Y.-M. He

Analysis for complete genomic sequence of HLA-B and HLA-C alleles in the Chinese Han population

In the present study, we have determined the complete genomic sequence and analysed the intron polymorphism of partial HLA‐B and HLA‐C alleles in the Chinese Han population. Over 3.0 kb DNA fragments of HLA‐B and HLA‐C loci were amplified by polymerase chain reaction from partial 5′ untranslated region to 3′ noncoding region respectively, and then the amplified products were sequenced. Full‐length nucleotide sequences of 14 HLA‐B alleles and 10 HLA‐C alleles were obtained and have been submitted to GenBank and IMGT/HLA database. Two novel alleles of HLA‐B*52:01:01:02 and HLA‐B*59:01:01:02 were identified, and the complete genomic sequence of HLA‐B*52:01:01:01 was firstly reported. Totally 157 and 167 polymorphism positions were found in the full‐length genomic sequence of HLA‐B and HLA‐C loci respectively. Our results suggested that many single nucleotide polymorphisms existed in the exon and intron regions, and the data can provide useful information for understanding the evolution of HLA‐B and HLA‐C alleles.

Distribution of MICA diversity in the Chinese Han population by polymerase chain reaction sequence-based typing for exons 2-6.

Major histocompatibility complex class I chain-related gene A (MICA) is located 46 kb centromeric to HLA-B locus and encodes a stress-inducible protein. MICA allelic variation is thought to be associated with disease susceptibility and immune response to transplants. In this study, polymerase chain reaction sequence-based typing (PCR-SBT) method for MICA alleles has been established. Genomic DNAs from 100 healthy Chinese Han individuals were typed for MICA alleles by this method. The microsatellite polymorphism in the exon 5 of MICA gene, MICA*Del allele, and human leukocyte antigen-B alleles was also detected by the polymerase chain reaction-GeneScan, polymerase chain reaction sequence-specific primer, and PCR-SBT methods, respectively. Fourteen MICA alleles were found in the population, with MICA*00801/04 having the highest frequency of 27.0%. MICA*A4, *A5, *A5.1, *A6, and *A9 microsatellites were identified. Two samples with HLA-B*4801 were MICA*Del positive, with the frequency of 1.0%. The data showed that the new PCR-SBT method for MICA alleles was reliable and Chinese Han population was distinct in distribution of MICA alleles.

Analysis of the complete genomic sequence of HLA-A alleles in the Chinese Han population

To analyse the complete genomic sequences and investigate the intron polymorphism of the human leucocyte antigen (HLA)‐A locus, the full‐length nucleotide sequences of each major allelic group of HLA‐A in the Chinese Han population were determined, including HLA‐A*01, A*02, A*03, A*11, A*23, A*24, A*26, A*29, A*30, A*31, A*32, A*33, A*34, A*68, A*69. More than 3.0‐kb DNA fragment of HLA‐A locus was amplified from 5′‐untranslated region to 3′‐noncoding region for sequencing. Full‐length sequences of the HLA‐A alleles were determined using an ABI BigDye® Terminator Cycle Sequencing kit and the HLA‐A phylogenetic tree was analysed by dnaman software. Full‐length nucleotide sequences of 15 HLA‐A alleles (GenBank Accession numbers EU445470–EU445484) were obtained. HLA‐A*110101, A*2301, A*300101, A*310102, A*330301, A*340101, A*680102 and A*6901 alleles were firstly reported for complete genomic sequences. Total 247 polymorphism positions were found in the complete genomic sequences of HLA‐A alleles and a insertion of 17 nucleotides within intron 3 was observed in several allelic groups. According to the phylogenetic tree of the full‐length nucleotide sequences, HLA‐A locus was classified into seven major allelic lineages. In this study, complete genomic sequences of common HLA‐A alleles were obtained and the data will help us understand the evolution of HLA‐A.

Distribution of MICB diversity in the Zhejiang Han population: PCR sequence-based typing for exons 2–6 and identification of five novel MICB alleles

The polymorphism of major histocompatibility complex class I chain-related gene B (MICB) and variations in MICB alleles in a variety of populations have been characterized using several genotyping approaches. In the present study, a novel polymerase chain reaction sequence-based typing (PCR-SBT) method was established for the genotyping of MICB exons 2–6, and the allelic frequency of MICB in the Zhejiang Han population was investigated. Among 400 unrelated healthy Han individuals from Zhejiang Province, China, a total of 20 MICB alleles were identified, of which MICB*005:02:01, MICB*002:01:01, and MICB*004:01:01 were the most predominant alleles, with frequencies of 0.57375, 0.1225, and 0.08375, respectively. Nine MICB alleles were detected on only one occasion, giving a frequency of 0.00125. Of the 118 distinct MICB ∼ HLA-B haplotypes identified, 42 showed significant linkage disequilibrium (P < 0.05). Haplotypes MICB*005:02:01 ∼ B*46:01, MICB*005:02:01 ∼ B*40:01, and MICB*008 ∼ B*58:01 were the most common haplotypes, with frequencies of 0.0978, 0.0761, and 0.0616, respectively. Five novel alleles, MICB*005:07, MICB*005:08, MICB*027, MICB*028, and MICB*029 were identified. Compared with the MICB*005:02:01 sequence, a G > A substitution was observed at nucleotide position 210 in MICB*005:07, and a 1,134 T > C substitution in MICB*005:08 and an 862 G > A substitution in MICB*027 were detected. In addition, it appears that MICB*028 probably arose from MICB*004:01:01 with an A to G substitution at position 1,147 in exon 6. MICB*029 had a G > T transversion at nucleotide position 730 in exon 4, compared with that of MICB*002:01:01. On the basis of the new PCR-SBT assay, these observed results demonstrated MICB allelic variations in the Zhejiang Han population.

Identification of a novel HLA-B*35:42:02 allele in a Chinese bone marrow donor.

HLA-A*11:57 allele was different from HLA-A*11:16 by single nucleotide substitution at codon 145(CAC>CGC), resulting in one amino acid change His to Arg.

A novel HLA-DPA1*0204 allele was identified in a Chinese individual

We report here the identification of a novel human leukocyte antigen-DPA1*0204 allele that was detected by polymerase chain reaction sequence-based typing.

HLA-A, -B and -DRB1 allele and haplotype frequencies of 8333 Chinese Han from the Zhejiang province, China

The distribution of human leucocyte antigen (HLA) allele and haplotype is varied among different ethnic populations. In this study, HLA‐A, ‐B and ‐DRB1 allele and haplotype frequencies were determined in 8333 volunteer bone marrow donors of Zhejiang Han population using the polymerase chain reaction sequence‐based typing. A total of 52 HLA‐A, 96 HLA‐B and 61 HLA‐DRB1 alleles were found. Of these, the top three frequent alleles in HLA‐A, HLA‐B and HLA‐DRB1 loci, respectively, were A*11:01 (24.53%), A*24:02 (17.35%), A*02:01 (11.58%); B*40:01 (15.67%), B*46:01 (11.87%), B*58:01 (9.05%); DRB1*09:01 (17.54%),DRB1*12:02 (9.64%) and DRB1*08:03 (8.65%). A total of 171 A‐B‐DRB1 haplotypes with a frequency of >0.1% were presented and the five most common haplotypes were A*33:03‐B*58:01‐ DRB1*03:01, A*02:07‐B*46:01‐DRB1*09:01, A*30:01‐B*13:02‐DRB1*07:01, A*33:03‐B*58:01‐RB1*13:02 and A*11:01‐B*15:02‐DRB1*12:02. The information will be useful for selecting unrelated bone marrow donors and for anthropology studies and pharmacogenomics analysis.

Identification of two novel HLA-B*54 alleles, B*54:01:03 and B*54:01:04 by polymerase chain reaction sequence-based typing

HLA-B*54:01:03 and HLA-B*54:01:04 show one nucleotide change compared to HLA-B*54:01:01.

Identification of a novel HLA-DQB1*03:03:04 allele by polymerase chain reaction sequence-based typing in a Chinese leukemia patient.

Nucleotide sequence of HLA-DQB1*03:03:04 allele was different from that of HLA-DQB1*03:03:02 by a single nucleotide substitution at position 603 C>T.

Identification of a novel HLA‐DQB1*03:38 allele by polymerase chain reaction sequence‐based typing in a Chinese bone marrow donor

HLA-DQB1*03:38 differs from HLA-DQB1*03:03:02:01 at nucleotide position 184 T>C in exon 2.