Figure 5

Profiling by proportional hybridization of HLA-A exon 2. Four patterns are described: a,a homozygosity (A); b,b homozygosity (B); a,b heterozygosity (C) and b,c heterozygosity (D). Each bar represents the _LogRatio for individual oligos sequentially positioned in 3' to 5' direction. Variant oligos are nested between homologous consensus oligos and appear as bright (_LogRatio >1) or light red (_LogRatio > 0.5 and ≤ 1). _LogRatio for any oligo between ≤ 0.5 or ≥ -0.5 are shown in yellow. Consensus oligos in various conditions of mismatch with test DNA are shown as light (_LogRatio < -0.5 and ≤ -1) or dark (_LogRatio < -1) green. The orange lines delimit _LogRatio between 1 and -1. The letter p points to a variant oligo with a double nucleotide variant (CA → GG at 256–257). Another double mismatch-containing oligo is pointed out by q (CA → AC at 99–100). The letter x points to a variant oligo (9-SP-A-02) spanning a region of b,c type heterozygosity (HLA-A*0201 and A*2901 differ A → G from the consensus). The letter y points to a situation where a variant oligo (14-SP-A-03, A29 at 263–280) encompasses also a "unknown" SNP present in the other allele (HLA-A*0201). z shows a variant oligo (10-SP-A-29 at 211–229) whose increased _LogRatio is not associated with decreased _LogRatio in the homologous consensus oligo. The orange asterisks and the dashed lines show a genomic region in which "unknown" HLA-A*0201 polymorphisms are associated (blue) or not associated (orange) with HLA-A*2901 polymorphic sites.