Cited by 179Genetic Associations and EpidemiologyRenal Transplantation Outcomes and TreatmentsHematopoietic Stem Cell Transplantation

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New HLA haplotype frequency reference standards: high-resolution and large sample typing of HLA DR-DQ haplotypes in a sample of European Americans

Klitz, W., Maiers, M., Spellman, S., Baxter‐Lowe, L.A., Schmeckpeper, B., Williams, T.M., Fernandez‐Viña, M.·2003·Tissue Antigens

DOI 10.1034/j.1399-0039.2003.00103.x

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Abstract

Abstract: 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 high‐resolution 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.

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Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma
Skibola, C., Akers, N. K., Conde, L., Ladner, M., Hawbecker, S., Cohen, F., Ribas, F., Erlich, H. A., Goodridge, D., Trachtenberg, E. A., et al. (2012) · Tissue Antigens · doi:10.1111/j.1399-0039.2012.01845.x · Cited by 35
The Association Between Broad Antigen HLA Mismatches, Eplet HLA Mismatches and Acute Rejection After Kidney Transplantation
Nguyen, H. T. D., Wong, G., Chapman, J., McDonald, S., Coates, P., Watson, N., Russ, G., D'Orsogna, L., & Lim, W. (2016) · Transplantation Direct · doi:10.1097/txd.0000000000000632 · Cited by 34
“However, the lack of acuity for all HLA-DR-DQ haplotypes introduces uncertainties.(28) Our study has focussed only on the risk of early acute rejection within 12 months.”
Background
HLA-DQ Barrier: Effects on cPRA Calculations
Tambur, A., Leventhal, J., Walsh, R., Zitzner, J. R., & Friedewald, J. (2013) · Transplantation · doi:10.1097/tp.0b013e3182a452a5 · Cited by 31
“(16), studying a large sample of European American subjects, demonstrated that there is strong linkage disequilibrium between the DQA1 and DQB1 loci in this homogenous Caucasian population.”
Background
HLA-DQA1*03:02/DQB1*03:03:02 is strongly associated with susceptibility to childhood-onset ocular myasthenia gravis in Southern Han Chinese.
Zhu, W.-H., Lu, J.-H., Lin, J., Xi, J., Lu, J., Luo, S.-S., Qiao, K., Xiao, B.-G., Lu, C.-Z., & Zhao, C. (2012) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2012.03.018 · Cited by 31
“16%) (Klitz et al., 2003; Trachtenberg et al., 2007).”
The immunopathogenesis of celiac disease reveals possible therapies beyond the gluten-free diet
McAllister, C. S., & Kagnoff, M. F. (2012) · Seminars in Immunopathology · doi:10.1007/s00281-012-0318-8 · Cited by 32
Single-nucleotide polymorphisms in the IL2RA gene are associated with age at diagnosis in late-onset Finnish type 1 diabetes subjects
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“HLA-DQA1-DQB1 haplotypes (HLA-DQ) and 4-digit resolution of HLA-DQA1 were then inferred using reported European Caucasian haplotype frequencies ( Klitz et al. 2003 ), and confirmed by the E-M algorithm.”
Method
Role of Human Leucocyte Antigen DQ in the Presentation of T Cell Epitopes in the Major Cow’s Milk Allergen αs1-Casein
Ruiter, B., Rozemuller, E., van Dijk, A. V., Garssen, J., Bruijnzeel-koomen, C., Tilanus, M., Knol, E., & van Hoffen, E. (2007) · International Archives of Allergy and Immunology · doi:10.1159/000098660 · Cited by 28
Immune perturbations in human pancreas lymphatic tissues prior to and after type 1 diabetes onset
Golden, G. J., Wu, V. H., Hamilton, J. T., Amses, K. R., Shapiro, M. R., Japp, A. S., Liu, C., Pampena, M. B., Kuri-Cervantes, L., Knox, J. J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59626-0 · Cited by 27
“Phasing of HLA-DQA1 and HLA-DQB1 genotypes was inferred via comparison with published haplotype frequencies from European Americans 104 .”
Impact of de novo donor‐specific anti‐HLA antibodies on grafts outcomes in simultaneous pancreas–kidney transplantation
Malheiro, J., Martins, L., Tafulo, S., Dias, L., Fonseca, I., Beirão, I., Castro-henriques, A., & Cabrita, A. (2016) · Transplant International · doi:10.1111/tri.12687 · Cited by 27
“The loci within the DR-DQ region present a tight linkage and high linkage disequilibrium as shown by a study done in a population with European ancestry [23].”
Background
Human leukocyte antigen–A, -B, -C, -DRB1 allele and haplotype frequencies in Americans originating from southern Europe: Contrasting patterns of population differentiation between Italian and Spanish Americans
Mack, S. J., Tu, B., Yang, R., Masaberg, C., Ng, J., & Hurley, C. K. (2010) · Human Immunology · doi:10.1016/j.humimm.2010.10.017 · Cited by 24
LIMITED HLA SEQUENCE VARIATION OUTSIDE OF ANTIGEN RECOGNITION DOMAIN EXONS OF 360 10/10 MATCHED UNRELATED HEMATOPOIETIC STEM CELL TRANSPLANT DONOR - RECIPIENT PAIRS
Hou, L., Vierra-Green, C., Lazaro, A. M., Brady, C., Haagenson, M., Spellman, S., & Hurley, C. K. (2016) · HLA · doi:10.1111/tan.12942 · Cited by 25
“Although HLA-DQA1 was not typed at the time of transplant, the tight linkage between HLA-DQA1 and -DQB1 predicts that, if HLA-DQB1 is matched, HLA-DQA1 will also be matched (24).”
BackgroundSelf-citation
HLA DR and DQ alleles and haplotypes associated with clinical response to glatiramer acetate in multiple sclerosis
Dhib-Jalbut, S. S., Valenzuela, R. M., Ito, K., Kaufman, M., Picone, M. A., & Buyske, S. G. (2013) · Multiple Sclerosis and Related Disorders · doi:10.1016/j.msard.2013.02.005 · Cited by 27
The rare HLA-DQA1*03-DQB1*02 haplotype confers susceptibility to type 1 diabetes in whites and is preferentially associated with early clinical disease onset in male subjects.
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Unrelated Stem Cell Donor HLA Match Likelihoods in the US Registry Incorporating HLA-DPB1 Permissive Mismatching
Gragert, L., Spellman, S. M., Shaw, B., & Maiers, M. (2022) · medRxiv · doi:10.1101/2022.11.14.22282311 · Cited by 23
Self-citation
Failed Genetic Protection: Type 1 Diabetes in the Presence of HLA-DQB1*06:02
Simmons, K. M., Mitchell, A. M., Alkanani, A. K., McDaniel, K. A., Baschal, E. E., Armstrong, T., Pyle, L. L., Yu, L., & Michels, A. W. (2020) · Diabetes · doi:10.2337/db20-0038 · Cited by 27
Prediction of duration and success rate of unrelated hematopoietic stem cell donor searches based on the patient's HLA-DRB1 allele and DRB1-DQB1 haplotype frequencies
Hirv, K., Bloch, K. E., Fischer, M. D., Einsiedler, B., Schrezenmeier, H., & Mytilineos, J. (2009) · Bone Marrow Transplantation · doi:10.1038/bmt.2009.53 · Cited by 23
The role of human leukocyte antigen DRB1-DQB1 haplotypes in the susceptibility to acquired idiopathic thrombotic thrombocytopenic purpura.
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Association with HLA DQ of early onset myasthenia gravis in Southeast Texas region of the United States
Deitiker, P., Oshima, M., Smith, R. G., Mosier, D. R., & Atassi, M. (2011) · International Journal of Immunogenetics · doi:10.1111/j.1744-313x.2010.00979.x · Cited by 22
“allele or haplotype based on a control data set (Klitz et al., 2003), and is a measure of significant deviations in the higher direction.”
BackgroundMethodInfluential
Association of human leukocyte antigen (HLA)-DQ and HLA-DQA1/DQB1 alleles with Vogt–Koyanagi–Harada disease
Liu, B., Deng, T., Zhu, L., & Zhong, J.-X. (2018) · Medicine · doi:10.1097/md.0000000000009914 · Cited by 21
Human genetic variation studies and HLA class II loci
Agrawal, S., Khan, F., & Bharadwaj, U. (2007) · International Journal of Immunogenetics · doi:10.1111/j.1744-313x.2007.00683.x · Cited by 16
“Frequency of DRB1*0301DQA1*0501-DQB1*0201 is found as high as 11% among Iranis and 12.7% and 13.4%, respectively, among English and American Caucasians (Klitz et al., 2003).”
BackgroundInfluential
Full-resolution HLA and KIR gene annotations for human genome assembliesPreprint
Zhou, Y., Song, L., & Li, H. (2024) · Genome Research · doi:10.1101/gr.278985.124 · Cited by 25
“The HLA class II region is highly structured (Klitz et al. 2003; Norman et al. 2017; Chin et al. 2023), which is commonly characterized by DR haplotype.”
A Diverse Repertoire of CD4 T Cells Targets the Immediate-Early 1 Protein of Human Cytomegalovirus
Ameres, S., Liang, X.-L., Wiesner, M., Mautner, J., & Moosmann, A. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00598 · Cited by 20
“However, DRB1*0701 is in linkage disequilibrium with DQA1*0201/DQB1*0202 as described (32), and thus carriers of this haplotype can instead target IE-1 through HLA-DQ-restricted CD4 T cells, as seen for two of our three donors with this haplotype (Table 1; Figure 3B).”
Background
Comparing transplant glomerulopathy in the absence of C4d deposition and donor‐specific antibodies to chronic antibody‐mediated rejection
Torres, I., Salcedo, M., Moreso, F., Sellarés, J., Castellá, E., Azancot, M., Perelló, M., Cantarell, C., & Serón, D. (2014) · Clinical Transplantation · doi:10.1111/ctr.12433 · Cited by 20
“In patients with positive HLA-DQ, the presence/ absence of DSA was assigned according to linkage disequilibrium for DR-DQ types (20).”
Method
Cord blood banks collect units with different HLA alleles and haplotypes to volunteer donor banks: a comparative report from Swiss Blood stem cells
Meyer-Monard, S., Passweg, J. R., Troeger, C., Eberhard, H., Roosnek, E., de Faveri, G. N., Chalandon, Y., Rovó, A., Kindler, V., Irion, O., et al. (2009) · Bone Marrow Transplantation · doi:10.1038/bmt.2008.391 · Cited by 20
HLA-DQ3 is a probable risk factor for CMV infection in high-risk kidney transplant patients.
Varga, M., Rajczy, K., Telkes, G., Hídvégi, M., Péter, A., Remport, Á., Korbonits, M., Fazakas, J., Toronyi, É., Sárváry, E., et al. (2008) · Nephrology, Dialysis and Transplantation · doi:10.1093/ndt/gfn111 · Cited by 18
“Since HLA-DQ3 has strong linkage disequilibrium with HLA-DR11 [ 13 ], we analysed the data concerning HLA-DR11 in complex with HLA-DQ3.”
Background
Association of HLA class II alleles with sensitization to cow dander Bos d 2, an important occupational allergen.
Kauppinen, A., Peräsaari, J. P., Taivainen, A., Kinnunen, T., Saarelainen, S. A., Rytkönen-Nissinen, M., Jeal, H., Jones, M. G., & Virtanen, T. (2012) · Immunobiology · doi:10.1016/j.imbio.2011.08.012 · Cited by 18
Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers
Lim, W. C., Costa, M. E. M. D., Godefroy, K., Jacquet, E., Gragert, L. A., Rondof, W., Marchais, A., Nhiri, N., Dalfovo, D., Viard, M., et al. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1265469 · Cited by 17
DR15-DQ6 remains dominantly protective against type 1 diabetes throughout the first five decades of life
Thomas, N. J., Dennis, J., Sharp, S. A., Kaur, A., Misra, S., Walkey, H. C., Johnston, D. G., Oliver, N. S., Hagopian, W., Weedon, M. N., et al. (2021) · Diabetologia · doi:10.1007/s00125-021-05513-4 · Cited by 19
Celiac disease risk stratification based on HLA-DQ heterodimer (HLA-DQA1 ~ DQB1) typing in a large cohort of adults with suspected celiac disease.
Choung, R., Mills, J., Snyder, M., Murray, J., & Gandhi, M. (2020) · Human Immunology · doi:10.1016/j.humimm.2020.01.006 · Cited by 17
HLA-DR-DQ haplotypes and type 1 diabetes in Macedonia.
Ilonen, J., Kocova, M., Lipponen, K., Sukarova-Angelovska, E., Jovanovska, A., & Knip, M. (2009) · Human Immunology · doi:10.1016/j.humimm.2009.03.014 · Cited by 17
Genetic association of HLA DQB1 with CD4+CD25+high T-cell apoptosis in type 1 diabetes
Glišić, S., Klinker, M. W., Waukau, J., Jailwala, P., Jana, S., Basken, J., Wang, T., Alemzadeh, R., Hagopian, W., & Ghosh, S. (2009) · Genes and Immunity · doi:10.1038/gene.2009.14 · Cited by 19
Why can Sensitization by a HLA-DR2 Mismatch lead to Antibodies that react also with HLA-DR1?
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The incidence of HLA-DQ2/DQ8 in Turkish children with celiac disease and a comparison of the geographical distribution of HLA-DQ
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“During the interpretation of the HLA-DQ2 and HLA-DQ8 allele levels, the detection of 0201 and 0202 for HLA-DQ2 B1 and the detection of 0302 for HLA-DQ8 B1 are regarded as positive [10].”
Background
HLA-DR7 and HLA-DQ2: Transgenic mouse strains tested as a model system for ximelagatran hepatotoxicity
Lundgren, H., Martinsson, K., Cederbrant, K., Jirholt, J., Mucs, D., Madeyski-Bengtson, K., Havarinasab, S., & Hultman, P. A. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184744 · Cited by 17
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“Figure 1a schematically depicts the variation in the HLA-DR b1 domain per amino acid of the top 15 most prevalent HLA-DRB1 chains present in the Caucasian population (together covering 91% of the variations in Caucasians [21]).”
Background
Interaction between Treg Apoptosis Pathways, Treg Function and HLA Risk Evolves during Type 1 Diabetes Pathogenesis
Glišić, S., & Jailwala, P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0036040 · Cited by 17
“[35].”
Association of HLA Class II alleles and haplotypes with cervical dystonia: HLA DR13-DQ6 (DQB1*0604) homozygotes are at greatly increased risk of cervical dystonia in Caucasian Americans
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Immunogenetic Correlates of Neisseria gonorrhoeae Infection in Adolescents
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Mapping MHC-resident transplantation determinants.
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Self-citation
microRNAs: Novel Markers in Diagnostics and Therapeutics of Celiac Disease
Chamani, E., Sargolzaei, J., Tavakoli, T., & Rezaei, Z. (2019) · DNA and Cell Biology · doi:10.1089/dna.2018.4561 · Cited by 13
“2 (Klitz et al. , 2003; Meresse et al. , 2009). downregulation and reduced expression concerns with miR-31-5p in children and miR-338-3p in the duodenum of adults suffering from CD. miR-21-5p upregulation is sig-niﬁcantly involved in the regulation of the immune response in the duodenum of CD…”

Authors: Klitz, W., Maiers, M., Spellman, S., Baxter‐Lowe, L. A., Schmeckpeper, B., Williams, T. M., & Fernandez‐Viña, M.
Affiliations: National Marrow Donor Program (US)
University of California, San Francisco (US)
American Red Cross (US)
University of New Mexico Health Sciences Center (US)
Corresponding author: Klitz, W.
ORCID: Maiers, M.
Spellman, S.
Baxter‐Lowe, L.A.
Williams, T.M.
Venue: Tissue Antigens
Publisher: Wiley
Published: 2003-09-16
Volume: 62
Issue: 4
Pages: 296-307
ISSN: 0001-2815 (ISSN-L)
1399-0039
DOI: 10.1034/j.1399-0039.2003.00103.x
OpenAlex: W1976319355
Cited by: 179
References: 0
Citations by year: 2026: 5 · 2025: 5 · 2024: 9 · 2023: 5 · 2022: 1 · 2021: 9 · 2020: 9 · 2019: 4 · 2018: 6 · 2017: 11 · 2016: 6 · 2015: 12 · 2014: 7 · 2013: 8 · 2012: 12
FWCI: 3.89
Type: journal article
Language: en
Open access: closed
Licence: onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations: Tissue Antigens (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Health Sciences › Medicine › Transplantation › Renal Transplantation Outcomes and Treatments
Health Sciences › Medicine › Hematology › Hematopoietic Stem Cell Transplantation
Keywords: HLA haplotype frequencies, HLA-DRB1, HLA-DQA1, HLA-DQB1, haplotype inference, linkage disequilibrium, European Americans, allogeneic transplantation, rare haplotypes
MeSH terms: Histocompatibility Antigens Class II, Gene Frequency, Haplotypes, Histocompatibility Testing, HLA-DQ Antigens, HLA-DR Antigens, Humans, Reference Standards, HLA-A Antigens, HLA-B Antigens, White People, HLA-DRB1 Chains, HLA-DQ alpha-Chains, HLA-DQ beta-Chains

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New HLA haplotype frequency reference standards: high-resolution and large sample typing of HLA DR-DQ haplotypes in a sample of European Americans

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