Novel HLA-A*31 allele, A*3111 identified by sequence-based typing

In this report, we describe the identification of an HLA-A*31 nucleotide sequence variant, a new HLA-A*3111, in three members of a Korean family by using sequence-based typing (SBT). The new allele was detected during routine HLA typing by high-resolution SBT. Allele A*3111 showed one nucleotide difference with A*310102 at codon 165 (GTG-->CTG) resulting in an amino acid change from valine to leucine (V165L). Serologic reactivity was shorter than normally expected.     

人类白细胞抗原新等位基因HLA-A*3020的鉴定及确认

目的 鉴定及确认1名中国人的人类白细胞抗原(human leukocyte antigen,HLA)新等位基因.方法 应用聚合酶链式反应-序列特异性寡核苷酸探针(polymerase chain reaction-sequence specific oligonucleotide probes,PCR-SSOP)方法基因分型、PCR产物测序和基因克隆DNA测序方法,通过软件分析该基因序列及与最相近HLA等位基因序列的差异.结果 PCR-SSOP基因分型结果显示该样品HLA-A谱型为与已知HLA-A等位基因谱型不一致的新谱型;测序结果显示该样品HLA-A位点第2外显子序列与所有已知HLA-A等位基因序列不一致.软件分析表明该基因序列与序列最相近的等位基因A*300101,在所检测的第1～3外显子中的差异只是在第2外显子区域产生了nt 294 C→A一个碱基替代,并导致相应的密码子98由GAC(D)→GAA(E).结论 该基因为HLA新等位基因,被世界卫生组织HLA因子专用术语命名委员会正式命名为HLA-A*3020.     

Identification of a novel HLA-A allele,HLA-A*01:195, in a UAE national

A novel human leucocyte antigen (HLA)-A allele, HLA-A*01:195, was identified by sequence-based typing (SBT) in a UAE national subject. The novel allele is identical to its closest known allele, HLA-A*01:01:01:01, in exon 2, 3 and 4, except for a single nucleotide mutation of A to G at position 442 in exon 3 (codon 124 in the α2 domain of the α chain of the mature protein). This A to G mutation results in an amino acid change of isoleucine #124 to valine.     

Identification of a new HLA allele,A*1114, in a Chinese family

A novel HLA-A allele, A*1114, was initially detected in two generations of a Chinese family by unusual polymerase chain reaction based sequence-specific primers ( PCR-SSP) reaction patterns and ambiguous sequence-based typing (SBT). Molecular cloning and sequencing analysis indicated that this new allele differs from HLA-A*1102 by three nucleotide substitutions in exon 3, 524 A-->G, 526 G-->C, and 527 C-->G, thus changing codon 175 from His to Arg (CAT-->CGT) and codon 176 from Ala to Arg (GCG-->CGG). Segregation analysis showed that the proband inherited his mother's HLA haplotype A*1114, B*5801, DRB1*1405. The serologic equivalent of A*1114 is a split antigen HLA-A11.2. A PCR-SSP method was developed to distinguish A*1114 from other A*11 alleles. No further individuals with A*1114 were found in 5000 Chinese bone marrow donors.     

New HLA-A*11 allele,A*1112, identified by sequence-based typing

In this report, we describe the identification of HLA-A*1112, a novel HLA-A*11 allele found in two Italian families. The new allele was detected during routine HLA typing by a polymerase chain reaction sequence-specific primer and was confirmed by high-resolution sequencing-based typing. The nucleotide sequences of HLA-A*1112 exons 2 and 3 are identical to HLA-A*11011 except for a single nucleotide substitution in codon 90 (GAC-->GCC).     

Identification of a new human leukocyte antigen A allele, HLA-A*3020

A new human leukocyte antigen (HLA) A allele, HLA-A*3020, was found during routine HLA genotyping by polymerase chain reaction–sequence specific oligonucleotide probes and sequencing-based typing. The A*3020 allele has one nucleotide change at position 294 of exon 2 from the closest matching allele A*300101, resulting in an amino acid change from D (GAC) to E (GAA) at codon 98.     

Identification and sequence characterization of a novel HLA-A11 serological variant (HLA-A*1108)

In this report we describe the identification of a novel HLA-A*11 allele, HLA-A*1108, found in two individuals of a Spanish family. This new allele was detected during routine HLA typing by an atypical serological reactivity pattern and by inconclusive patterns obtained in DNA-based typing methods. The nucleotide sequence of exons 2 and 3 of HLA-A*1108 was identical to HLA-A*11011 except for two nucleotide substitutions at codons 152 (GCG-->GAG) and 156 (CAG-->CGG). These mutations change the non-charged amino acid alanine, at codon 152, to negative glutamic acid, and also non-charged glutamine, at codon 156, to positive arginine, which may explain its anomalous serological reactivity.     

Identification of a novel allele HLA-A*1113 in a Japanese donor

Anew HLA-A*11 allele, A*1113, was identified in a healthy Japanese female. She was typed as HLA-A11?, A2, B46, B67, Cw1, Cw7 (Bw6) with unusual serological reactivity of A11, suggesting possible presence of a new A*11 allele. The novel A*1113 allele was identified by haplotypic group-specific allele amplification using A*11 allele-specific primer pairs and sequence-based typing. The A*1113 allele differs from A*11011 by one nucleotide substitution in exon 3 at position 503 (A --> G) which causes an amino acid change in the alfa2 domain at residue 144 (lysine : K --> arginine : R), thus resulting in the unusual serological reactivity.     

HLA-A*3306, a novel variant in the Indian population

We describe a new HLA-A allele, A*3306, which was identified by sequencing based typing (SBT) in an individual of Indian origin. A*3306 is similar to A*3303, with a difference at position 228 (A to G). This difference leads to an amino-acid change at codon 52 from Ile (ATA) to Met (ATG). Until now this position has been considered conserved.     

Description and molecular modeling of a novel human leukocyte antigen allele: A*32:22

We describe here the sequence and the molecular modeling of a new variant of HLA-A*32 allele officially named A*32:22. This novel allele has been detected in an Italian cord blood sample by sequence-based typing (SBT). The mutation (CAT →CGT), which has occurred at codon 151, at nucleotide position 524, implies an amino acidic change from Histidine to Arginine. Residue 151 is located on top of the molecule inside the region contacted by T cell receptor (TCR) and it is possibly involved in docking TCR. A positively charged residue is maintained on this position determining a slight change of electrostatic potential on the molecular surface. This suggests a limited functional relevance of the amino acid substitution encoded by A*32:22.     

A new HLA-A*24 variant, A*2475, identified by sequence-based typing in the Korean population

A novel human leukocyte antigen (HLA) A*24 allele was identified in the Korean population and designated HLA-A*2475. The HLA-A*2475 allele shows one nucleotide difference from A*24020101 in exon 3 at nucleotide position 575 (T→C), resulting in an amino acid change, Leu168Arg.     

Detection of a novel HLA-A allele by polymerase chain reaction-sequence-specific oligonucleotide typing: HLA-A*0252

Anew human leukocyte antigen (HLA) class I allele, HLA-A*0252, has been found during routine typing of samples for the Australian Bone Marrow Donor Registry. A*0252 differs from A*020101 at four codon positions, with all the new polymorphisms resulting in an amino acid change. The amino acids involved are located in the antigen-binding region of the HLA protein.     

A nucleotide insertion in exon 4 is responsible for the absence of expression of an HLA-A*01 allele

HLA class I typing performed in parallel by molecular biology and serology has revealed cases where an HLA class I allele was identified whereas the corresponding antigen was not detected on the cell surface. In the present report, we describe four members of a family in whom an HLA-A 1 allele identified at the molecular level was typed as A "blank" by lymphocytotoxicity. This serologically blank antigen was undetectable by isoelectric focusing (IEF). Sequencing of the HLA-A*01 allele from the promoter region to the eighth exonic region revealed insertion of a "C" nucleotide at the beginning of the fourth exon as compared to the common HLA-A*0101 allele. This mutation causes a frame shift, giving rise to an early stop codon in the fourth exon.     

Identification and characterization of three novel HLA alleles, HLA-A*240214, HLA-A*3215 and HLA-DQB1*060302

We describe three novel human leukocyte antigen (HLA) alleles found in three different Caucasians, HLA-A*240214, HLA-A*3215 and HLA-DQB1*060302. As compared with HLA-A*24020101, HLA-A*240214 has a synonymous nucleotide (nt) exchange in codon 132. HLA-A*240214 may have arisen from intergenic recombination between HLA-A*24020101 and an HLA-B or HLA-C allele. The second novel allele, HLA-A*3215, has three nucleotide exchanges as compared with HLA-A*320101. These variations result in amino acid exchanges in codons 62 and 63, generating the public epitope of the serological HLA-A10 group. The third novel allele, HLA-DQB1*060302, has one synonymous nucleotide exchange within codon 38 as compared with HLA-DQB1*060301. In a family segregation study, we found that HLA-DQB1*060302, similar to the known HLA-DQB1*060301 allele, cosegregates with HLA-DRB1*1301.     

Sequencing based typing for HLA-C. Identification of three new alleles: Cw*0307, Cw*0502 and Cw*0504

HLA-C has been described as a transplantation locus in the unrelated bone marrow transplantation setting, and noticeably the number of mismatches between HLA-A,-B,-DRB1 compatible pairs is considerably high. Sequencing based typing (SBT) is an accurate and efficient methodology utilised in the HLA class I and II allele level of resolution. SBT for HLA-C locus was applied on a sample of 40 HLA-A,B,DRB1,DRB3/4/5,DQB1-compatible bone marrow recipient-donor pairs, and 3 new HLA-C alleles have been found. Cw*0307, well defined by serology as Cw3, showed two amino acid changes at the NK motif 77-80 regarding all described Cw*03 alleles, N77K80 instead of S77N80. Two new Cw*05 alleles were described, Cw*0502 properly typed by serology, and Cw*0504 that behaves as a short antigen. Cw*0502 differed from Cw*0501 by only one nucleotide at exon 3, that generated an amino acid replacement at codon 177, K to E. Cw*0504 differs from Cw*0501 by two clustered amino acid positions (114 and 116) placed at the peptide binding site. The rate of new HLA-C alleles found in this small series evidences a high grade of hidden HLA-C diversity in the Spanish population, particularly in the well-defined serologic specificities.     

Characterization of a new HLA-A allele,A*0256, identified in a Caucasian individual

HLA-A typing by the PCR-SSP method in a male 21-year-old Caucasian individual revealed a very rare allele combination corresponding to a unique reaction pattern. Therefore, the result was examined using sequence-based typing. Sequencing of exons 2 and 3 of the HLA-A locus after allelic separation with specific primers revealed the sequence of a new allele, similar to A*0245. Sequencing of exons 1 and 4 resulted in no additional inconclusive positions. The sequence pattern of the new allele HLA-A*0256 might have been generated as a result of a double crossing over recombination of an A*0201 and either an A*03 or an A*11.     

Identification of HLA-A*11 variant (A*1107) in the Korean population

We report here a new HLA-A*11 allele, A*1107, identified by sequencing based typing in the Korean population. The full-length sequencing of A*1107 was conducted on cDNA. HLA-A*1107 differs from HLA-A*1101 by a single nucleotide at position 399 of codon 109 in exon3 (TTC-->TTA), leading to an amino acid change from phenylalanine to leucine. But the serological profile of HLA-A*1107 did not exhibit the altered HLA-A11.     

Point mutation in the alpha helix of the HLA-C alpha2 domain generates a novel HLA-C allele,HLA-Cw*0106, in a Han Chinese individual in Taiwan

We report herein the identification of a new HLA-C allele using sequence-based typing (SBT). This novel allele, HLA-Cw*0106, was found in a Han Chinese individual from Taiwan. This individual was typed using SBT as having a class I HLA genotype of HLA-A*0206/0207, HLA-B*4601/5601, and HLA-Cw*0102/0106. This new allele differs from HLA-Cw*0102 in one of the nucleotides of the polymorphic exon 3 at codon 152 (GAG-->GTG; E152V). This residue is located in the alpha helix of the HLA-C alpha2 domain and may have the potential to affect the binding of HLA-C molecules with antigenic peptides and/or the interactions with the T cell receptor. This new allele was detected in a few individuals of Han Chinese in Taiwan, but has not yet been observed in the aboriginal populations in Taiwan.     

Identification of the new HLA-A*31:48 allele in an Italian patient

Human leukocyte antigen (HLA) class I sequence-based typing (SBT) for hematopoietic unrelated donor searching in an Italian Caucasian patient showed the presence of a novel HLA-A allele defined as A*31:48. HLA-A*31:48 has one nucleotide change from A*31:01:02 at nt 727 from C to T, resulting in an amino acid change at codon 219 of exon 4 from Arg to Trp.     

An intronic mutation responsible for a low level of expression of an HLA-A*24 allele

HLA class I typing performed in parallel by molecular biology and serology has revealed cases where an HLA class I allele was identified but the corresponding antigen on the cell surface was not detected. In the present report, we describe three members of a family in whom an HLA-A24 allele identified at the molecular level was typed as A "blank" by lymphocytotoxicity. This serologically blank antigen was nevertheless faintly detectable by isoelectric focusing (IEF) and FACS analyses. Sequencing of the HLA-A*24 allele from the promoter region to the eighth exonic region revealed a point mutation in the acceptor site of the second intron as compared to the normal HLA-A*24 allele. This mutation could lead to incorrect processing of mRNA through a cryptic acceptor site located at the beginning of the third exon and hence to alternative splicing with a frame shift introducing an early stop codon into the fourth exon.