Three new DP alleles identified in sub-Saharan Africa: DPB1*74O1, DPAl*02013, and DPAl*0302

Abstract: HLA-DP genotyping of over 400 individuals from sub-Saharan Africa identified three new DP alleles: DPB1*7401, DPAl*02013, and DPAl*0302. DNA sequencing confirmed that DPB1*7401, found in one individual, is a novel combination of previously described sequence motifs in the six variable regions of DPB1. DPA1*02013, found in one individual, is identical to DPAl*02012 except for two silent substitutions, a T to C transition in codon 37, and an A to G transition in codon 38. DPAl*0302, identified in seven individuals, is identical to DPAl*0301 except for a C to T transition at the second position of codon 66. The identification of these novel alleles brings the total number of reported DPB1 alleles to 77 and DPA1 alleles to 11.     

HLA-DPA1*/DPB1* en asociación con leucemias linfoides agudas y leucemias mieloides crónicas en mestizos venezolanos

More is now known of the involvement of HLA-DP region in the pathogenesis of the leukemias through several previousstudies showing interference of these molecules in modulating the immune response to pathogens. For evaluation of HLA alleles and haplotypes DPA1*/DPB1* (28 alleles HLA DPA1* and 123 of HLA- DPB1*) Olerup SSP ™PCR (Genovision) was used in 48 patients with ALL, 48 CML, and 48 Venezuelan twins as controls. For HLA/leukemias, a relative risk (RR) > 3 was considered to be a positive association and negative with an RR < 3, with a p corrected P<.05. ALL patients confirmed positive associations with DPA1*0105 allele, and negative with DPA1*010301-010302. In addition, they were positively associated with DPA1*0106 and *0107, with DPA1*020101-020106 being negatively associated with ALL. DPA1*0105, *0108 and *0109 were negatively associated with CML. The observed frequencies of HLA-DPB1* 01:01, 02:01, 03:01, 04:01 and 4:02 alleles in Venezuelan, which twins were between 7 and 16%, were higher than those of leukemic patients. Negative associations of DPB1*2:01, *3:01 and LLA were confined. No positive associations were observed with ALL. Non-confirmed positive associations were observed between DPB1*99:01 and CML. Haplotypes HLA-DPA1*01:03-DPB1*4:01, *2:01, *99:01 were strongly positively associated with CML. DPA1*1:09-DPB1*2:01, *4:01 were negatively associated with the CML. DPA1*1:03-DPB1*4:02; DPA1*01:09-DPB1*2:01, *4:01 and DPA1*02:01-DPB1*04:02 were negatively associated with ALL. The DPB1* single region does not appear to be associated with leukemia in the Venezuelan population. The strong association with several haplotypes DPA*1/DPB1* and LMC suggests massive differences between the pathogenesis of both diseases.     

DPB1*8501, a novel DPB1 variant in the US Black population

We describe a new DPB1 allele, DPB1*8501, which was identified by sequencing-based typing (SBT) in the UCLA exchange. DPB1*8501 is similar to DPB1*2701 with a difference at position 272, (G to A). This difference leads to an amino-acid change of codon 91 from arginine (CGC) to histidine (CAC). Until now this position has been considered conserved. This substitution is located at the 3' site of exon 2, and may interfere with typing strategies using primers or probes located in this region.     

DPB1*8601, a previously unrecognized DPB1 variant in the Caucasoid population

A new, previously unrecognized DPB1* allele, DPB1*8601, was found in a Swedish family. The new allele was carried on the common North European haplotype HLA A1-B8-DR3. Both individuals carrying the new allele were initially typed as clear DPB1*4601,*6601 but after family studies and further typing with allele-specific primers it was concluded that a new allele was present together with the common DPB1*0401. The new allele was investigated by direct sequencing of exon 2 in both forward and reverse directions employing intron primers combined with either an allele-specific sense or anti-sense biotinylated primer for bi-directional sequencing. The new allele is identical to DPB1*1701 in the five first variable regions. In the sixth region, however, DPB1*8601 carries the GGPM motif shared by several common alleles such as DPB1*0201 and 0401and 0402.     

浙江汉族人群HLA-DPA1和-DPB1基因多态性分析

目的 检测浙江地区汉族人群HLA-DPA1和HLA-DPB1等位基因及单倍型频率.方法 应用PCR-直接测序分型法对100名健康、无血缘关系的浙江汉族人外周血标本进行HLA-DPA1和HLADPB1等位基因分析.结果 在100份标本中检出8个HLA-DPA1等位基因和19个HLA-DPB1等位基因.HLA-DPA1等位基因频率较高的依次为DPA1*020202(47.0%)、DPA1*010301(38.5%)和DPA1*020101(10.5%).HLA-DPB1等位基因中,频率较高的依次为DPB1*0501(39.5%)、DPB1*020102(13.5%)和DPB1*040101(13.0%).连锁分析发现共有44个HLA-DPA1-DPB1单倍型,单倍型频率最高为DPA1*020202-DPB1*0501(29.5%).结论 浙江地区汉族人群HLA-DPA1和DPB1基因座等位基因具有丰富的多态性,2个基因座呈现连锁不平衡.     

A new HLA-DPA1 allele, DPA1*02016, identified in African-American population

A new HLA-DPA1 allele has been found in the African-American population. This newly discovered type is homologous with the DPA1*02011 allele, except in codon 38 of the DPA1 sequence. The variant of DPA1 was detected by sequence-specific oligonucleotide (SSO) typing, and specified by cloning and sequencing methods. GenBank accession number is AF165160. The WHO Nomenclature Committee has officially assigned the name DPA1*02016.     

HLA-DPA1 and DPB1 polymorphism in four Pacific Islands populations determined by sequencing based typing

Class II HLA-DP antigens are heterodimers comprised of alpha and beta chains coded by HLA-DPA1 and HLA-DPB1 genes. Both genes are polymorphic with substantial variation between different populations world wide. This work describes DPA1 and DPB1 polymorphism in four Pacific Island populations of Cook Islands, Samoa, Tokelau and Tonga, living in New Zealand. Using sequencing based typing four DPA1 alleles and twelve DPB1 alleles were observed in total among the four populations. There are two predominant DPA1 alleles DPA1*01031 and DPA1*02022 and three predominant DPB1 alleles DPB1*02012, DPB1*0401 and DPB1*0501. Fourteen DPA1-DPB1 haplotypes in total are present in these four populations with three predominant haplotypes: DPA1*02022-DPB1*0501, DPA1*01031-DPB1*02012, and DPA1*01031-DPB1*0401. Strong positive and negative disequilibrium was observed for individual DPA1-DPB1 haplotypes. Significant differences in DPA1 and DPB1 allele and haplotype frequencies were observed between Tokelauan and other three populations. Phylogenetic analysis of genetic distances between the four Pacific Island populations and other Asian Oceanian populations have shown that Cook Islanders, Samoans and Tongans are more closely related to Asian populations whereas Tokelauans cluster towards non-Austronesian populations of Papua New Guinea Highlanders and Australian Aborigines.     

浙江汉族人群HLA-DPA1和-DPB1基因多态性分析

目的 检测浙江地区汉族人群HLA-DPA1和HLA-DPB1等位基因及单倍型频率.方法 应用PCR-直接测序分型法对100名健康、无血缘关系的浙江汉族人外周血标本进行HLA-DPA1和HLADPB1等位基因分析.结果 在100份标本中检出8个HLA-DPA1等位基因和19个HLA-DPB1等位基因.HLA-DPA1等位基因频率较高的依次为DPA1*020202(47.0%)、DPA1*010301(38.5%)和DPA1*020101(10.5%).HLA-DPB1等位基因中,频率较高的依次为DPB1*0501(39.5%)、DPB1*020102(13.5%)和DPB1*040101(13.0%).连锁分析发现共有44个HLA-DPA1-DPB1单倍型,单倍型频率最高为DPA1*020202-DPB1*0501(29.5%).结论 浙江地区汉族人群HLA-DPA1和DPB1基因座等位基因具有丰富的多态性,2个基因座呈现连锁不平衡.     

Four new DP alleles identified in a study of 500 unrelated bone marrow donor-recipient pairs

HLA-DP genotyping of 500 donor recipient pairs in a retrospective analysis sponsored by the National Marrow Donor Program (NMDP) identified four new DP alleles, two DPB1 and two DPA1. DNA sequencing confirmed that DPB1*8001 and *8101, each found in a single individual, are novel combinations of previously described sequence motifs in the six variable regions of DPB1. DPA1*02014, found in two individuals, is identical to DPA1*02011 except for a novel silent substitution, a G to A transition at the third position of codon 14. DPA1*01032, found in one individual, is identical to DPB1*01031 except for a silent G to A transition at the third position of codon 20. The identification of these novel alleles brings the total number of reported DPB1 alleles to 85 and DPA1 alleles to 15.     

浙江汉族人群HLA-DPA1和-DPB1基因多态性分析

目的 检测浙江地区汉族人群HLA-DPA1和HLA-DPB1等位基因及单倍型频率.方法 应用PCR-直接测序分型法对100名健康、无血缘关系的浙江汉族人外周血标本进行HLA-DPA1和HLADPB1等位基因分析.结果 在100份标本中检出8个HLA-DPA1等位基因和19个HLA-DPB1等位基因.HLA-DPA1等位基因频率较高的依次为DPA1*020202(47.0%)、DPA1*010301(38.5%)和DPA1*020101(10.5%).HLA-DPB1等位基因中,频率较高的依次为DPB1*0501(39.5%)、DPB1*020102(13.5%)和DPB1*040101(13.0%).连锁分析发现共有44个HLA-DPA1-DPB1单倍型,单倍型频率最高为DPA1*020202-DPB1*0501(29.5%).结论 浙江地区汉族人群HLA-DPA1和DPB1基因座等位基因具有丰富的多态性,2个基因座呈现连锁不平衡.     

Gene polymorphism of HLA-DPB1 and DPA1 loci in caucasoid population: Frequencies and DPB1-DPA1 associations

The genetic polymorphism of the HLA-DPB1 and DPA1 loci was studied in 60 unrelated caucasoid individuals by PCR-RFLP. The polymorphic second exon of DPB1, the third exon of DPA1, and the trans-membrane DPA1 exon were specifically amplified in vitro by polymerase chain reaction (PCR). Amplified DNAs were digested with selected enzymes. Twenty patterns were obtained with DPB1 defining 20 DPB1 alleles. Thirty-nine homozygous cell lines were used as HLA-DP reference cells. The results obtained with these cell lines were compared to those obtained by PLT, RFLP, and SSO. Although three subdivisions of the allele DPA1^*01 were reported, DPA1^*0103 was the only represented one in the caucasoid population. In the studied population, it was the most frequent DPA1 allele (76.6%), whereas DPA1^*0201 frequency is 23.3%. DPB1^*0401 and DPB1^*0402 are the most frequent among the DPB1 alleles (40.0% and 13.3%, respectively). This may lead to a lower HLA-DPB1 diversity among caucasoids. Certain HLA-DPB1 alleles associate exclusively with one DPA1 allele (DPB1^*0401, 0402, and 0301 with DPA1^*01 and DPB1^*0101, 0501, and 1701 with DPA1^*0201) whereas the others can associate with both DPA1 alleles. This by itself can create another kind of polymorphism, indicating the importance of HLA-DPA1 typing. Thus, PCR-RFLP seems to be one of the best DNA typing methods: it represents direct, accurate, fast, and nonradioactive typing for both HLA-DPA1 and HLA-DPB1 alleles.     

Identification of a novel HLA-DPB1 allele, DPB1*02014, by sequence-based typing

In this report we describe the identification of a novel DPB1 allele, DPB1*02014, found in an Italian Caucasian individual.The new allele was detected during routine HLA sequence-based typing (SBT) for an individual undergoing bone marrow transplantation. DPB1*02014 was identical to DPB1*02012 except for a single nucleotide substitution in codon 72 (GTG-->GTT). This nucleotide change represents a synonimous mutation, as both triplets code for a valine.This new allele has been submitted to GenBank and assigned the accession number AF326565. The WHO Nomenclature Committee has officially assigned the name DPB1*02014.     

HLA class II DRB1, DQB1, DPB1 polymorphism and cardiomyopathy due to Trypanosoma cruzi chronic infection

Trypanosomiasis is an important cause of cardiomyopathy in endemic rural areas of Latin America. Previous studies have suggested participation of HLA molecules in the immune response regulation of T. cruzi infection, and association of HLA antigens with heart damage.One hundred and eleven unrelated T. cruzi antigen-seropositive individuals were tested for HLA class II alleles by the polymerase chain reaction and sequence specific oligonucleotide (PCR-SSO) method. Patients were classified in 3 groups according to clinical and electrocardiographic characteristics: asymptomatics (group A), with arrhythmia (group B), and with overt congestive heart failure (group C). Statistical analysis confirmed the significant increment of the DRB1*01 DQB1*0501 haplotype (p = 0.03) previously reported by our laboratory in patients with cardiomyopathy. The DPB1*0401 allele frequency is also significantly increased in patients with heart disease (groups B + C) (p = 0.009) while DPB1*0101 frequency is higher among the asymptomatic group (p = 0.04) compared with individuals of group C. The DPB1*0401 allele in homozygous form or in combination with allele DPB1*2301 or 3901, was found present more often in patients of groups B and C. Thus, the combination of two of these three alleles, sharing specific sequence motifs in positions 8, 9, 76, and 84-87 confers a relative risk of 6.55 to develop cardiomyopathy in seropositive patients (p = 0.041). Furthermore, 32% of the cardiomyopathics have either DRB1*01 DQB1*0501 and/or DPB1*0401/*0401, 0401/*2301, or* 0401/*3901 compared with 9% of the seropositive asymptomatics (OR = 5.0; p = 0.006).     

High resolution sequence-based DPB1 typing identified two novel DPB1 alleles,DPB1*9401 and DPB1*9501, from a Kenyan population

Two novel DPB1 alleles, DPB1*9401 and DPB1*9501, were identified from a Kenyan population during sequence-based HLA-DPB1 typing. Molecular cloning and sequencing of multiple clones confirmed that one of the new DPB1 alleles is identical to DPB1*0402 at exon 2 except for a single nucleotide substitution (CGG -->TGG), changing codon 70 from Arg to Trp. The new allele has been named DPB1*9401. This is the first report of polymorphism at codon 70 of HLA-DPB1 alleles. New codon combinations have been identified in another novel DPB1 allele named DPB1*9501. The extensive diversity at DPB1 locus of this East African population is being revealed by high resolution sequence-based DPB1 typing.     

Nucleotide sequence of the corrected DQB1*06011 allele

The DQB1*06011 allele first classified and registered with the codon ACC at position 51(1) was recently corrected to ACG by Dr. Akinori Kimura (2) and in independently confirmed in our laboratory (3). The correct nucleotide sequence for this allele is shown below. The DQB1*06011 allele was found in two sisters of Turkish nationality who had been serologically typed for class I as HLA-A11, A33, B44, B52, Cw4. Nucleotide sequencing based typing of HLA class II alleles disclosed DRB1*0701, *15021, DRB4*01011/*0103, DRB5*0102, DQA1*0103, *0201, DQB1*02, *06011, DPB1*0401,*11011.     

High-resolution sequence-based DPA1 typing identified two novel DPA1 alleles, DPA1*010303 and DPA1*0303, from a Kenyan population

We report here two novel DPA1 alleles, DPA1*010303 and DPA1*0303, identified from a Kenyan population during sequence-based HLA-DPA1 typing. Molecular cloning and sequencing of multiple clones confirmed that one of the new DPA1 alleles is identical to DPA1*010301 at exon 2, except for a single nucleotide substitution (ACG ACC) at codon 15. The new allele has been named by the WHO Nomenclature Committee as DPA1*010303. The second novel DPA1 allele is identical to DPA1*0301, except for a single nucleotide difference (GAA GAC) at codon 28 that changed the amino acid from Glu to Asp. The new allele has been named by the WHO Nomenclature Committee as DPA1*0303. Identification of the two novel DPA1 alleles reflects the genetic diversity of this East African population.     

HLA-DP polymorphism in Sudanese controls and patients with insulin-dependent diabetes mellitus

Human leukocyte antigen (HLA) genes are candidates for susceptibility to insulin-dependent diabetes mellitus (IDDM). The association of IDDM with particular DR and DQ alleles has been reported in all populations studied, but its association with HLA-DP alleles has been controversial. To address this question we analyzed 19 DPB1 and 2 DPA1 alleles and their associations in well-characterized Sudanese (an admixture of Arab and Black) IDDM patients (n = 71) and ethnically matched controls (n = 86) using polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) typing. There were no significant differences between the patient and control groups in the DPB1 frequencies. DPB1*0201, *0401 and DPA1*01 were the most frequent alleles in both IDDM patients and control subjects. Significant positive and negative associations between DPB1 and DPA1 alleles were detected in both groups. A novel DPB1 allele included in DPB1*1701 was identified.     

Linkage disequilibrium between DPA1 and DPB1 alleles among Norwegian caucasoids and Japanese

Associations between alleles at the DPA1 and DPB1 loci were analyzed in 181 Norwegian caucasoids. Associations were observed between the DPA1*0201 and the DPB1*0101, *0901, *1001 and *1101 alleles. An association between DPA1*0201 and the DPB1*0901 allele was also observed among 23 healthy Japanese and 24 Japanese MS patients. In addition, it appeared that among Japanese the DPA1*0201 allele may be associated to the DPB1*0501. In conclusion, alleles at the DPA1 and DPB1 loci display different associations among Norwegian caucasoids and Japanese.     

Three new DP alleles identified in a study of 800 unrelated bone marrow donor-recipient pairs

HLA-DP genotyping of 800 unrelated donor-recipient pairs in phase 5 of a retrospective analysis of unrelated bone marrow transplantation, sponsored by the National Marrow Donor Program (NMDP), has identified two new DPB1 alleles (DPB1*8701 and DBP1*8801) and one new DPA1 (DPA1*0108) allele. Sequencing confirmed that all three of these new alleles represent novel combinations of previously described sequence motifs, reinforcing the notion that "gene conversion-like" events play an important role in generating HLA allelic diversity. The identification of these new alleles brings the total number of DPA1 alleles to 20 and the total number of DPB1 alleles to 94.     

High-resolution HLA typing for the DQB1 gene by sequence-based typing

Abstract: The ideal high-resolution typing strategy for polymorphic genes is sequence-based typing. SBT of genomic DNA has been developed for the HLA class H genes DRB1, DRB3/4/5 and DPB1. For the DQB1 gene the sequence-based typing method was shown to cause a number of problems. To resolve those problems, different primers to amplify and sequence exon 2 of DQB1 were designed and tested. With several primer combinations, preferential amplification was observed in individuals heterozygous for DQB1*02/*03 and DQB1*02/*04. The preference was for DQB1*02 in many instances but could also be demonstrated for DQB1*03 or *04 and resulted occasionally in allelic drop-out. The best primer combination was selected and successfully used to type individuals heterozygous for DQB1*02, *03 and*04. To distinguish DQB1*0201 and *0202, primers for amplification and sequencing of exon 3 were developed and correct subtyping was obtained. The ambiguous typing DQB1*0301/*0302 and DQB1*0303/*0304 was resolved by allele-specifk amplification and sequencing. A total of 258 individuals were fully typed for their DQB1 subtypes. All samples had been previously typed by PCR-SSP and serology. Concordant typing results were obtained for all individuals tested. The DQB1 alleles detected included *0501, *0502, *0503, *0601, *0602, *0603, *0604, *0609, *0201, *0202, *0301, *0302, *0303, *0304, *0401 and *0402. Sequence-based typing of the DQB1 gene proved a reliable typing strategy for assignment of the different DQB1 alleles after intensive selection of primers and test conditions.