Genetic dissection of the human leukocyte antigen region by use of haplotypes of Tasmanians with multiple sclerosis

Abstract

Association of multiple sclerosis (MS) with the human leukocyte antigen (HLA) class II haplotype DRB1*1501-DQB1*0602 is the most consistently replicated finding of genetic studies of the disease. However, the high level of linkage disequilibrium (LD) in the HLA region has hindered the identification of other loci that single-marker tests for association are unlikely to resolve. In order to address this issue, we generated haplotypes spanning 14.754 Mb (5 cM) across the entire HLA region. The haplotypes, which were inferred by genotyping relatives of 152 patients with MS and 105 unaffected control subjects of Tasmanian ancestry, define a genomic segment from D6S276 to D6S291, including 13 microsatellite markers integrated with allele-typing data for DRB1 and DQB1. Association to the DRB1*1501-DQB1*0602 haplotype was replicated. In addition, we found that the class I/extended class I region, defined by a genomic segment of approximately 400 kb between MOGCA and D6S265, harbors genes that independently increase risk of, or provide protection from, MS. Log-linear modeling analysis of constituent haplotypes that represent genomic regions containing class I (MOGCA-D6S265), class III (TNFa-TNFd-D6S273), and class II (DRB1-DQB1) genes indicated that having class I and class II susceptibility variants on the same haplotype provides an additive effect on risk. Moreover, we found no evidence for a disease locus in the class III region defined by a 150-kb genomic segment containing the TNF locus and 14 other genes. A global overview of LD performed using GOLD identified two discrete blocks of LD in the HLA region that correspond well with previous findings. We propose that the analysis of haplotypes, by use of the types of approaches outlined in the present article, should make it possible to more accurately define the contribution of the HLA to MS.

Figure 1

An integrated physical map of the HLA region, showing the locations of the 13 SSLP markers: pTer-D6S276, D6S105, MOGCA, D6S265, D6S1571, D6S1568, TNFa, TNFd, D6S273, G51152, RINGCA, D6S439, and D6S291-cen. Selected genes (not drawn to scale) involved in functions of the immune system are represented by hatched boxes. The boundary between the “extended” and “classical” class I region lies between MOGCA and HLA-F. The “classical” class I region extends 1.8 Mb centromeric of HLA-F. The telomeric boundary of the class III region lies between HLA-B and the TNF locus. The class III region extends 0.75 Mb to the centromeric boundary with class II, which is located between D6S273 and DRA. The “classical” class II region extends 0.85 Mb, just centromeric of DPB1. This physical map was assembled with information from a number of sources (MHC Consortium ; Foissac et al. 2000; National Center for Biotechnology Information).

Figure 2

Comparison of haplotype frequencies between case and control subjects. For the class I region (A), MOGCA-D6S265 haplotypes were analyzed; for the class III region (B), TNFa-TNFd-D6S273 haplotypes were analyzed and for the class II region (C), DRB1-DQB1 haplotypes were analyzed. Haplotypes with a frequency of ⩾1% in cases and controls were plotted for MOGCA-D6S265 and DRB1-DQB1, but only haplotypes with a frequency ⩾2% were plotted for TNFa-TNFd-D6S273. Coding of haplotypes is describe in the Appendix. Asterisks (*) indicate haplotypes selected for association testing.

Figure 3

Two-point LD analysis, using GOLD, for case (A) and control (B) haplotypes. The relative location of markers used to construct the haplotypes is represented on the X-axis but is more clearly depicted in figure 1. The X-axis has been rotated left through 90° for the Y-axis, with the ticks identifying the relative marker location for both axes. The LD measure, D′, is graphically represented adjacent to each GOLD plot. For cases, D′ values are 0.07–0.87, and, for controls, they are 0.09–0.84. Between the top and bottom D′ value, the range has been divided into 10 intervals, each represented by a colored box. The D′ value delineating each interval is indicated.