TAP2 recombination analysis

Cullen et al. (1995) used families showing meiotic crossovers in the class II region of the MHC to identify a putative recombination hotspot in intron 2 of the human TAP2 gene.

We have identified 45 SNPs and two indel polymorphisms in 9.7 kb of DNA surrounding this hotspot, extending from the end of the LMP7 gene to intron 6 of TAP2, and have used this to investigate haplotype diversity and to map crossover breakpoints in 176 recombinants recovered from sperm DNA. Both approaches revealed a 1.2 kb long meiotic crossover hotspot in TAP2 intron 2 that shows a peak intensity of 8-10 cM/Mb in male meiosis and an activity probably an order of magnitude greater in female meiosis.

A fully annotated sequence of the LMP7-TAP2 region investigated, with information on all SNPs detected and their ancestral state plus location of PCR primers, is available here:

TAP2 sequence and SNPs

A full listing of allele-specific oligonucleotides (ASOs) used to type each of the TAP2 polymorphisms is available here:

TAP2 allele-specific oligonucleotides

To download these files in pdf format, select the option below:

pdf formatted files

A full listing of allele frequencies at each polymorphic site analysed within the LMP7-TAP2 region is also available here:

LMP7-TAP2 SNP allele frequencies

If you refer to this data in any publication, please cite:

High-resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot. Jeffreys, A.J., Richie, A. and Neumann, R. Hum. Mol. Genet., 9, 724-733 (2000).