Visualizing human leukocyte antigen class II risk haplotypes in human systemic lupus erythematosus

Abstract

Human leukocyte antigen (HLA) class I and class II alleles are implicated as genetic risk factors for many autoimmune diseases. However, the role of the HLA loci in human systemic lupus erythematosus (SLE) remains unclear. Using a dense map of polymorphic microsatellites across the HLA region in a large collection of families with SLE, we identified three distinct haplotypes that encompassed the class II region and exhibited transmission distortion. DRB1 and DQB1 typing of founders showed that the three haplotypes contained DRB1*1501/ DQB1*0602, DRB1*0801/ DQB1*0402, and DRB1*0301/DQB1*0201 alleles, respectively. By visualizing ancestral recombinants, we narrowed the disease-associated haplotypes containing DRB1*1501 and DRB1*0801 to an approximately 500-kb region. We conclude that HLA class II haplotypes containing DRB1 and DQB1 alleles are strong risk factors for human SLE.

Figures

Figure 1

Association between the HLA class II region and SLE. A, PDT global association results for 55 markers across the length of chromosome 6 in 187 sib-pair families with SLE. B, PDT results for 41 HLA markers in 211 multiplex families (unfilled triangles), 123 simplex families (unfilled circles), and all 334 families (filled circles). The heterozygosity index for each marker was >0.70. C, PDT association results in 275 families (filled circles), where at least one parent was available and where phase could be determined unambiguously. Of these, 191 families carried at least one of the three risk haplotypes (unfilled circles), whereas 84 families lacked a risk haplotype (unfilled triangles). The position of selected HLA genes are indicated by the arrows. Dashed lines indicate P=.05.

Figure 2

Visualization of founder risk haplotypes carrying DRB1*1501 (DR2). Shown are all founder haplotypes carrying allele 6 at marker D6S2446 (D6S2446-6). The consensus ancestral haplotype containing D6S2446-6 was determined, and individual alleles were color-coded: marker alleles identical to consensus are shown in maroon, alleles different from consensus are shown in gold, and missing data or alleles with ambiguous phase are shown in gray. After sorting by length, groups of founder haplotypes were tested by TDT, with the numbers shown referring to the ratio of T:NT haplotypes. Blue boxes indicate significant transmission distortion (P<.05) for the larger groups; white boxes indicate nonsignificant TDTs. A, Founder haplotypes (N=176) were sorted by telomeric (left) length, and TDTs were performed. B, Founder haplotypes (N=176) were sorted, first by centromeric (right), and then by telomeric (left) length, to define the centromeric “breakpoint” by TDT. C, Founder haplotypes (N=155) carrying the TNF-α allele found on the DRB1*1501 extended haplotype were sorted on the basis of centromeric (right) length. Only those haplotypes extending to DRB1/DQB1 were significant by TDT. At the bottom of panel C are four “double recombinant” haplotypes, showing consensus markers for the TNF and class II regions but showing nonconsensus in-between; T:NT ratio is 3:1. Asterisks (*) represent the approximate boundaries of the haplotype length showing convincing evidence for transmission distortion. Haplotype groupings that failed to show significant transmission disequilibrium (white boxes) did not contain DRB1*1501, despite carrying D6S2446-6.

Figure 3

Haplotypes containing DRB1*0301 (DR3) and DRB1*0801 (DR8) show significant transmission disequilibrium in families with SLE. Founder haplotypes were sorted and analyzed as described in figure 2. A and B, Founder haplotypes (N=110) carrying D6S2446-8 (DRB1*0301 linked) were sorted on the basis of telomeric (left) length (A), and centromeric (right) length (B). C, Founder haplotypes (N=68) carrying D6S2446-5 (DRB1*0801 linked) sorted on the basis of overall length. Asterisks (*) represent the approximate boundaries of the haplotypes showing convincing evidence for transmission distortion. Haplotypes that failed to show significant transmission disequilibrium (white boxes) did not contain DRB1*0301 or DRB1*0801, despite carrying D6S2446-8 (A and B) or D6S2446-5 (C), respectively.

Online-Only Figure

Physical map of the HLA complex, showing the 52 genotyped microsatellite markers. This map is based on the current consensus 3,673,778-bp sequence available from the Sanger Centre. The positions of the markers indicate the centromeric end of the amplimer, and the positions of genes indicate the translation start codon. The 16 markers with designations beginning with “MN6S” were developed during the course of the present study and have been submitted to the Genome Database. The 11 microsatellite markers with heterozygosities