Rana, Naheed Akhter; (2002) Investigation of recombination hotspots within human phosphoglucomutase 1 (pgm1): an allelic association and mapping approach. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

Human phosphoglucomutase 1 (PGM1) is a highly polymorphic protein coded by a single locus on chromosome lp31. Eight different alleles, four of them common, have been generated by a mixture of mutation and intragenic recombination. Previous work has suggested an elevated rate of recombination within the PGM1 gene, an observation supported by population studies, showing collapse of linkage disequilibrium across two distinct regions of the gene. Site A, comprising 17 kb between exons 4 and 8, has been studied previously; Site B, spanning 38.5 kb between the 5' region of the gene and exon 4, is the subject of this thesis. Initially CRIMAP was used to construct a genetic map of the region from CEPH families using locally typed intragenic PGM1 markers and more than 100 markers downloaded from the CEPH database, resulting in female and male maps of 76.5 cM and 64.0 cM, respectively. The sex averaged recombination rate derived from this map across 55.5 kb within PGM1 is 50 times higher than the genomic average and strikingly different from the recombination rate in regions bordering PGM1. Recombination within PGM1 is more frequent in males than females. Sequencing of 8 individuals across 6 kb of targeted regions across Site B revealed 18 new SNPs, nine of which were used in subsequent investigations. Detailed analysis of PGM1 haplotypes in CEPH families has demonstrated an increase in recombination frequency estimated to be 2.1% (37.8 cM/Mb) across 55.5 kb within the PGMl gene. Estimation of intragenic recombination frequencies confirmed that both Sites A and B are hotspots for recombination, showing female and male rates of recombination to be 0.7% (12.6 cM Mb-1) and 3.5% (63.1 cM m -1), respectively. Three additional maternal recombinants from other multi-generation families were also identified, and shown to involve PGM1 and a flanking marker. Patterns of linkage diseqiulibrium across 14 polymorphic markers have been mapped in the previously uncharacterised Site B region in three population samples; Caucasian (n=264), Chinese (n=222) and Vietnamese (n=187). Allelic association and haplotype analysis in this region revealed extremely variable recombination rates, implicating the presence of, (i) at least two hotspots, mapping to regions spanning ~2.7 kb and ~3.3 kb, and (ii) two haplotype blocks that extend ~8.7 kb and 658 bp. where two common haplotypes account for 80-90% of the chromosomes. There was no heterogeneity in the position of the blocks of LD in the three populations. Furthermore, this finding is supported by meiotic data, where all recombination events map within the sites of equilibrium observed in the three populations. A consensus 21 bp origin of replication motif, four perfect x sequences and two (TG)n (n > 20 bp) repeats have also been found within Site B. The data described for the PGM1 gene in this thesis, derived from genetic mapping, meiotic and population studies, are indicative of the presence of clustered hotspot activity with intervening blocks of linkage disequilibrium.

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