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Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex

Abstract

There is considerable interest in understanding patterns of linkage disequilibrium (LD) in the human genome, to aid investigations of human evolution and facilitate association studies in complex disease1,2,3,4,5. The relative influences of meiotic crossover distribution and population history on LD remain unclear, however5. In particular, it is uncertain to what extent crossovers are clustered into 'hot spots,6,7,8 that might influence LD patterns. As a first step to investigating the relationship between LD and recombination, we have analyzed a 216-kb segment of the class II region of the major histocompatibility complex (MHC) already characterized for familial crossovers9. High-resolution LD analysis shows the existence of extended domains of strong association interrupted by patchwork areas of LD breakdown. Sperm typing shows that these areas correspond precisely to meiotic crossover hot spots. All six hot spots defined share a remarkably similar symmetrical morphology but vary considerably in intensity, and are not obviously associated with any primary DNA sequence determinants of hot-spot activity. These hot spots occur in clusters and together account for almost all crossovers in this region of the MHC. These data show that, within the MHC at least, crossovers are far from randomly distributed at the molecular level and that recombination hot spots can profoundly affect LD patterns.

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Figure 1: Patterns of linkage disequilibrium (LD) in the class II region of the MHC.
Figure 2: Analysis of sperm crossover distribution near HLA-DNA and HLA-DMB.
Figure 3: Distribution of sperm crossovers within hot-spot DNA3.
Figure 4: Decay of association with distance within domains of linkage disequilibrium.
Figure 5: Sperm crossover activity in the class II region of the MHC.

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Acknowledgements

We thank J. Blower and numerous volunteers for supplying semen and blood samples, K. Lilley for assistance with automated sequencing and oligonucleotide synthesis, R. Dalgleish for advice on PCR, J. Stead for web site construction and other colleagues for helpful discussions. This work was supported by grants to L.K. from the Instrumentarium Science Foundation and the Finnish Cultural Foundation and to A.J.J. from the Medical Research Council, Wellcome Trust and Royal Society.

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Correspondence to Alec J. Jeffreys.

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Jeffreys, A., Kauppi, L. & Neumann, R. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29, 217–222 (2001). https://doi.org/10.1038/ng1001-217

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