Rapid HLA-DRB1 genotyping by nested PCR amplification

State of the art genotyping of HLA class II alleles with group-specific DNA amplification by the polymerase chain reaction (PCR) (1) and subsequent probing with sequence-specific oligonucleotides (2-4) is not suitable for typing cadaveric organ donors since the typing procedure takes far more than one working day. We designed specific oligonucleotide primer sets for nested PCR amplification which allowed typing for all serological HLA-DR specificities (DR1-DRw18) solely by the detection of amplified DNA in the reaction mixtures after agarose gel electrophoresis. Exon 2 of the DRB genes and a DRw52-group-specific part of DRB1 exon 2 was amplified directly from cell lysates without prior DNA extraction. The amplified DNA was subjected to a second round of amplification, which employed a set of 18 nested allele- or group-specific primer pairs. All alleles which have at least a single mismatched base at the terminal 3'-nucleotide of one primer were completely refractory to amplification. This assay is easy to perform and takes less than one working day to complete. Thus, this method may prove to be suitable for DNA typing of organ donors for prospective HLA-DR matching in renal transplantation.     

HLA-DRB101 subtyping by allele-specific PCR amplification: A sensitive, specific and rapid technique

The two DR1-associated cellular specificities Dw1 and Dw20, as well as DR'Br' (Dw'BON'), cannot be unequivocally assigned by serological typing or restriction fragment length polymorphism (RFLP) analysis. We have developed and compared two polymerase chain reaction-based (PCR) typing methods for distinguishing these DRB1 alleles; allele-specific amplification of DRB1*01 alleles followed by an agarose gel electrophoresis detection step and group-specific DRB1*01 amplification followed by hybridization with sequence-specific oligonucleotide probes. The two typing strategies gave completely concordant results in the 33 DRB1*01-positive and the 46 DRB1*01-negative individuals and cell lines studied. No false-negative or false-positive typing results were obtained. All possible heterozygous combinations of the DRB1*0101-0103 alleles could be distinguished by both typing methods. DRB1*01 subtyping by allele-specific PCR amplification was performed in less than 3 hours, including PCR amplification, detection and interpretation steps. The technique will be a valuable complement to DR typing by serology and RFLP analysis. Allele-specific DRB1 amplifications or group-specific amplifications followed by directed allele-specific amplifications of DRB1 alleles, typing based on the absence or presence of amplified products, may well prove to be the technical innovation that will firmly establish PCR-based DR typing in routine clinical tissue typing.     

Positive association of HLA-DRB1*15 with Dupuytren's disease in Caucasians

Dupuytren's disease (DD) is a permanent nodular condition affecting the palms and digits of the hands, leading to progressive shortening and contractures of the digits often resulting in diminished function and severe deformity. DD is thought to be one of the most common hereditary connective tissue disorders in Caucasians. To elucidate further the aetiology of DD, we compared the HLA-DRB1 phenotype frequencies of DD patients (n=67) against the HLA-DRB1 phenotype frequencies observed in a control population (n=537). HLA-DRB1*15 phenotype frequency was higher in DD positive Caucasoids (37.3%) when compared with control data (20.9%) (corrected P=0.029): we conclude that in Caucasoids of European origin, HLA-DRB1*15 is associated with risk of developing DD.     

A novel DRB1*13 allele (DRB1*1327) on a DR17, DQ2 haplotype with a DRB1*0301 sequence motif in the 2nd hyperpolymorphic region

In a sample from a Netherlands Caucasian, we found a new DRB1*13 allele ( DRB1*1327 ). The nucleotide sequence of the second exon of the novel allele was identical to DRB1*1301 except for a single productive base substitution changing codon 26 from TTC to TAC, encoding phenylalanine and tyrosine, respectively. The new allele shares sequence with DRB1*03011 from codons 5 to 66. The haplotype carrying the new allele was, from known linkage disequilibria, deduced to be DRB1*1327, DRB3*0101, DQA1*05011, DQB1*0201 , i.e. similar to the DR17, DQ2 haplotype, which suggests that the DRB1*1327 allele has arisen by a double recombination event between a DR13 donor haplotype and a DR17, DQ2 recipient haplotype.     

A rapid HLA-DRB1*04 subtyping method using PCR and DNA heteroduplex generators

We describe here a rapid polymerase chain reaction (PCR)-based method for the identification of HLA-DRB1*0401-*0412 alleles. The method is based on the generation of specific DNA heteroduplex patterns between PCR products derived from selective group-specific amplification of the various DRB1*04 alleles and PCR products derived from two synthetic DNA heteroduplex generator (DHG) molecules following non-denaturing polyacrylamide minigel electrophoresis. One DHG was designed to detect DRB1*0401, *0405, *0407, *0408, and *0409 alleles, whilst the other was designed to detect DRB1*0402, *0403, *0404, *0406, *0410, *0411, and *0412 alleles. Characteristic heteroduplex patterns were obtained for all DRB1*04 alleles tested both in homozygous and heterozygous situations. Both DHG and PCR-SSP (sequence-specific primer) typing were performed on 41 DRB1*04 positive DNAs from Singaporean Chinese blood donors and complete concordance in results was obtained. HLA-DRB1*0403, *0405, and *0406 were found to account for 95% of the DRB1*04 alleles in the population studied. The DHG technique described is technically simple and rapid since it essentially involves only two PCR amplifications per individual subtyping. The technique is particularly useful for resolving DRB1*04 combinations which are indistinguishable by PCR-SSO (sequence-specific oligonucleotide) or PCR-SSP subtyping.     

SSOP typing of the Tenth International Histocompatibility Workshop reference cell lines for HLA-C alleles

Abstract: HLA-C gene products are the most poorly understood of the HLA class I molecules because they express at low level on the cell surface compared to HLA-A and -B. However, recent evidence shows that HLA-C molecules are functionally competent in eliciting T-cell responses and in controlling NK-cell recognition. Approximately 20 to 50% of HLA-C alleles type "blank" in most populations. To provide a better definition of the HLA-C alleles, we analyzed 98 extensively characterized B-cell lines from the 10th International Histocompatibility Workshop. Selective HLA-C-specific DNA amplification of exons 2 and 3 from DNA prepared from the cell panel was achieved with the use of two sets of locus-specific primers. We used 64 sequence-specific oligonucleotide probes (SSOPs) complementary to variable sites in exons 2 and 3 to generate hybridization patterns. Twenty-five alleles were found among these patterns, including seven new alleles in the homozygous cell lines and seven potential new alleles in heterozygous cell lines. Differences between the new alleles and known alleles were generally small. Five major groups were identified in the Cw "blank" cells by the SSOP patterns. In addition, linkage between HLA-B specificities and HLA-C alleles was similar to previous observations. The present study demonstrated that SSOP typing was effective in identifying new alleles in homozygous typing cells but not in the heterozygous cells. Also, DNA typing can facilitate the identification of all HLA-C alleles, including those that serologically type as blanks. The HLA-C locus may be more polymorphic than was previously recognized.     

Diversity of HLA-DR2 in North Indians: the changed scenario after the discovery of DRB1*1506

Abstract: DRB1*1506, a new allele of DR2, differs from DRB1*1501 only at codon 50 in the second exon, where the nucleotide sequence has changed from GTG to GCG resulting in an amino acid substitution from valine to alanine in DRB1*1506. Since codon 50 was considered non-polymorphic until the discovery of this new allele by sequence-based typing, it became necessary to study what fraction of subjects thought to have DRB1*1501 actually had DRB1*1506. For this purpose, 116 DNA samples with DR2 coming from normal healthy individuals, leprosy patients and childhood tuberculosis patients were amplified using PCR and hybridized with ³²P-labeled probes specific for DRB1*1501, DRB1*1502, DRB1*1503, DRB1*1506, DRB1*1601 and DRB1*1602. The oligonucleotide probe for DRB1*1506 was designed to span codons 47–52 based on the published nucleotide sequence. DRB5, DQA1 and DQBl-specific amplifications and hybridizations were also carried out to study the diversity of DR2 haplotypes. It was found that 21 % of the samples identified previously as DRB1*1501 were actually DRB1*1506. DRB1*1506 was found to be associated with DQBl*0502 and DQB1*0601. Haplotypes of DRB1*1501, DRB1*1502, DRB1*1506 and DRB1*1602 showed a marked heterogeneity. Besides the rare haplotypes which have not yet been reported in any other populations, haplotypes characteristic of different ethnic groups, such as Croatians, South Chinese and Gypsies, were also found in the North Indians, suggesting the extent of racial admixture and migrations to and from India.     

Allele walking: a new and highly accurate approach to HLA-DRB1 typing: Application to DRB1*04 alleles

We have developed a typing method, which can be used even in small laboratories, to produce a highly accurate and reliable allele assignment in any homozygous or heterozygous situation. We have called the method allele walking (AW) and it consists of sequential rounds of PCR-RFLP. After digestion, electrophoresis separates alleles positive for the mutation from the negative alleles; the cleaved fragment is then recovered from the gel and analyzed for mutations at another codon. In this way, AW is able to positively ascertain which mutations are in the same chromosome (cis-linkage) and assigns alleles independently from each other. Artificial sites are created in the PCR step in order to positively detect substitutions not naturally recognized by any of the existing or convenient enzymes. We report the application of AW for typing the 22 DRB1*04 alleles. The first PCR-RFLP round groups DRB1*04 alleles. Subsequently, the mutations at codons 86, 74, 71, 57 and 37 can be analyzed for the unambiguous assignment of the majority of the alleles. Additional polymorphisms at different codons can be assayed to resolve any undetermined alleles. The viability of all the restriction sites used as well as the feasibility of AW were successfully tested.     

HLA-DRB1*01 and DRB1*04 alleles in Sardinian rheumatoid arthritis patients

In Sardinia, like in other Caucasoid populations, rheumatoid arthritis (RA) is significantly associated with HLA-DR4 and DR1 antigens. To discover which DR4 and DR1 alleles were associated with the disease we selected 22 Sardinian patients affected by RA. Fifty DR4+ and 28 DR1+ healthy individuals coming from the same geographical area were used as controls. In the Sardinian patients only two DRB1*04 alleles were observed: DRB1*0405 in 11 and DRB1*0403 in three patients. The DRB1*0102 allele was observed in two patients and DRB1*0101 in six patients. Hereditary predisposition to RA in Sardinia therefore seems to be almost exclusively associated with the DRB1*0405 and DRB1*0101 alleles which share the 67LLEQRRAA74-85VG86 epitope in the peptide binding groove.     

昆明白族和彝族人群HLA-DRB1/DQB1等位基因遗传特点及频率分布比较

目的研究昆明白族和彝族儿童HLA-DRB1／DQB1等位基因多态性,分析比较昆明白族和彝族人群的遗传特点。方法采用PCR-SSP基因分型技术,分别对70名白族儿童和70名彝族儿童进行HLA-DRB1／DQB1基因分型。结果昆明白族儿童在HLA-DRB1位点上共检出13种等位基因,依次为DRB1*08(20．7％)、*04(16．4％)、*12(16．4％)、*15(8．57％)、*0901(8．57％)、*14 (6．43％)、*11(5．71％)、*16(5．00％)、*13(4．29％)、*07(2．86％)、*03(2．86％)、*01 (1．43％)、*10(0．71％);HLA-DQB1位点上共检出7种等位基因,依次为DQB1*0301(23．6％)、*06(21．4％)、*05(18．6％)、*04(18．6％)、*0303(7．14％)、*0302(6．43％)、*0201(4．29％)。彝族儿童在HLA-DRB1位点上共检出12种等位基因,依次为DRB1*12(33．57％)、*0901 (11．43％)、*04(11．43％)、*01(8．57％)、*11(7．86％)、*14(7．14％)、*15(7．14％)、*08 (5．00％)、*03(2．83％)、*13(2．14％)、*07(1．43％)、*16(1．43％);HIA-DQB1位点上共检出7种等位基因,依次为DQB1*0301(45％)、*05(22．14％)、*0303(12．14％)、*04(6．43％)、*06 (6．43％)、*0201(4．29％)、*0302(3．57％)。组间比较HLA-DRB1／DQB1等位基因总体分布及诸多等位基因频率均有显著差异。结论昆明白族和彝族人群HLA-DRB1／DQB1等位基因分布具有各自遗传特点。     

Identification of a novel HLA-DRB1*12 allele, DRB1*1218, in Chinese population

Here, we report the identification of a novel human leukocyte antigen-DRB1*12 variant, DRB1*1218 allele, in a Chinese Han individual. The novel DRB1*12 variant allele differed from the closest allele DRB1*120201 by nucleotide 262 G>C (codon 59 GAG>CAG) missense mutation in exon 2, which resulted in an amino acid substitution of Glu>Gln.     

Limited diversity of HLA-DRB1*02 alleles and DRB1-DRB5 haplotype associations in four United States population groups

At least 60 DRB1*02 positive individuals from each of four US population groups found within a hematopoietic stem cell volunteer donor registry - Caucasoids, African Americans, Asians/Pacific Islanders, and Hispanics - were randomly selected from a database of 82,979 individuals. DRB1*02 alleles were identified by DNA sequencing. A total of five of 23 known DRB1*02 alleles were detected. DRB1*15011 was the predominant DRB1*02 allele in Caucasoids and Hispanics. The most common DRB1*02 allele observed in African Americans was DRB1*1503, and DRB1*15021 in Asians/Pacific Islanders. Caucasoids were found to be the least diversified; only DRB1*15011 and DRB1*16011 were observed. A subset of individuals was also typed for DRB5 alleles by DNA sequencing. DRB5*01011, DRB5*0102, DRB5*0103, DRB5*0108N and DRB5*0202 were detected and nine DRB1-DRB5 haplotypes defined.