The Class II region of the human MHC: analysis of linkage disequilibrium and meiotic crossover patterns

To investigate the fine-scale distribution of meiotic crossovers along human chromosomes, a 216 kb segment extending from upstream of the HLA-DNA gene to the TAP2 gene in the MHC Class II region was selected for study. Studies of familial meiotic crossovers in this region by Cullen et al. (1997) showed evidence of non-random distribution, with definite clustering between the HLA-DNA and RING3 genes, plus a possible cluster in the TAP2 gene. Sperm crossover analysis in TAP2 confirmed the presence of a localised hotspot about 1 kb long within an intron (Jeffreys, Ritchie & Neumann, 2000). To extend the hotspot investigation, SNPs were characterised across the entire 216 kb region and genotyped by ASO hybridisation in a panel of 50 unrelated UK Caucasian semen donors. These genotypes were used to identify regions of strong linkage disequilibrium that are likely to be recombinationally inert, plus intervals of local breakdown of linkage disequilibrium that might signal the presence of a local recombination hotspot. Breakdown intervals were then subjected to sperm crossover analysis to characterise any local hotspots.

This analysis revealed the existence of 5 crossover hotspots in addition to the TAP2 hotspot. Three of the hotspots form a cluster around the HLA-DNA gene (hotspots DNA 1, DNA 2, DNA 3). The other two were located in and downstream of the HLA-DMB gene (hotspots DMB 1, DMB 2). Together, these hotspot clusters account for the great majority (probably 94%) of all male meiotic crossovers in this region of the MHC.

Data on the TAP2 hotspot, SNPs and their locations, ASOs used for SNP typing, semen donor genotypes, and procedures for recovering crossover molecules from sperm DNA by single molecule PCR, can be found below:

The TAP2 meiotic recombination hotspot

Annotated sequence around hotspots DNA 1-3

showing the location of SNPs and PCR primers used for resequencing,
plus approximate position of the centre of each crossover hotspot

Annotated sequence around hotspots DMB 1,2

showing the location of SNPs and PCR primers used for resequencing,
plus approximate position of the centre of each crossover hotspot

Details of each SNP

including location, allele frequencies
and the sequences of ASOs used for SNP typing

SNP genotypes

established by genotyping a panel of semen donors

Sperm crossover analysis at hotspots DNA 1-3, DMB 1,2

with details of allele-specific and universal primers
used for recovering crossover molecules from sperm DNA,
plus information on PCR cycling conditions for each primer combination.

Last updated: 8 September, 2005 Celia A. May The views expressed in this document are those of the document owner, Alec J. Jeffreys.