Molecular mapping of a recombination hotspot located in the second intron of the human TAP2 locus

Am J Hum Genet. 1995 Jun;56(6):1350-8.


Recombination across the HLA class II region is not randomly distributed, as indicated by both strong linkage disequilibrium within the 100 kb encompassing the DRB1-DQA1-DQB1 loci and complete equilibrium between TAP1 and TAP2, the closest variant sites of which are < 15 kb. In an attempt to explain these observations, 39 novel polymorphic markers in a region encompassing the TAP, LMP, and DOB genes were used to delineate the site of crossover in 11 class II recombinant chromosomes. SSCP demonstrated that two recombination events occurred within an 850-bp interval in the second intron of TAP2, which separates the variant sites of TAP1 and TAP2. These data indicate the presence of a recombination hotspot, the first to be identified from the analysis of familial transmission in the human major histocompatibility complex. The region of crossover was cloned and sequenced from one of the recombinants, further defining the crossover site to a 138-bp segment nested within the 850-bp region. This represents the most precisely defined region of recombination in the human genome.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • ATP Binding Cassette Transporter, Subfamily B, Member 3
  • ATP-Binding Cassette Transporters / genetics*
  • Base Sequence
  • Chromosome Mapping
  • Chromosomes, Human / genetics*
  • Cloning, Molecular
  • Crossing Over, Genetic / genetics*
  • Female
  • Genes, MHC Class II / genetics
  • Genetic Variation
  • HLA-D Antigens / genetics
  • Humans
  • Introns / genetics*
  • Male
  • Molecular Sequence Data
  • Pedigree
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA


  • ATP Binding Cassette Transporter, Subfamily B, Member 3
  • ATP-Binding Cassette Transporters
  • HLA-D Antigens
  • TAP2 protein, human

Associated data

  • GENBANK/S78269