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

<b>OBJECTIVEb>The purpose of this research was to identify a novel HLA-B allele in Chinese population.

<b>METHODSb>The HLA typing of bone marrow donors was performed by PCR-SBT. The ambiguous novel HLA allele was confirmed with GSSP method.

<b>RESULTSb>The sequence of a sample was different from all alleles in the HLA-B databases. The sequence analysis showed that it differed from the closet matching allele HLA-B*13:01:01 at one nucleotide substitution, 137 T > C in Exon2, which resulted in an amino acid change from Phenylalanine (Phe) to Serine (Ser) at codon 22.

<b>CONCLUSIONb>A novel allele was identified and named as HLA-B*13:68 by the WHO Nomenclature Committee.

Alleles ; Asian Continental Ancestry Group ; Base Sequence ; HLA-B Antigens ; Histocompatibility Testing ; Humans ; Polymerase Chain Reaction ; 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

<b>OBJECTIVEb>To confirm a new allele HLA-B*13:01:06 and analyze its nucleotide sequence.

<b>METHODSb>Genomic DNA was extracted using a Qiagen DNA extraction kit. Nucleotide sequences of HLA-A, HLA-B, HLA-C and HLA-DRB1 were analyzed by polymerase chain reaction-sequence based typing (PCR-SBT). HLA high-resolution results were assigned, and the nucleotide sequences of HLA-B locus was compared with that of HLA-B*13:01:01.

<b>RESULTSb>The nucleotide sequence of the new allele shows a strong similarity to that of HLA-B*13:01:01. One nucleotide in exon 2 has changed from G to A at position 219 (codon 49 GCG>GCA), which however did not result in amino acid change.

<b>CONCLUSIONb>The novel allele verified by sequencing has been submitted to GenBank and officially named as HLA-B*13:01:06 by the World Health Organization HLA Nomenclature Committee.

Alleles ; Amino Acid Sequence ; Base Sequence ; Exons ; HLA-B Antigens ; genetics ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; Sequence Analysis, DNA

The aim of this study was to identify a novel HLA-B allele in Chinese population. The HLA typing of bone marrow donors was performed by PCR-SBT. The ambiguous novel HLA allele was confirmed with GSSP and single stranded SBT method. The result indicated that there was a sample, the sequence of which was different from all alleles in the HLA databases. The sequence analysis showed that it differed from the closet matching allele B(*)40:06:01 in one nucleotide substitution, 272 C>T in Exon 2, which resulted in an amino acid change from Serine (Ser) to Phenylalanine (Phe) at codon 63. It is concluded that the novel allele has been identified and is named HLA-B(*)40:162 by the WHO Nomenclature Committee.
Alleles ; Female ; HLA-B Antigens ; genetics ; Histocompatibility Testing ; Humans ; 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

<b>OBJECTIVEb>To identify a novel human leukocyte antigen(HLA) allele in Chinese population.

<b>METHODSb>HLA typing was carried out with polymerase chain reaction-sequence specific oligonucleotide probes (PCR-SSOP). The HLA-B exons 1-7 of the proband were amplified and the product was cloned using a TOPO TA cloning sequencing kit to separate the two alleles. Both strands of exons 2 and 3 of selected colonies were sequenced. Sequence-based typing (SBT) was used to identify and analyze the difference between the new allele and the closest matching HLA-B allele.

<b>RESULTSb>HLA typing indicated a SSOP pattern which did not match with known HLA-B alleles. The results of the sequencing suggested the HLA-B alleles of the proband as B*59:01 and a novel allele. The HLA-B exon 3 sequence of the novel allele was different from any known alleles. This allele differs from the closest matching B*54:06 allele by 6 nucleotides, which included nt486 (G to C), nt527 (A to T), nt538 (T to C), nt539 (G to T), nt559 (C to A) and nt560 (T to C) in exon 3, resulting in substitutions of three amino acids including Glu to Val at codon 152, Trp to Leu at codon 156 and Leu to Thr at codon 163.

<b>CONCLUSIONb>A novel HLA-B allele has been identified and has been designated as HLA-B*54:09 by WHO Nomenclature Committee for Factors of the HLA System.

Alleles ; Base Sequence ; China ; Exons ; HLA-B Antigens ; genetics ; Humans ; Molecular Sequence Data ; Sequence Analysis, DNA ; methods

This study was purposed to analyze and identify a novel HLA allele in Chinese population. A new HLA-B allele which is closely related to HLA-B*35:03:01 was initially detected by PCR-SSOP, then DNA sequencing was performed to identify the difference between the novel allele and HLA-B*35:03:01 allele. The result showed that the sequence of the new allele was different from all other known sequence. It differs from the closest matching HLA-B*35:03:01 by a single substitution at position 387 C→G in exon 3, no resulting in amino acid change. It is concluded that this allele is a novel one and has been officially named B*35:03:07 by the WHO Nomenclature Committee.
Alleles ; Asian Continental Ancestry Group ; genetics ; HLA-B Antigens ; genetics ; Humans ; Male ; Sequence Analysis, DNA

This study was aimed to discriminate the alleles in the HLA-C*07:01:01G and HLA-C*07:02:01G groups and analyze their associations with HLA-B locus. Samples previously typed as HLA-C*07:01:01G and HLA-C*07:02:01G were collected. The nucleotide sequences in exons 1 to 7 of the HLA-C locus were sequenced by polymerase chain reaction sequence-based typing (PCR-SBT) and HLA-B genotyping was also preformed by PCR-SBT in these samples. The results showed that 4 samples (30.8%) were confirmed as HLA-C*07:01:01 and 9 samples (69.2%) were HLA-C*07:06 among 13 samples previously typed as HLA-C*07:01:01G. Linkage disequilibrium (LD) analysis showed that HLA-C*07:06 allele was strongly related with HLA-B*44:03. All samples were typed as C*07:02:01 among 102 individuals previously typed as C*07:02:01G. LD analysis showed that C*07:02:01 was strongly related with HLA-B*51:01, B*46:01, B*39:01, B*40:01, B*38:02, B*15:02 alleles. It is concluded that HLA-C*07:01:01 and HLA-C*07:06 alleles are confirmed in the HLA-C*07:01:01G group and HLA-C*07:02:01 is a preferred allele in the HLA-C*07:02:01G.
Alleles ; Base Sequence ; Exons ; HLA-B Antigens ; genetics ; HLA-C Antigens ; genetics ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; methods ; Sequence Analysis, DNA

<b>OBJECTIVEb>To investigate the molecular basis for a novel human leukocyte antigen (HLA) allele B*5827.

<b>METHODSb>DNA from the proband was analyzed by polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) typing. The amplified product was sequenced bidirectionally.

<b>RESULTSb>Abnormal HLA-B locus was observed and its nucleotide sequence was different from the known HLA-B allele sequences, with highest homology to HLA-B*5820 allele. It differs from HLA-B*5820 by 8 nucleotide substitutions in exon 3, i.e., nt 290 (G > C), nt 346 (T > A), nt 390 (A > C), nt 404 (G > C), nt 413 (C > G), nt 471 (A > G), nt 486 (A > G) and nt 487 (C > A), resulting in an amino acid change from ser > arg at nt 97, phe >tyr at nt 115, ser > arg at nt 130, thr > ala at nt 157 and thr > glu at nt 162. Nucleotide differences of nt 404 (G > C) and nt 413( C > G) did not change amino acid.

<b>CONCLUSIONb>The sequences of the novel allele have been submitted to GenBank (access No.GU071234). A novel HLA class I allele B*5827 has been officially assigned by the WHO HLA Nomenclature Committee in Jan. 2010.

Alleles ; Base Sequence ; Cloning, Molecular ; Genotype ; HLA-B Antigens ; chemistry ; genetics ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA