNP identities shared between B8HM1 and B8HM2 (the HLA-A*01, B*08 CEH) cell lines. Only those SNPs for which there was an unequivocal call for all four cell lines were included. Fourth panel: SNP variations between the HLA-A*26, B*38 CEH and the L2DB cell line homozygous for the independent HLA-A*03, B*07 CEH ([HLA-A*0301, E*010302, Cw*0702, B*0702, SC31, DRB1*1501, DQA1*0102, DQB1*0602]. Bottom panel: SNP variations between the HLA-A*01, B*08 CEH and the L2DB cell line homozygous for the HLA-A*03, B*07 CEH.