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Park BL, Kim TH, Kim JH, Bae JS, Pasaje CFA, Cheong HS, Kim LH, Park JS, Lee HS, Kim MS, Choi IS, Choi BW, Kim MK, Shin S, Shin HD, Park CS. Genome-wide association study of aspirin-exacerbated respiratory disease in a Korean population. Hum Genet 2012. [PMID: 23180272 DOI: 10.1007/s00439-012-1247-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aspirin-exacerbated respiratory disease (AERD) is a nonallergic clinical syndrome characterized by a severe decline in forced expiratory volume in one second (FEV1) following the ingestion of non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin. The effects of genetic variants have not fully explained all of the observed individual differences to an aspirin challenge despite previous attempts to identify AERD-related genes. In the present study, we performed genome-wide association study (GWAS) and targeted association study in Korean asthmatics to identify new genetic factors associated with AERD. A total of 685 asthmatic patients without AERD and 117 subjects with AERD were used for the GWAS of the first stage, and 996 asthmatics without AERD and 142 subjects with AERD were used for a follow-up study. A total of 702 SNPs were genotyped using the GoldenGate assay with the VeraCode microbead. GWAS revealed the top-ranked variants in 3' regions of the HLA-DPB1 gene. To investigate the detailed genetic effects of an associated region with the risk of AERD, a follow-up targeted association study with the 702 single nucleotide polymorphisms (SNPs) of 14 genes was performed on 802 Korean subjects. In a case-control analysis, HLA-DPB1 rs1042151 (Met105Val) shows the most significant association with the susceptibility of AERD (p = 5.11 × 10(-7); OR = 2.40). Moreover, rs1042151 also shows a gene dose for the percent decline of FEV1 after an aspirin challenge (p = 2.82 × 10(-7)). Our findings show that the HLA-DPB1 gene polymorphism may be the most susceptible genetic factor for the risk of AERD in Korean asthmatics and confirm the importance of HLA-DPB1 in the genetic etiology of AERD.
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Affiliation(s)
- Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc, Seoul, Republic of Korea
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DEKKER JW, NIZANKOWSKA E, SCHMITZ-SCHUMANN M, PILE K, BOCHENEK G, DYCZEK A, COOKSON WOCM, SZEZEKLIK A. Aspirin-induced asthma and HLA-DRB1 and HLA-DPB1 genotypes. Clin Exp Allergy 2006. [DOI: 10.1111/j.1365-2222.1997.tb00747.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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FAUX JA, MOFFATT MF, LALVANI A, DEKKER J, WARRELL DA, COOKSON WOC. Sensitivity to bee and wasp venoms: association with specific IgE responses to the bee and wasp venom and HLA DRB1 and DPB1. Clin Exp Allergy 2006. [DOI: 10.1111/j.1365-2222.1997.tb00748.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Tréjaut J, Kennedy A, Hobart D, Le T, Greville WD, Ng G, Taverniti A, Dunckley H. PCR-RFLP typing detects new HLA-DRB1 alleles: DRB1*13022, DRB1*1336 and DRB1*1435. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 2001; 28:441-7. [PMID: 11532019 DOI: 10.1046/j.1365-2370.2001.00243.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It is difficult to resolve all heterozygous combinations of the HLA-DRB1*03, *08, *11, *12, *13 and *14 allele group in a one-step generic HLA-DRB1 typing system. Therefore, it is common to employ a secondary technique utilizing group-specific primers to amplify this group of alleles separately from the other HLA-DRB1, -DRB3, -DRB4 and -DRB5 alleles. This paper describes a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for broad typing of the HLA-DRB1*03, *08, *11, *12, *13 and *14 alleles which, as well as being time-efficient and cost-effective, has so far allowed the detection of 10 new alleles. The new alleles were identified after following up unusual or novel PCR-RFLP patterns. Of the 10 novel alleles found so far with this method, seven have been described previously while three, DRB1*13022, DRB1*1336 and DRB1*1435, are presented here.
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Affiliation(s)
- J Tréjaut
- Tissue Typing Department, Australian Red Cross Blood Service, NSW Division, Sydney
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5
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Weissensteiner T, Lanchbury JS. An integrated multiplex-PCR and PCR-RFLP typing system for markers associated with seronegative arthritides. Hum Immunol 1998; 59:119-32. [PMID: 9536435 DOI: 10.1016/s0198-8859(97)00260-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The system was designed with emphasis on the identification HLA-B alleles and genotypes associated or potentially associated with seronegative arthritides. By using a combination of multiplex SSP and PCR-RFLPs, the assays can be economically performed on a large range of sample sizes in diagnosis and epidemiology. 24 HLA-B alleles and subtypes can be discriminated, including options for PCR-RFLP or sequence specific amplification of the allele groups B27 and B60 (B*4001 and B*4007). In addition, the internal control carries central MHC polymorphisms, which can help to identify HLA extended halplotypes. False negatives, caused by preferential amplification of the internal control under suboptimal PCR conditions, were prevented by employing new, optimized PCR buffer. Four of the HLA-B primers were pooled into a multiplex reaction whose products were subtyped by digestion with seven restriction endonucleases. Specificity and sensitivity were verified in a panel of 68 homozygous cell lines and 200 heterozygous samples. An HLA-B*27-B*40 hybrid allele was observed in 3 out of 95 B*27-positive individuals from Berlin, Germany. Such an allele could be mistyped by some published assays as a B*27/B*40 heterozygote, a genotype reported to confer an increased risk for ankylosing spondylitis.
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6
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Saito S, Ota S, Hashizume K, Yamada E, Kaneshige T, Kinoshita T, Hashimoto M, Oguchi H, Ishii E, Fukushima H. A new HLA-DQB1*0306 allele sharing motifs from DQB1*03032 and DQB1*04 sequences. TISSUE ANTIGENS 1996; 48:580-5. [PMID: 8988541 DOI: 10.1111/j.1399-0039.1996.tb02672.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have discovered a new HLA-DQB1 allele in a Japanese family, MAT. In the family the new allele segregates in three generations and demonstrates the positive association with DRB1*0901. We observed a novel RFLP pattern in the course of examining the modified PCR-RFLP method for HLA-DQB1 genotyping. The PCR-SSOP analysis also showed a new hybridized pattern. Sequence analysis of the allele indicates that it was generated by a gene conversion-like event between the HLADQB1*03032 and one of DQB1*04 contemporary alleles. This new allelic product did not react with all of allosera and monoclonal antibodies against DQ1, DQ2, DQ3, DQ4 and DQ7. The HLA molecule encoded by the allele is not defined by serology. This new allele was officially recognized and named DQB1*0306 by the WHO Nomenclature Committee in November 1995.
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Affiliation(s)
- S Saito
- Nagano Red Cross Blood Center, Japan.
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7
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Djilali-Saiah I, Benini V, Daniel S, Assan R, Bach JF, Caillat-Zucman S. Linkage disequilibrium between HLA class II (DR, DQ, DP) and antigen processing (LMP, TAP, DM) genes of the major histocompatibility complex. TISSUE ANTIGENS 1996; 48:87-92. [PMID: 8883297 DOI: 10.1111/j.1399-0039.1996.tb02612.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
TAP, LMP and DM genes map within the major histocompatibility complex (MHC) class II region between the DQB1 and DPB1 loci, and are involved in the processing of peptides bound to HLA class I or class II molecules. In order to determine the various linkage disequilibria existing between these genes and HLA class II genes, we have analyzed TAP1, TAP2, LMP2, DMA, DMB, DRB1, DQA1, DQB1 and DPB1 polymorphisms in 162 unrelated healthy Caucasian individuals. Many positive or negative associations were observed between alleles at these loci, such as between DR/DQ and TAP2, DM or LMP, between DP and DMB, and between TAP2 and DM, TAP2 and LMP. Conversely, no linkage disequilibrium was detected between some closely related genes (DR/DQ and TAP1, TAP1 and TAP2, LMP2 and DM), in agreement with the existence of recombination hot spots in this region. Other weak linkage disequilibria are likely to exist in this region. These data allow to define some conserved MHC class II haplotypes including HLA class II and TAP, LMP and DM alleles. Furthermore, the knowledge of such linkage disequilibria is of outstanding importance in order to avoid misinterpretation of the data when studying MHC class II associations with autoimmune diseases.
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8
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Naughton MJ, Limm TM, Ashdown ML, Simons MJ. DPB1 locus PCR-RFLP typing of the fourth Asia-Oceania Histocompatibility Workshop cell panel reveals a novel DPB1 allele. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 1994; 21:351-64. [PMID: 9098444 DOI: 10.1111/j.1744-313x.1994.tb00205.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
DPB1 locus typing of the 155 cell 4AOHW panel was performed using a PCR-RFLP method. Ambiguity of allele assignment was resolved by amplification using sequence-specific primers. Of the 150 cells for which typings were achieved, three exhibited unusual restriction enzyme fragment patterns, suggesting the possibility of novel DPB1 alleles. Sequence analysis revealed one allele present in the currently reported 46, one novel allele (4AOHW/107) not present among the 46, and one from a non-human primate which is being investigated. Twenty-six (26) of the 34 10IHW cells have been studied previously by cDNA RFLP, and strong haplotypic associations have been demonstrated between DPA1 and DPB1 locus alleles. It is proposed that exploitation of intron polymorphisms making haplotypes will be an integral part of future DPB1 typing as a "first-pass' stratification process to minimize the requirement for sequence-based methods to definitively assign DPB1 alleles.
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9
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Young RP, Dekker JW, Wordsworth BP, Schou C, Pile KD, Matthiesen F, Rosenberg WM, Bell JI, Hopkin JM, Cookson WO. HLA-DR and HLA-DP genotypes and immunoglobulin E responses to common major allergens. Clin Exp Allergy 1994; 24:431-9. [PMID: 8087654 DOI: 10.1111/j.1365-2222.1994.tb00931.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In order to test for human histocompatibility leucocyte antigens (HLA) class II restriction of IgE responses, 431 subjects from 83 families were genotyped at the HLA-DR and HLA-DP loci and serotyped for IgE responses to six major allergens from common aero-allergen sources. A possible excess of HLA-DR1 was found in subjects who were responsive to Fel d I compared with those who were not (Odds Ratio (OR) = 2, P = 0.002), and a possible excess of HLA-DR4 was found in subjects responsive to Alt a I (OR = 1.9, P = 0.006). Increased sharing of HLA-DR/DP haplotypes was seen in sibling pairs responding to both allergens. Der p I, Der p II, Phl p V and Can f I were not associated with any definite excess of HLA-DR alleles. No significant correlations were seen with HLA-DP genotype and reactivity to any of the allergens. The results suggest class II HLA restriction is insufficient to account for individual differences in reactivity to common allergens.
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Affiliation(s)
- R P Young
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, UK
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10
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Koshizaka T, Taguchi M, Onishi H, Kobayashi S, Inoko H. A new HLA-DPB1 allele, DPB1*SUT (DPB1*4701). TISSUE ANTIGENS 1994; 43:50-3. [PMID: 7912859 DOI: 10.1111/j.1399-0039.1994.tb02297.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- T Koshizaka
- Department of Medical Business, Sumitomo Metal Industries Ltd., Kanagawa, Japan
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11
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Versluis LF, Rozemuller E, Tonks S, Marsh SG, Bouwens AG, Bodmer JG, Tilanus MG. High-resolution HLA-DPB typing based upon computerized analysis of data obtained by fluorescent sequencing of the amplified polymorphic exon 2. Hum Immunol 1993; 38:277-83. [PMID: 8138423 DOI: 10.1016/0198-8859(93)90555-f] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
To differentiate 32 HLA-DPB alleles, conventional techniques such as serology and cellular typing are inadequate for high-resolution DPB typing. The most refined DNA typing until now is SSO typing and new selected oligonucleotides can be added to this system to distinguish new allele sequences. DNA sequencing, however, reveals directly the sequence information of all polymorphic HVRs and has the advantage of being independent from exon polymorphisms. We have developed a new DNA-based typing approach that is rapid, fully automated, and therefore suitable for routine typing. The system is based upon direct sequencing of amplified DNA with fluorescent-labeled primers. The designation of alleles is obtained by a comparison of all polymorphic positions in the determined sequence with all known allele sequences retained in a database along with their heterozygous combinations. Sequence data at both constant and polymorphic positions are used for quality control. In this study, the typing results of a panel of 91 previous SSO-typed DNA samples are described. After comparison with the SSO-typing results, we conclude that with this SBT system allele assignment is reliable. The method is easy to perform since both sequencing and assignment are automated. Furthermore, the system is easily applicable to other gene systems.
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Affiliation(s)
- L F Versluis
- Diagnostic DNA Laboratory, Utrecht Academic Hospital, The Netherlands
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12
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Limm TM, Ashdown ML, Naughton MJ, McGinnis MD, Simons MJ. HLA-DQA1 allele and suballele typing using noncoding sequence polymorphisms. Application to 4AOHW cell panel typing. Hum Immunol 1993; 38:57-68. [PMID: 7905870 DOI: 10.1016/0198-8859(93)90520-b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
HLA-DQA1 typing of the 4AOHW cell panel is presented using a novel strategy that exploits both intron and exon polymorphisms. Intron sequences adjacent to the variable HLA-DQA1 second exon exhibit stable polymorphisms that are specific for locus alleles and certain suballelic DR/DQ haplotypes. A PCR-RFLP method has been developed that is based on amplification of a 780-bp segment extending from intron 1 through exon 2 to intron 2. Stable sequence polymorphisms provide restriction enzyme sites and confer mobility variations detected on polyacrylamide minigel electrophoresis. Direct band comparison of amplified products and restriction fragments with known standards facilitates pattern comparison, obviating the requirement for accurate molecular weight determination. This method, using only two enzymes, identifies a total of 11 allelic and suballelic groups, including all eight DQA1 alleles encoded at the second exon.
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Affiliation(s)
- T M Limm
- GeneType Pty Ltd., Fitzroy, Australia
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13
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Easteal S, Grooms A, Croft L. A second new HLA-DPB1 allele from Santa Cruz Island, Solomon Islands. Immunogenetics 1993; 38:79. [PMID: 8463002 DOI: 10.1007/bf00216399] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- S Easteal
- Human Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra, A.C.T
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14
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van Eijk MJ, Stewart-Haynes JA, Lewin HA. Extensive polymorphism of the BoLA-DRB3 gene distinguished by PCR-RFLP. Anim Genet 1993; 23:483-96. [PMID: 1362859 DOI: 10.1111/j.1365-2052.1992.tb00168.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A polymerase chain reaction (PCR)-based method is described for typing of alleles of the bovine lymphocyte antigen (BoLA)-DRB3 gene. A total of 30 DRB3 alleles were distinguished by digestion of PCR amplification products of BoLA-DRB3 exon 2 with RsaI, BstYI and HaeIII (PCR-RFLP). All restriction fragment patterns, with the exception of one HaeIII pattern, were consistent with restriction sites that were found among 14 previously sequenced DRB3 alleles. The PCR-RFLP typing method was evaluated on 168 genomic DNA samples collected from animals of 10 cattle breeds, 48 of which were typed in the Fourth International BoLA Workshop for BoLA-DRB and -DQ by conventional restriction fragment length polymorphism (RFLP) analysis using heterologous and homologous DNA probes. Thirty-one DRB/DQ haplotypes containing 23 DRB3 alleles were identified among the 48 workshop animals analysed. Using PCR-RFLP, 11 DRB3 alleles were identified in 18 workshop animals for which DRB RFLPs were not informative. PCR-RFLP typing of additional animals revealed five new DRB3 alleles, of which three contained a putatively located three basepair deletion in the identical position as found for the sequenced allele DRB*2A. PCR-RFLP was shown to be a rapid and sensitive method for the detection of polymorphism in a functionally relevant domain of the BoLA-DRB3 gene and should be useful for studying the evolution of DRB polymorphism in cattle and other Bovidae.
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Affiliation(s)
- M J van Eijk
- Department of Animal Sciences, University of Illinois at Urbana-Champaign 61801
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15
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Dekker JW, Easteal S, Jakobsen IB, Gao X, Stewart GJ, Buhler MM, Hawkins BR, Higgins DA, Yu YL, Serjeantson SW. HLA-DPB1 alleles correlate with risk for multiple sclerosis in Caucasoid and Cantonese patients lacking the high-risk DQB1*0602 allele. TISSUE ANTIGENS 1993; 41:31-6. [PMID: 8456441 DOI: 10.1111/j.1399-0039.1993.tb01974.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multiple sclerosis (MS) is a demyelinating disease associated with the HLA-DR2-related haplotype DRB1*1501, DQB1*0602 in Caucasoids and with DQB1*0602 in DR2-positive Cantonese. However, many MS patients do not have the high-risk HLA-D determinants and alternative genes may contribute to the pathogenesis of MS. One candidate gene is HLA-DPB1. Our reanalysis of five earlier reports of HLA-DPB1 antigen distributions in Caucasoid MS patients shows a consistent and highly significant increase (p = 1.5 x 10(-5)) in frequency of HLA-DPw3 in the combined data set. This study tests whether HLA-DPw3 (DPB1*0301) is also increased in frequency in Australian and Cantonese MS patients and whether any distortion in DPB1 allelic distributions can be attributed to linkage disequilibrium with DQB1*0602. PCR-RFLPs were used to determine distributions of 20 HLA-DPB1 alleles in 41 Australian MS patients and 67 controls of known DQB1*0602 status and in 11 Cantonese MS patients and 33 controls positive for HLA-DR2. HLA-DP distributions in Australian MS patients and controls positive for DQB1*0602 did not differ, but in those MS patients lacking DQB1*0602, the DPB1*0301 antigen (phenotype) frequency was significantly (p = 0.006) increased (50.0%) when compared with DQB1*0602-negative controls (9.1%). DPB1*0301 was associated (p = 0.003) with DQB1*0402 (DR8) in Caucasoid MS patients.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J W Dekker
- Human Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra
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16
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Hviid TV, Madsen HO, Morling N. HLA-DPB1 typing with polymerase chain reaction and restriction fragment length polymorphism technique in Danes. ACTA ACUST UNITED AC 1992; 40:140-4. [PMID: 1359673 DOI: 10.1111/j.1399-0039.1992.tb02106.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We have used the polymerase chain reaction (PCR) in combination with the restriction fragment length polymorphism (RFLP) technique for HLA-DBP1 typing. After PCR amplification of the polymorphic second exon of the HLA-DPB1 locus, the PCR product was digested with seven allele-specific restriction endonucleases: RsaI, FokI, ApaI, SacI, BstUI, EcoNI, and DdeI, and the DNA fragments were separated by electrophoresis in agarose gels. Altogether, 71 individuals were investigated and 16 different HLA-DPB1 types were observed in 26 different heterozygotic combinations, as well as five possible homozygotes. Four heterozygotes could not be unequivocally typed with the PCR-RFLP method. The HLA-DPB1 typing results obtained with the PCR-RFLP method were compared with the typing results obtained with PCR allele-specific oligonucleotides (PCR-ASO) in 50 individuals. The results obtained with the two methods were concordant in 84% of the cases. One of the HLA-DPB1 types was discrepant in six heterozygotes, both HLA-DPB1 types were discrepant in one heterozygote, and in one individual two HLA-DPB1 types were identified with the PCR-RFLP technique while only one HLA-DPB1 type could be demonstrated with the PCR-ASO technique. The frequencies of the HLA-DPB1 genotypes deduced from the results of PCR-RFLP typing were estimated in 71 healthy Danes.
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Affiliation(s)
- T V Hviid
- Institute of Forensic Genetics, University of Copenhagen, Denmark
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17
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Harada H, Kimura A, Dong RP, Xu XP, Bhatia K, Sasazuki T. Sequencing and population analysis of four novel HLA-DPA1 alleles. Hum Immunol 1992; 35:173-8. [PMID: 1363422 DOI: 10.1016/0198-8859(92)90102-s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We determined the base sequences of the HLA-DPA1 gene from four B-lymphoblastoid cell lines (CB6B, LKT3, AMAI, and T7526) that showed distinct electrophoretic patterns of single-stranded polymerase chain reaction products of the HLA-DPA1 gene. The novel HLA-DPA1 alleles of CB6B, LKT3, AMAI, and T7526 were designated DPA1*02021, DPA1*02022, DPA1*0301, and DPA1*0401, respectively. Although there was only one base substitution between DPA1*02021 and DPA1*02022, the single-strand conformation polymorphism of these two alleles was clearly demonstrated by electrophoresis in a nondenaturing polyacrylamide gel containing 10% glycerol. In addition, we genotyped for the HLA-DPA1 gene of healthy unrelated Oriental individuals--i.e., 227 Japanese, 88 Papua New Guineans, and 41 Buyi-Chinese--to demonstrate the ethnic distribution of the HLA-DPA1 alleles.
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Affiliation(s)
- H Harada
- Department of Genetic, Kyushu University, Fukuoka, Japan
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18
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Sawitzke AD, Sawitzke AL, Ward RH. HLA-DPB typing using co-digestion of amplified fragments allows efficient identification of heterozygous genotypes. TISSUE ANTIGENS 1992; 40:175-81. [PMID: 1361686 DOI: 10.1111/j.1399-0039.1992.tb02042.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Twenty-four alleles have been defined for HLA-DPB based on their second exon sequences. This paper describes a novel method, co-digested amplified fragment length polymorphisms (CAFLP), for assigning these alleles to heterozygous patients, as well as to homozygous cell lines. The method depends on co-digestion of amplified DNA by restriction endonucleases and separation of the resultant fragments with polyacrylamide gel electrophoresis. Co-digestion by selected restriction enzymes produces a set of readily discernible fragments that are unique for a given haplotype because the selected restriction sites occur in cis. Consequently, this method provides haplotype information not available from independent digests and allows all known heterozygous genotypes to be identified. Analysis of 103 trios of mother, father, and child, plus 120 normal caucasians, demonstrates the reliability and simplicity of this procedure. This simple typing method results in unambiguous assignment of all current HLA-DPB genotypes in random samples with a high proportion of heterozygous individuals.
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Affiliation(s)
- A D Sawitzke
- Department of Human Genetics, University of Utah, Salt Lake City
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19
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Affiliation(s)
- J L Bidwell
- Clinical Services, United Kingdom Transplant Support Service, Bristol, UK
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20
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Mizuki N, Ohno S, Sugimura K, Seki T, Kikuti YY, Ando A, Ota M, Tsuji K, Inoko H. PCR-RFLP is as sensitive and reliable as PCR-SSO in HLA class II genotyping. ACTA ACUST UNITED AC 1992; 40:100-3. [PMID: 1357778 DOI: 10.1111/j.1399-0039.1992.tb01967.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- N Mizuki
- Department of Ophthalmology, Yokohama City University School of Medicine, Kanagawa, Japan
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21
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Dormoy A, Urlacher A, Tongio MM. Complexity of the HLA-DP region: RFLP analysis versus PLT typing and oligotyping. Hum Immunol 1992; 34:39-46. [PMID: 1356955 DOI: 10.1016/0198-8859(92)90083-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A total of 84 individuals were DP typed in parallel with the restriction fragment length polymorphism (RFLP) analysis and the primed lymphocyte test (PLT). Whereas 80% of the cases gave concordant results, the other 20% showed discrepancies for one of the two alleles carried by the typed individuals. Oligotyping, PCR-RFLP and sequencing confirmed the results found by PLT. The 20% discordant results obtained with RFLP led us to conclude that RFLP typing cannot replace PLT typing. From a more general point of view, the RFLP analysis revealed the DP region to be more complex than expected since for each given PLT DP defined specificity, more than one RFLP DP haplotype could be determined. These were possibly induced by crossing-overs or gene conversion events.
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Affiliation(s)
- A Dormoy
- Regional Center for Blood Transfusion, Strasbourg, France
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22
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Salazar M, Yunis I, Alosco SM, Chopek M, Yunis EJ. HLA-DPB1 allele mismatches between unrelated HLA-A,B,C,DR (generic) DQA1-identical unrelated individuals with unreactive MLC. ACTA ACUST UNITED AC 1992; 39:203-8. [PMID: 1356283 DOI: 10.1111/j.1399-0039.1992.tb01936.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have used a PCR-RFLP method with one generic amplification of HLA-DPB1 second exon and 6 endonucleases to differentiate the 19 HLA-DPB1 alleles and 171 heterozygous combinations. The set of primers used in our studies produced fragment sizes different from those published before (1). The HLA-DPB1 alleles in Caucasians showed a higher frequency of DPB1*0401 and DPB1*0402, when compared to a small group of Colombians who showed a higher frequency of DPB1*0402 and DPB1*0201. We found three HLA-DPB1 alleles associated with two HLA haplotypes that result from non-random association of alleles: DPB1*0401 with HLA-A26, B38, DR4, DQA1*0301 and DPB1*0101 and DPB1*0401 with HLA-A1, B8, DR3, DQA1*0501. We also report that 70% of combinations between HLA (generic A,B,C,DR) and DQA1-identical MLC-unreactive cell mixtures showed HLA-DPB1 mismatches, suggesting that HLA-DPB1 differences are not important in MLC reactivity.
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Affiliation(s)
- M Salazar
- Dana Farber Cancer Institute, Boston, Mass
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23
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Hoshino S, Kimura A, Fukuda Y, Dohi K, Sasazuki T. Polymerase chain reaction—single-strand conformation polymorphism analysis of polymorphism in DPA1 and DPB1 genes: A simple, economical, and rapid method for histocompatibility testing. Hum Immunol 1992; 33:98-107. [PMID: 1348744 DOI: 10.1016/0198-8859(92)90059-v] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new technical trial was carried out to detect polymorphism in HLA-DP genes, based on the diversity in electrophoretic mobility of single-stranded DNA (single-strand conformation polymorphism, SSCP). Genomic DNAs from 31 cell lines homozygous for 2 and 14 different DPA1 and DPB1 alleles, respectively, and from peripheral blood cells of a normal individual homozygous for another DPB1 allele were subjected to polymerase chain reaction (PCR) to amplify the polymorphic exon 2 of DPA1 or DPB1 genes. The PCR samples were denatured by heating in the presence of formamide to obtain single-stranded DNA, electrophoresed in a neutral polyacrylamide gel, and visualized by silver staining. Allelic differences were detected by the distinctive electrophoretic pattern of each single strand, depending on the sequence-specific conformation. Fifteen DPB1 alleles showed 11 distinct electrophoretic patterns, leaving four allelic combinations not distinguished. These four allelic combinations could be further distinguished by using another couple of primers in PCR, with which a part of the exon was amplified, and by subsequent SSCP analysis. The use of four pairs of primers in PCR allowed for discrimination of all the 15 DPB1 alleles tested. Two allelic differences in exon 2 of DPA1 gene could be clearly demonstrated. In addition, putative new alleles of DPA1 and DPB1 genes were detected by SSCP analyses. The PCR-SSCP analysis is simple and rapid, requires neither radioactive materials nor restriction enzymes, and is expected to be a useful tool for investigating the fine HLA-matching required for clinical transplantation of organs.
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Affiliation(s)
- S Hoshino
- Department of Genetics, Kyushu University, Fukuoka, Japan
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24
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Rubocki RJ, Wisecarver JL, Hook DD, Cox SM, Beisel KW. Histocompatibility screening by molecular techniques: Use of polymerase chain reaciton products and heteroduplex formation. J Clin Lab Anal 1992; 6:337-41. [PMID: 1357120 DOI: 10.1002/jcla.1860060515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Novel molecular approaches have recently become available allowing improved major histocompatibility complex (MHC) matching of potential allogeneic bone marrow donors and recipients. Current cellular and serological assays are hindered by aberrant cell populations and limited reagents which only detect an individuals' phenotype. Therefore, a molecular screening protocol which discriminates at the genotypic level would be advantageous. Here we describe a two-step DNA-based approach that can be applied to large-scale screening of potential donors. A primary screen, utilizing polymerase chain reaction (PCR), reduces the potential donor population, whereas a secondary or fine resolution screen uses DNA heteroduplex analysis to determine identity or non-identity at specific loci. Heteroduplex analysis generates a DNA migration pattern that is unique for alleles at a given locus, and is more sensitive than serology in discriminating among individuals. Here we demonstrate the potential feasibility of this approach by analyzing results at one MHC locus, HLA-DQ. Since this method does not rely on typing sera or viable lymphocytes, it is not subject to the variability found in the traditional methods. In contrast to traditional methods, these molecular techniques can provide the critical information needed to select a potential bone marrow donor.
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Affiliation(s)
- R J Rubocki
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha 68198-3135
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25
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al-Daccak R, Wang FQ, Theophille D, Lethielleux P, Colombani J, Loiseau P. Gene polymorphism of HLA-DPB1 and DPA1 loci in caucasoid population: frequencies and DPB1-DPA1 associations. Hum Immunol 1991; 31:277-85. [PMID: 1680839 DOI: 10.1016/0198-8859(91)90100-n] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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 transmembrane 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.
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Affiliation(s)
- R al-Daccak
- Laboratoire d'Immunologie et d'Histocompatibilité-Hôpital Saint Louis Paris, France
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26
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Drover S, Codner D, Gamberg J, Hutchings L, Marshall WH. A site-specific anti-HLA-DP monoclonal antibody recognizes molecules bearing "DE" at positions 55 and 56 on the beta chain. TISSUE ANTIGENS 1991; 38:37-40. [PMID: 1681600 DOI: 10.1111/j.1399-0039.1991.tb02034.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- S Drover
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
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27
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Smrzka OW, Faé I, Pickl WF, Fischer GF. HLA-DRB3 typing by restriction digestion of locus-specific amplified DNA. TISSUE ANTIGENS 1991; 37:205-10. [PMID: 1685265 DOI: 10.1111/j.1399-0039.1991.tb01873.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Locus HLA-DRB3 codes for the serologically defined supertypic specificity DRw52 in HLA-DR3, -5 and -w6 haplotypes. Three specificities of DRw52 (DRw52a, -b and -c) can further be distinguished by cellular techniques or by DNA typing with allele-specific oligonucleotide probes. These specificities were recently reported to have significant importance in antigen presentation. To avoid a time-consuming hybridization procedure, we have developed a simple typing system using PCR and subsequent digestion by allele-specific restriction endonucleases. A system was established with locus-specific amplification of HLA-DRB3 and digestion by the enzymes KpnI, ScaI and HinfI which recognize unique restriction sites within the amplified region. This allowed HLA-DRB3 typing on agarose gel by determining whether the amplification product has been digested or not. This typing system was compared to conventional oligotyping by analyzing 145 RFLP-typed individuals for their DRw52 specificity using both methods. Agarose typing correlated well with oligotyping and was shown to be more simple and practical even in heterozygous individuals.
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Affiliation(s)
- O W Smrzka
- Institute for Blood Group Serology University of Vienna, Austria
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28
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Howell WM, Sage DA, Haegert DG, Evans PR, Smith JL. PCR-SSO typing for HLA-DPB alleles. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 1991; 18:81-95. [PMID: 1676913 DOI: 10.1111/j.1744-313x.1991.tb00008.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- W M Howell
- Wessex Histocompatibility Group, Southampton General Hospital, U.K
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