HLA-DR antigen and gene frequencies were studied in 150 unrelated Koreans in Seoul. HLA-DR4 was the most common DR specificity encountered and HLA-DR1 and -DR3 occurred with the lowest frequencies. The frequency of HLA-DR blank allele was 27.1%. HLA-B:DR haplotypes involving positive delta values differing significantly from zero were DR1:B7, DR2:Bw22, DR3:B17, DR5:Bw35, DRw6:B17, DR7:B12, DR7:B13, and DRw8:Bw16. The supertypic groups (MT1, MT2 and MT3) differ somewhat in frequencies from Other populations. These findings suggested that the Korean population, while having many similarities in HLA-DR antigen frequencies with those of neighboring Orientals, has not only different features in the distribution of HLA-DR antigens but also has unique HLA-B:DR haplotypes.
Gene Frequency ; HLA Antigens/analysis* ; HLA-B Antigens ; HLA-DR Antigens ; Haploidy ; Histocompatibility Antigens Class II/analysis* ; Human ; Korea ; Mongoloid Race*

<b>OBJECTIVEb>To investigate the genetic diversity in Chinese populations. And HLA-A, -B alleles and haplotypes of 190 unrelated healthy individuals of Tu nationality from Wufeng county Hubei province were identified for the associated studies of HLA gene polymorphism and disease.

<b>METHODSb>The high-resolution typing methods--sequence-based typing(SBT) was used to define the most polymorphism of exons 2 and 3 of the HLA-A, -B locus alleles. The allele and haplotype frequencies were calculated by maximum likelihood estimation with Arlequin software.

<b>RESULTSb>HLA-A, -B alleles were found to be in Hardy-Weinberg equilibrium(P>0.05). A total of 26 HLA-A and 41 HLA-B alleles were detected. The most frequent alleles were A*0201(0.16053), A*110101(0.14737), A*24020101(0.14211), B*4001(0.14737), B*4601(0.13947), followed by A*0207(0.08947), A*0206(0.08158), B*1301(0.07632), B*5801(0.08947), B*1501(0.09737). The frequencies of following alleles to be A*330301(0.05526), B*1502(0.05526), B*3501(0.05263) were all higher than 0.05. The extensive HLA-A-B haplotypes were observed, and the most common haplotypes were A*0202-B*4001(0.04196), A*0201-B*4601(0.03625).

<b>CONCLUSIONb>In the present study, we first analyzed the HLA-A, B gene typing with SBT, all of these results will be the basic and reference data for Tu race, and also will have the applications available to trace the population migration, clinical organ transplantation, disease-associated study, HLA genetic feature and forensic identification.

Alleles ; Asian Continental Ancestry Group ; ethnology ; genetics ; China ; ethnology ; Ethnic Groups ; genetics ; HLA Antigens ; analysis ; genetics ; HLA-A Antigens ; analysis ; genetics ; HLA-B Antigens ; genetics ; Humans

OBJECTIVE: To verify a rare allele of human leukocyte antigen (HLA) and analyze its inheritance and 3D molecular structure. METHODS: PCR-sequence-based typing, PCR-single strand oligonucleotide polymorphism and single allele-specific sequencing were carried out to characterize the rare HLA-C allele and its transmission in the family. Its protein structure was modeled by using SWISS-MODEL, Phyre2 and FATCAT software. RESULTS: Analysis indicated that the rare allele (HLA-C*08:84) has transmitted from the proband's mother and has differed from HLA-C*08:01 by a single base (g.512G>C), resulting in substitution of an amino acid (p.Trp147Ser). Modeling of the 3D structure of the encoded protein indicated that the amino acid residue variation is located at the alpha 2 helix, which participates the formation of pocket F. Modeling of the structures of C*08:84, C*08:01, C*08:02, C*08:03 and C*08:22 has suggested significant variation in the peptide binding regions of the backbone, with root mean square errors being 1.70 nm, 1.79 nm, 0.71 nm and 1.70 nm, respectively. CONCLUSION A rare HLA-C*08:84 allele has been identified, and its clinical significance has been analyzed.
Alleles ; Base Sequence ; HLA-B Antigens/genetics* ; HLA-C Antigens/genetics* ; Humans ; Molecular Structure ; Sequence Analysis, DNA

BACKGROUND: Data on allele frequencies (AFs) and haplotype frequencies (HFs) of HLA-C and -DQB1 are limited in Koreans. We investigated AFs and HFs of HLA-A, -B, -C, -DRB1, and -DQB1 in Koreans by high-resolution sequence-based typing (SBT). METHODS: Hematopoietic stem cells were obtained from 613 healthy, unrelated donors to analyze HLA-A, -B, -C, -DRB1, and -DQB1 genotypes by using AlleleSEQR HLA-A, -B, -C, -DRB1, and -DQB1 SBT kits (Abbott Molecular, USA), respectively. Alleles belonging to HLA-C*07:01/07:06 group were further discriminated by using PCR-sequence specific primer analysis. AFs and HFs were calculated by direct counting and maximum likelihood method, respectively. RESULTS: In all, 24 HLA-A, 46 HLA-B, 24 HLA-C, 29 HLA-DRB1, and 15 HLA-DQB1 alleles were identified. AFs and HFs of HLA-A, -B, and -DRB1 were similar to those reported previously. For the HLA-C locus, C*01:02 was the most common allele, followed by C*03:03, C*03:04, C*14:02, C*03:02, and C*07:02 (AF > or =7%). AFs of C*07:01 and C*07:06 were 0.16% and 3.18%, respectively. For the HLA-DQB1 locus, DQB1*03:01 was the most common allele, followed by DQB1*03:03, *03:02, *06:01, *05:01, *04:01, and *06:02 (AF > or =7%). AFs of DQB1*02:01 and DQB1*02:02 were 2.12% and 6.69%, respectively. HFs of A*33:03-C*07:06 and C*07:06-B*44:03 were 3.09% and 3.10%, respectively, while those of DRB1*07:01-DQB1*02:02 and DRB1*03:01-DQB1*02:01 were 6.61% and 2.04%, respectively. CONCLUSIONS: This study reported AFs and HFs of HLA, including HLA-C and -DQB1, in Koreans by using high-resolution SBT. These data can be used to resolve ambiguous results of HLA typing for organ and hematopoietic stem cell transplantations.
Alleles* ; DNA Fingerprinting* ; Gene Frequency ; Genotype ; Haplotypes* ; Hematopoietic Stem Cells ; Histocompatibility Testing ; HLA Antigens ; HLA-A Antigens ; HLA-B Antigens ; HLA-C Antigens ; HLA-DRB1 Chains ; Humans ; Korea ; Leukocytes* ; Sequence Analysis ; Unrelated Donors

HLA genes constitute a highly polymorphic multigene system. In the present study, HLA-B oligonucleotide chips were manufactured by using a set of sequence-specific oligonucleotide probes derived from polymorphic regions in exon 2 and exon 3 of HLA-B gene spotted by microarrayer onto the aldehyde modified glass slides. In addition, the sequenced HLA-B gene clones used as standard samples were amplified from exon 2 and exon 3 by PCR. Together with the correct hybridization and wash conditions, the PCR products were bound with the array probes on the chip, and the hybridization patterns were transformed to HLA-B genotypes. The results showed that the genotypes of standard samples by the HLA-B oligonucleotide chips were completely identical with the sequenced clones. In conclusion, the oligonucleotide chip method presented here for HLA-B genotyping is a rapid, accurate, sensitive and attractive high throughput biochemical way.
Genotype ; HLA-B Antigens ; classification ; genetics ; Humans ; Oligonucleotide Array Sequence Analysis ; Sequence Analysis, DNA

<b>OBJECTIVEb>To identify a novel human leukocyte antigen (HLA) B allele and explore its family heritage.

<b>METHODSb>A novel HLA allele was suspected upon routine HLA typing using a polymerase chain reaction-sequence specific oligonucleotide probe (PCR-SSOP) assay. The sequence was confirmed with DNA sequencing and compared with its closest matching allele, B*55:02. The family was also investigated.

<b>RESULTSb>An unusual reaction pattern was detected during routine HLA typing. The sequence was confirmed to be a novel HLA-B allele, which differed from the closest matching allele, B*55:02 in 7 nt positions in exon 2. Among the 7 mutations from 6 codons, there were two amino acids changes including 69Glu→Met and 70Glu→Ala.

<b>CONCLUSIONb>A novel HLA-B allele has been identified and officially named as B*55:35 by the WHO Nomenclature Committee for Factors of the HLA System (GenBank accession number FJ898284).

Alleles ; Base Sequence ; HLA-B Antigens ; genetics ; Histocompatibility Testing ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA

BACKGROUND: HLA-B*15 alleles encode molecules belonging to several serologic subtypes, B62, B63, B71, B72, B75, B76, and B77. Using the conventional serologic typing method, assignment of B15 subtypes has often been prone to error specifically in samples exhibiting either an ambiguous or a B15 homozygous reaction pattern. The goal of this study was to establish a supplementary DNA typing method for accurate assignment of B15 subtypes in 'problematic B15 positive samples'. METHODS: B*15 specific gene amplification was performed using a pair of PCR primers that specifically annealed to B*15 and B*46 alleles. Nested PCR was applied to the amplified DNA using 14 sequence specific PCR primer sets. DNA sequencing was used to clarify the assigning of samples exhibiting discrepancies between the results obtained by B*15-specific nested PCR-SSP typing and serology. RESULTS: The B*15-specific nested PCR-SSP typing could clearly discriminate the 9 B*15 alleles expressed in the Korean population. In application of the system to 30 B15 positive serologically typed samples, 4 exhibited discrepancies between serology to PCR-SSP results. DNA sequencing results obtained from the samples were concordant with those from B*15-specific nested PCR-SSP typing. CONCLUSIONS: The established B*15-specific nested PCR-SSP method is superior to serology in accuracy and resolution. Therefore, the method will be useful as a supplementary DNA typing method to clarify HLA-B assignments of 'problematic B15 positive samples' in Koreans.
Alleles ; DNA Fingerprinting* ; DNA* ; Gene Amplification ; HLA-B Antigens ; Polymerase Chain Reaction ; Sequence Analysis, DNA

This study was purposed to investigate the nucleotide sequences of a novel HLA-B*15:124 allele and its molecular mechanism. The genomic DNA from whole blood was extracted by using commercial DNA extraction kit. The sequences of exon 2, 3 and 4 of HLA-B locus in the proband were amplified by PCR with group-specific primers, the PCR products were purified by enzymes digestion, then exon 2 to 4 of HLA-B locus for both orientations was sequenced. The results showed that 2 HLA-B alleles of proband were gained after amplification and sequencing of group-specific primers, among them one was a B*40:03, another was a novel allele. After BLAST analysis, the novel allele showed nucleotides different from HLA-B*15:52 in exon 3 at nucleotide position 427 A > T and 440 G > T which resulted in amino acid change from Thr to Ser at codon 143 and Trp to Leu at conon 147. It is concluded that a novel HLA-B allele has two different nucleotides. This HLA-B allele is identified and has been officially named B*15:124 by the WHO Nomenclature Committee.
Alleles ; Base Sequence ; Exons ; Female ; HLA-B Antigens ; classification ; genetics ; Humans ; Sequence Analysis, DNA

<b>OBJECTIVEb>To identify a novel HLA allele in Chinese population.

<b>METHODSb>A new HLA-B allele was initially detected by an usual PCR-SSP and PCR-SSOP in routine typing HLA allele. Sequence-based typing (SBT) was used to identify and analysis the difference between the new allele and HLA-B 4409 allele.

<b>RESULTSb>The HLA-B exon 3 nucleotide sequence of the novel allele was different from all other known alleles. The allele had 3 nucleotides replaced of the closest matching B 4409 allele at nt538(G>C), nt539(A>T) and nt540 (C>G) in exon 3, resulting in an amino acid change from D(GAC) to L(CTG) at codon 180.

<b>CONCLUSIONb>A novel HLA allele was confirmed by the SBT and it was officially designated as HLA-B 4446 by WHO Nomenclature Committee for Factors of the HLA System in September,2005.

Alleles ; Base Sequence ; HLA-B Antigens ; classification ; genetics ; Humans ; Male ; Molecular Sequence Data ; Sequence Analysis, DNA

The study was purposed to investigate the molecular genetic basis for HLA novel allele HLA-B*5408N in Chinese population. DNA was extracted from whole blood by commercial DNA extraction kit, the HLA-B exons 2 - 4 of the proband was amplified by allele specific primers PCR and the amplified product was sequenced for exons 2, 3 and 4 bidirectionally. The sequencing results showed HLA-B alleles of the proband as B*1527 and the novel allele. The sequences of the novel allele have been submitted to Genbank (DQ295998, DQ295999, DQ296000). After blast analysis, the novel allele showed a single nucleotide mismatch with HLA-B*5401 in exon 3 at position 553 G-->T, which resulted in an amino acid changing from Glu to premature stop codon at position 161. No the HLA-B54 antigen specificity expression in the proband cells was found using HLA-AB serological Typing Trays. It is concluded that this allele is a novel null allele and has been officially named B*5408N by the WHO Nomenclature Committee.
Alleles ; China ; Exons ; genetics ; HLA-B Antigens ; genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA