173-P HLA-DQA1 locus sequencing assay (original) (raw)
Related papers
Tissue Antigens, 2003
A collaborative study involving a large sample of European Americans was typed for the histocompatibility loci of the HLA DR-DQ region and subjected to intensive typing validation measures in order to accurately determine haplotype composition and frequency. The resulting tables have immediate application to HLA typing and allogeneic transplantation. The loci within the DR-DQ region are especially valuable for such an undertaking because of their tight linkage and high linkage disequilibrium. The 3798 haplotypes, derived from 1899 unrelated individuals, had a total of 75 distinct DRB1-DQA1-DQB1 haplotypes. The frequency distribution of the haplotypes was right skewed with haplotypes occurring at a frequency of less than 1% numbering 59 and yet constituting less than 12% of the total sample. Given DRB1 typing, it was possible to infer the exact DQA1 and DQB1 composition of a haplotype with high confidence (>90% likelihood) in 21 of the 35 highresolution DRB1 alleles present in the sample. Of the DRB1 alleles without high reliability for DQ haplotype inference, only *0401, *0701 and *1302 were common, the remaining 11 DRB1 alleles constituting less than 5% of the total sample. This approach failed for the 13 serologically equivalent DR alleles in which only 33% of DQ haplotypes could be reliably inferred. The 36 DQA1-DQB1 haplotypes present in the total sample conformed to the known pattern of permissible heterodimers. Four DQA1-DQB1 haplotypes, all rare, are reported here for the first time. The haplotype frequency tables are suitable as a reference standard for HLA typing of the DR and DQ loci in European Americans.
European Journal of Immunogenetics, 1994
HLA-DRBI, DQAI and DQBl alleles have been determined in 42 families with one IDDM proband and 64 healthy controls, by oligotyping (PCR-SSO) using primers and probes from the XI International Histocompatibility Workshop. A positive DRB 1 *03 and DRB 1 *04 association with the disease was observed, whereas DRB 1 * 1 1 and DRB 1 *07 showed negative association but 19% of patients carried DRBl alleles different to DRB I *03 or *04. When single alleles were considered, DQA 1 *03 showed the strongest association with susceptibility to the disease (RR = 8.2, Pc = 0.ooOOl) but this association was outgrown by 2 and 3 allele combinations, with genotype DRBI*M-DQA1*03-DQB I *0302/DRB 1 *03-DQA 1 *050 1 -DQB 1 *020 1 showing the strongest association (RR = 28, Pc = 0.002). Application of the relative predispositional effect (RPE) method to our data, revealed a further susceptibility risk provided by the DRB I * 13-DQAI *0102-DQB1*0604 haplotype once DR3 and DR4 haplotypes were removed. When DQAI-DQB I genotypes were analysed for presence of Arg 52 (DQ a) and absence of Asp 57 (DQ p). genotypes S S / S S were found significantly increased in diabetics. Interestingly, one of the strongest associations with the disease was observed with the DQA1*03-DQB 1 *020 1 combination encoded mainly by genes in trans (RR = I 1.7 Pc = 0.00004). These observations and their comparison with DR-DQ haplotypes in more homogeneous ethnic groups support the stronger influence of the DQ molecule rather than the individual DR or DQ alleles in the susceptibility to IDDM. They also emphasize the need for detailed HLA haplotype studies in non-Caucasian and ethnically mixed populations to gain further insight into the nature of genetic and environmental factors contribution to autoimmunity.
HLA-DRB1, -DQB1 and -DPB1 polymorphism in the Slovak population
Tissue Antigens, 1998
Aim of the study was to investigate an association between HLA class II alleles and type 1 diabetes mellitus in the Slovak population. Methods. 460 patients suffering from diabetes were typed for DQB1 alleles; 97 out of them also for DQA1 and 146 for DRB1 alleles, respectively. The HLA-typing was performed by a PCR-SSP method. Primer sets originated from the GenoVision (Olerup SSP TM AB Sweden). Results. Out of DQA1 and DQB1 alleles, the most frequent were found: DQA1*0301 (30.93% compared to 17.09 % in the healthy population; P < 0.0002), DQA1*0501 (34.02% compared to 25.76% in the healthy population; P < 0.0413, DQB1*0201 (22.93% vs. 12.94%, P < 0.0002), and DQB1*0302 (30.33 % vs. 5.59 %; P < 0.0001). Similarly, DRB1*0301 and DRB1*0401, respectively, were found to have the highest occurrence rates among 13 DRB1 alleles tested (DRB1*03: 26.37 % vs. 9.62 %, P < 0.0001; DRB1*04: 34.93% vs. 11.16 %, P < 0.0001). Statistically significant decreased occurrence rates were also observed, too: DQA1*0102 (8.76% vs. 16.58 %, P < 0.0111), DQA1*0201 (6.18% vs. 13.51 %, P < 0.0077), DQB1*0602 (2.17% vs. 10.14 %, P < 0.0001), DRB1*15 (2.74% vs. 12.31 %, P < 0.0001) and DRB1*07 (7.18% vs. 14.23%, P < 0.0081). The DQB1*0302 and DQA1*0301, respectively, were present in the same individual in all DRB1*0401 positive patients, suggesting they belong to the haplotype DQB1*0302-DQA1*0301-DRB1*0401. The same situation was observed with the alleles DQB1*0201, DQA1*0501, and DRB*0301, respectively, forming the haplotype DQB1*0201-DQA1*0501-DRB1*0301. These findings are in concordance with similar studies done in Czech, Polish or other Caucasoid populations. However, some findings, i.e. decreased frequencies of DQA*0301, DQA1*0603, and DRB*11 were not reported till now. Conclusion. The results of our study confirm previous studies done in various Caucasoid populations that HLA-DQ2, -DQ8, -DR3, and DR4 represent for autoimmune diabetes mellitus susceptible and HLA-DQ6, DR15, and DR7 protective molecules
Human Immunology, 1990
HLA class Il polymorphism is functionally important in the control of immune responses, in transplantation immunology, and in the suceptibility to autoimmune diseases. HLA-DQA1 and -DQB1 genes exhibit a larger degree of allelic polymorphism than usually recognized by routine serology. We have therefore performed an extensive analysis of DQB1 polymorphism by oligotyping. A set of 12 oligo probes was hybridized on polymerase chain reaction-amplified DNA, thus allowing the detection of 12 DQB1 alleles, as demonstrated in homozygous as well as in heterozygous individuals. This highly sensitive detection system is particularly relevant within the DQwl specificity where the 7 allelic sequences can easily be identified. The DQ-DR linkage disequilibrium was analyzed by oligotyping of 80 Caucasoid heterozygous individuals (160 haplotypes), and very tight associations were observed between DRBI and DQB1 alleles. Five DRB1 alleles, DR-BON, DR4/Dw4 or Dwl4, DR7, DRw8.3, and DRwll, however, can be associated with different DQB1 alleles. Moreover the DRB1 and DQB1 oligotyping analysis performed on 20 randomly chosen DRw8 Caucasoid individuals showed a high prevalence of the DRB1 *0801-DQB I *0402 haplotype. By combining the analysis of allelic variations at DRB1, DRB 3, and DQB1 loci, we can detect 33 different DR-DQ combinations in our panel of Caucasoid individuals. We now apply DQB 1 oligotyping on a routine basis for optimal matching of unrelated donors for bone marrow transplantation. ABBREVIATIONS BMT bone marrow transplantation HTC homozygous typing cell PCR polymerase chain reaction RFLP restriction fragment length polymorphism bp base pair IDDM insulin-dependant diabetes mellitus
Human Immunology, 1999
The frequencies of 30 HLA-DRB1*13 alleles and 15 DRB3 alleles were determined for the 5 major U.S. ethnic populations: Caucasians, African Americans, Asian/Pacific Islanders, Hispanics, and Native Americans. A random sampling (163) of DRB1*13-positive individuals from each self-described ethnic group was selected out of a pool of 82,979 unrelated individuals, providing at least an 80% probability of detecting a rare allele that occurred at 1%. These 815 samples were subjected to allele-level SSOP typing and/or DNA sequencing which identified 11 different DRB1*13 alleles. DRB1*1301 and DRB1*1302 were the most common alleles seen in the five major ethnic groups while DRB1*1304 was not detected among Caucasians and DRB1*1305 was not detected among African Americans. DRB1*13 allele diversity was surprisingly more limited among African Americans compared to both Caucasians and Asian/Pacific Islanders. To determine the extent of DRB1*13-DRB3 associations, 504 of these samples expressing only one DRB3-associated DRB1 allele were subjected to PCR-SSOP typing and 14 DRB1*13-DRB3 haplotypes were detected. The distribution revealed that African Americans were significantly different from Caucasians, Asian/Pacific Islanders, and Hispanics. Allele frequency studies such as this further support previous findings that the distribution of HLA types can differ significantly among different ethnic populations.
Tissue Antigens, 2009
The 2008 report of the human leukocyte antigen (HLA) data dictionary presents serologic equivalents of HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, and -DQB1 alleles. The dictionary is an update of the one published in 2004. The data summarize equivalents obtained by the World Health Organization Nomenclature Committee for Factors of the HLA System, the International Cell Exchange, UCLA, the National Marrow Donor Program, recent publications, and individual laboratories. The 2008 edition includes information on 832 new alleles (685 class I and 147 class II) and updated information on 766 previously listed alleles (577 class I and 189 class II). The tables list the alleles with remarks on the serologic patterns and the equivalents. The serological equivalents are listed as expert assigned types, and the data are useful for identifying potential stem cell donors who were typed by either serology or DNA-based methods. The tables with HLA equivalents are available as a searchable form on the IMGT/HLA database Web site (http:// www.ebi.ac.uk/imgt/hla/dictionary.html).
Tissue Antigens, 2002
The study of the genetics of the Major Histocompatibility Complex (MHC) in Amerindians is of great value in understanding the origins and migrations of these native groups, as well as the impact of immunogenetics on the epidemiology of diseases affecting these populations. We analyzed, using Polymerase Chain Reaction and Sequence Specific Oligonucleotide Probes (PCR-SSOP), DRB1, DQA1, DQB1 alleles and the promoter regions of DQA1 and DQB1 genes in 31 unrelated and 24 related Seri, a Mexican Indian group, from the state of Sonora (Northwest Mexico). The class II genotypes of this population were found to be in genetic equilibrium. The allele frequency (AF) of the prevalent DRB1 alleles were DRB1*0407 (48.4%), DRB1*0802 (33.9%) and DRB1*1402 (16.1%). The most frequent DQA1 and DQB1 alleles were DQA1*03011 (AF ϭ 50.00%), DQA1*0401 (AF ϭ 33.87%) and DQA1*0501 (AF ϭ 16.13%); DQB1*0302 (AF ϭ 50.00%), DQB1*0402 (33.87%) and DQB1*0301 (16.13%); which were in combination with DRB1*0407, DRB1*0802 and DRB1*1402, respectively. Three QAP and three QBP alleles were present (QAP 3.1, 4.1, 4.2; QBP 3.1, 3.21, 4.1) associated with the typical published DQA1 and DQB1 alleles. Four class II haplotypes were present in family members:
Diabetes Care, 1995
OBJECTIVE To study the human leukocyte antigen (HLA)-DQ heterodimers in the susceptible DR haplotypes for patients with insulin-dependent diabetes mellitus (IDDM) in Taiwan. RESEARCH DESIGN AND METHODS Extended class II HLA haplotypes were studied in 57 unrelated IDDM patients, 31 simplex IDDM families, and 105 unrelated control subjects recruited from the same area in Taiwan. Class II HLA genotyping was based on PCR-SSO DNA typing techniques. Extended class II HLA haplotypes were deduced unequivocally by the Taiwanese pedigree studies. RESULTS DR3/DR3, DR3/DR4, and DR3/DR9 genotypes were strongly associated with IDDM susceptibility in this population. In addition to the reported DR3/DR4 in Caucasians, the heterozygotic effect of DR3/DR9 for IDDM was remarkable in the Taiwanese population. Extended HLA haplotypes studies revealed that DRB1*0301/DQA1*0501/DQB1*0201, DRB1*0405/DQA1*0301/DQB1*0302, and DRB1*0405/DQA1*0301/DQB1*0401 were the susceptible haplotypes in this population. Th...
1999
This report presents serologic equivalents of 90 HLA-A, 190 HLA-B, and 145 HLA-DRB1 alleles. The equivalents cover over 70% of the presently identified HLA-A,-B, and-DRB1 alleles. The dictionary is an update of the one published in 1997 and now also includes equivalents for HLA-C, DRB3, DRB4, DRB5, and DQB1 alleles. The data summarize information obtained by the WHO HLA Nomenclature Committee, the International Cell Exchange (UCLA), the National Marrow Donor Program (NMDP), and by individual laboratories. In addition, a listing is provided of alleles that are expressed as antigens with serologic reaction patterns that differ from the well-established HLA specificities and that often lack official WHO nomenclature. The provided equivalents will be useful in guiding searches for unrelated donors in which patients and/or potential donors are typed by either serology or DNA-based methods. These equivalents will also serve typing and matching procedures for organ transplant programs where HLA typings from donors and from recipients on waiting lists represent mixtures of serologic and molecular typings. Some guidelines are provided for the use of appropriate WHO HLA nomenclature for serologic typings and for generic and allele specific typings obtained with molecular methods. The tables with HLA equivalents and the questionnaire for submission of serology on poorly identified alleles will also be available at the WMDA web page: www.bmdw. org/wmda.
HLA-A, -B, -C, -DRB1, and -DQB1 Allele Lineages and Haplotype Frequencies among Saudis
Immunology and Immunogenetics Insights, 2014
There are few reported studies on Saudi population for human leukocyte antigens (HLA) genes. We investigated allele lineages (two-digit) and haplotype frequencies of HLA-A, -B, -C, -DRB1, and -DQB1 loci in 499 healthy unrelated individuals, selected from potential bone marrow transplant (BMT) families' donors at King Fahad Medical City (KFMC), Saudi Arabia (SA). Genotyping was performed by Sequence Specific Oligonucleotide Probe (SSOP) utilizing a Luminex-based method. Allele lineages and haplotype frequencies were evaluated along with principal component analysis (PCA) to compare findings with previously reported data on Arab related populations. A total of 18 allele lineages for HLA-A, 28 for -B, 14 for -C, 13 for -DRB1, and 5 for -DQB1 were detected. High values for linkage disequilibrium indicators were found for B:C (D′ = 0.86599) and DRB1:DQB1 (D′ = 0.89468) loci. Additionally, PCA results confirmed previous findings on this population, but also indicated some genetic distances from other Arab related populations. The present study helps in further investigations of this population in anthropological analysis and HLA-associated disease studies. CITATION: osman et al. hla-a, -B, -c, -dRB1, and -dQB1 allele lineages and haplotype Frequencies among saudis.