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. Author manuscript; available in PMC: 2016 Feb 13.
Published in final edited form as: N Engl J Med. 2015 Aug 13;373(7):599–609. doi: 10.1056/NEJMoa1500140

Figure 2. Direct Chromosomal Phasing of HLA-DPB1, rs9277534, rs2281389.

Figure 2

A person with the genotype DPB1*04:01,14:01; rs9277534AG; rs2281389AG is heterozygous at all three genetic markers. The diploid genotype (both chromosomes together) can be produced by four theoretical haplotypes (Panel A). The physical linkage of HLA-DPB1, rs9277534, and rs2281389 alleles on each haplotype in a diploid sample requires separation of the chromosomes (a process known as phasing) (Panel B). The DNA was phased with the rs9277534A probe (red chromosome) and the rs9277534G probe (blue chromosome). The hap-loid DNA (one chromosome by itself) captured by the rs9277534A probe carries the HLA-DPB1*04:01 sequence (shown in reverse orientation for nucleotides 7 through 21, corresponding to residues 8 through 11 of HLA-DPβ; asterisks above the nucleotides indicate positions that distinguish DPB1*04:01 from 14:01) and is physically linked to rs9277534A (circled) and rs2281389A (circled), as ascertained by means of TaqMan genotyping. This is the HLA-DPB1*04:01-A-A haplotype. The haploid DNA captured by the rs9277534G probe carries the HLA-DPB1*14:01 allele and is physically linked to rs9277534G (circled) and rs2281389G (circled). This is the HLA-DPBl* 14:01-G-G haplotype. Controls shown for TaqMan genotyping include rs9277534AA (blue dot), rs9277534AG (green dot), rs9277534GG (red dot), and rs2281389AA (blue dot), rs2281389AG (green dot), rs2281389GG (red dot) cells from the International HLA Workshop panel (see the Materials and Methods section in the Supplementary Appendix). Black squares indicate the absence of template controls.