title: [Analysis of full intronic sequences of HLA-A alleles].
abstract: OBJECTIVE
  To analyze the full intronic sequences of human leukocyte antigen (HLA)-A alleles in Han Chinese.
  
  
  METHODS
  The full-length HLA-A alleles, including 8 exons and 7 introns, were amplified with a long-template PCR system from 165 donors from the Chinese Marrow Donor Program (CMDP). The products were cloned into a PGEM-T Vector System and sequenced from both directions. Genetic analysis was performed using a MEGA4.0 software. All sequences were aligned with a ClustalW algorithm. Phylogenetic trees were constructed with a neighbor-joining method. Genetic distances were estimated based on p-distance, and a bootstrap analysis was applied for assessing the confidence limits of the trees.
  
  
  RESULTS
  A total of thirty-three full-length sequences of HLA-A alleles, containing 2902-2918 nucleotides, were derived. A total of 138 point mutations and 9 insertions or deletions were found among the 7 introns, which showed remarkable group specificity. Intron 1 appeared to be most polymorphic with the highest average GC content and evolutionary distances. Eight phylogenetic trees were constructed respectively with the derived full-length sequences as well as each of the 7 introns sequences. Based on full-length sequences, sequences of the HLA-A locus were classified into five groups: group I consisted of A*01/03/11/30; group II consisted of A*23/24(A9); group III consisted of A*02/68/69(A2/28); group IV consisted of A*26/34(A10); and group V consisted of A*29/31/32/33/74(A19). The five groups were derived from two ancient lineages, one including groups I and II, and another including groups III, IV and V. No substantial difference was detected between the trees constructed with the 7 intronic sequences, except that group II belonged to different lineages based on introns 2-5 and introns 1 and 7. The A*30 variant cluster was close to group I (A*01/03/11/30) and differed from group V (A19).
  
  
  CONCLUSIONS
  The full-length sequences of 18 alleles have been submitted to GenBank and accepted by the international ImMunoGeneTics database (IMGT). Polymorphisms identified within the introns of HLA-A alleles showed remarkable group specificity. Such sequences seem to have substantially contributed to the recombination of the HLA-A alleles. The A*30 may represent an atypical group in which the rates of gene conversion and mutation have been unusually high.
authors.affiliation: Blood Center of Shenzhen, Shenzhen, Guangdong, People's Republic of China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Li
authors.forename: Liang-hong
authors.initials: LH
authors.lastname: Cheng
authors.forename: Hong-yan
authors.initials: HY
authors.lastname: Zou
authors.forename: Shi-zheng
authors.initials: SZ
authors.lastname: Jin
mesh_terms: D000483:Alleles; D015234:HLA-A Antigens / Q000235:genetics*; D006801:Humans; D007438:Introns; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D015234:HLA-A Antigens