HLA class II haplotype and sequence analysis support a role for DQ in narcolepsy

 A systematic haplotype and sequencing analysis of the HLA-DR and -DQ region in patients with narcolepsy was performed. Five new (CA)_n microsatellite markers were generated and positioned on the physical map across the HLA-DQB1-DQA1-DRB1 interval. Haplotypes for these new markers and the three HLA loci were established using somatic cell hybrids generated from patients. A four-marker haplotype surrounding the DQB1 ^* 0602 gene was found in all narcolepsy patients, and was identical to haplotypes observed on random chromosomes harboring the DQB1 ^* 0602 allele. Eighty-six kilobases of contiguous genomic sequence across the region did not reveal new genes, and analysis of this sequence for single nucleotide polymorphisms did not reveal sequence variation among DQB1 ^* 0602 chromosomes. These results are consistent with other studies, suggesting that the HLA-DQ genes themselves are among the predisposing factors in narcolepsy. Received: 18 March 1997 / Revised: 23 April 1997     

Cw * 1701 defines a divergent African HLA-C allelic lineage

 The complete sequence of a new HLA-C allele, Cw ^* 1701, was determined from a South African Zulu individual. Unique features that distinguish Cw ^* 1701 from other HLA-C alleles include multiple point substitutions and an 18 nucleotide insertion in exon 5, which encodes the transmembrane domain. In a phylogenetic analysis of HLA-C sequences, Cw ^* 1701 forms a third, distinct allelic lineage. A comparison of the transmembrane domain of Cw ^* 1701 with other HLA-B and -C alleles reveals that duplications and deletions have been common in the evolution of these loci. A polymerase chain reaction based typing method was used to determine the distribution of this unusual allele in human populations. In contrast to the other two lineages of HLA-C alleles, the Cw ^* 17 lineage is found at high frequencies only in populations of African descent. In addition, the HLA-B/Cw ^* 17 haplotype diversity is higher in Africa. Received: 29 June 1996  / Revised: 20 December 1996     

HLA-G gene polymorphism in a Japanese population

 Polymorphism of the HLA-G gene in a Japanese population was investigated employing polymerase chain reaction (PCR)-single-strand conformation polymorphism (SSCP) analysis, PCR sequence-specific oligonucleotide (SSO) analysis, and DNA direct sequencing. Nucleotide sequence variations in exons 2, 3, and 4 of the HLA-G gene in 54 healthy Japanese individuals were examined. In addition, seven Japanese samples carrying common HLA haplotypes were analyzed. In total, nine single-base substitutions compared with the sequence of G ^* 01011 were identified: one in intron 1 (nucleotide position 970), one in exon 2 (the third base of codon 57: G → A), three in intron 2 (1264, 1276, and 1292), three in exon 3 (the third base of codon 93: C → T, the third base of codon 107: A → T, and the first base of codon 110: C → A), and one in intron 3 (2334). The substitution at codon 110 was non-synonymous and led to an amino acid substitution from leucine to isoleucine. The other three nucleotide substitutions in exons were synonymous. Through analysis of combinations of the exon 2, 3, and 4 nucleotide sequences we identified four alleles, which we provisionally designated GJ1, GJ2, GJ3, and GJ4. The allele frequencies were estimated to be 0.33, 0.16, 0.45, and 0.06, respectively. Nucleotide sequences of GJ1, GJ2, and GJ4 were identical to G ^* 01011, the clone 7.0E, and G ^* 01013, respectively. GJ3 was a newly observed allele and was officially designated G ^* 0104 by the WHO Nomenclature Committee in January 1996. Strong positive associations were observed between HLA-G alleles and HLA-A, -B, or -DRB1 alleles. Received: 15 February 1996 / Revised: 26 March 1996     

Diversity associated with the second expressed H L A - D R B locus in the human population

Although diversity within the HLA-DRB region is predominantly focused in the DRB1 gene, the second expressed DRB loci, DRB3, DRB4, and DRB5, also exhibit variation. Within DRB1 ^* 15 or DRB1 ^* 16 haplotypes, four new variants were identified: 1) two new DRB5 alleles, DRB5 ^* 0104 and DRB5 ^* 0204, 2) a haplotype carrying a DRB1 ^* 15 or ^* 16 allele without the usual accompanying DRB5 allele, and 3) a haplotype carrying a DRB5^* 0101 allele without a DRB1 ^* 15 or ^* 16 allele. The evolutionary origins of these haplotypes were postulated based on their associations with the DRB6 pseudogene. Within HLA haplotypes which carry DRB3, a new DRB3 ^* 0205 allele and one unusual DRB3 association were identified. Finally, two new null DRB4 alleles are described: DRB4 ^* 0201N, which exhibits a deletion in the second exon, and a second allele, DRB4 ^* null, which lacks the second exon completely. Gene conversion-like events and variation in the number of functional genes through reciprocal recombination and inactivation contribute to the diversity observed in the second expressed HLA-DRB loci. Received: 2 November 1996 / Revised: 23 December 1996     

Trans-species origin of Mhc-DRB polymorphism in the chimpanzee

Trans-specific evolution of allelic polymorphism at the major histocompatibility complex loci has been demonstrated in a number of species. Estimating the substitution rates and the age of trans-specifically evolving alleles requires detailed information about the alleles in related species. We provide such information for the chimpanzee DRB genes. DNA fragments encompassing exon 2 were amplified in vitro from genomic DNA of ten chimpanzees. The nucleotide sequences were determined and their relationship to the human DRB alleles was evaluated. The alleles were classified according to their positioni in dendrograms and the presence of lineage-specific motifs. Twenty alleles were found at the expressed loci Patr-DRB1,-DRB3, -DRB4, -DRB5, and at the pseudogenes Patr-DRB6, -DRB7; of these, 13 are new alleles. Two other chimpanzee sequences were classified as members of a new lineage tentatively designated DRBX. Chimpanzee counterparts of HLA-DRB1 ^* 01 and ^* 04 were not detected. The number of alleles found at individual loci indicates asymmetrical distribution of polymorphism between humans and chimpanzees. Estimations of intra-lineage divergence times suggest that the lineages are more than 30 million year old. Predictions of major chimpanzee DRB haplotypes are made.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M94937-M94954.     

Family studies of complement C4 and HLA in man

Summary At least 12 different C4 gene products with a three band pattern have been identified after electrophoresis of sera pretreated with neuraminidase.Segregation analysis showed at least 12 different C4 haplotypes (or supergenes), of which five represent a single gene product and seven are duplications each composed of an F and an S gene. The data analyzed with respect to linkage showed one recombinant between the C4 and the HLAB loci in 154 meioses giving a map distance of C4 HLAB of 0.6 cM. Another recombinant between the C4 and the HLAD loci was found in 101 meioses giving a map distance of C4 HLAD of 1.0 cM.Linkage disequilibrium was found between at least eight C4 haplotypes and certain alleles at the HLAB as well as the HLAD loci. Examinations of 15 families selected through a proband with HLAA 25, HLAB 18 and C2 ^* Q0 showed that in almost all cases a slight variant of the C4 supergene F3S2 followed the haplotype HLAA ^* 25 HLAB ^* 18 C2 ^* Q0. No associations were found between the two duplications C4F ^* 3 C4S ^* 2 and C4F ^* 3 C4S ^* 1 and the HLA loci. These findings may indicate that these C4 haplotypes were the original ones preceding the other C4 haplotypes.     

Ancestral and recombinant 16-locus HLA haplotypes in the Hutterites

 Prior studies in the Schmiedeleut Hutterites of South Dakota have demonstrated associations between human leukocyte antigen (HLA) haplotype matching and fetal loss (Ober et al. 1992) and mate preferences (Ober et al. 1997), as well as deficiencies of homozygotes for HLA haplotypes (Kostyu et al. 1993). These studies were based on the serologically-defined five-locus HLA-A, -C, -B, -DR, -DQ haplotype. To further elucidate the effects of specific major histocompatibility (MHC) loci or regions on fetal loss and mate choice, we genotyped a sample of Hutterites for 14 MHC loci by DNA or biochemical methods. Typing for additional loci in the HLA-A to HLA-DPB1 region increased the number of recognized Hutterite MHC haplotypes to 67, and further localized the site of cross-over in 9 of 15 recombinant haplotypes. Hutterite MHC haplotype sequences are similar to those observed in outbred Caucasians, suggesting that the influence of HLA haplotypes on fetal loss and mating structure may be general. Received: 1 May 1998 / Revised: 2 December 1998     

The study of a French family with two duplicated C4A haplotypes

Summary The finding of two duplicated C4A haplotypes in a normal French family led to a detailed study of their C4 polymorphism. The father had an extremely rare A^*6A^*11, B^* QO haplotype inherited by all of his children and the mother had the more common A^*3A^*2, B^*QO haplotype. Two HLA identical daughters only have four C4A alleles. The father's A11 allotype expresses Ch: 1 (Chido) rather than Rg:1 (Rodgers) and represents a new Ch phenotype Ch: 1,-2,-3,-4,-5,-6. In order to clarify the genetic background in this unusual family, DNA studies of restriction fragment length polymorphisms (RFLPs) were undertake. The father's rare haplotype, which expresses two C4A allotypes, results from a long and a short C4 gene normally associated with the A^*6, B^*1 that also exhibits the BglII RFLP. As it travels in an extended MHC haplotype HLA A2, B57 (17), C2^*C, BF^*S, DR7 that is most frequently associated with A^*6, B^*1, we postulate that the short C4B has been converted in the chain region to a C4A gene which produces a C4A protein. This report of a short C4A gene is the first example in the complex polymorphism of C4.     

TNFB polymorphisms characterize three lineages of TNF region microsatellite haplotypes

 The human major histocompatibility complex (MHC) contains a variety of genes, many of which are highly polymorphic and of immunological importance. A database of MHC extended haplotypes was used to integrate experimental, cell line, and population data. Three alleles of the human TNF-beta (lymphotoxin-alpha) gene were identified, named TNFB ^*1SL, TNFB ^*2LL, and TNFB ^*1LS, each representing a different lineage in the evolution of TNF region haplotypes. Lower variability in the length of the associated microsatellite alleles indicates that ^*1SL characterizes the youngest of the three haplotype lineages. Microsatellite haplotypes in the two older lineages show evidence for a coevolution of alleles through concerted expansions. Genetic predispositions to high and low TNF-alpha (cachectin) responses seem to have evolved independently in more than one lineage. The literature data suggest different, or even opposite, associations concerning the regulation of TNF-alpha in macrophages and lymphoid cells. Microsatellite ud may be the most informative marker for studies of the associations of individual TNF region markers with secretion levels, immunity, and disease. Received: 10 December 1996 / Revised: 21 May 1997     

Generation of the HLA-B35, -B5, -B16, and B15 groups of alleles studied by intron 1 and 2 sequence analysis

 HLA-B is the most polymorphic of the major histocompatibility complex classical class I loci. This polymorphism is mainly in exons 2 and 3, which code for the molecule’s α1 and α2 domains and include the antigenic peptide binding site. Recent studies have indicated that not only exons but also the intron 2 region may be involved in the generation of certain HLA-B alleles such as B ^* 3906 and B ^* 1522. To study the degree of intron 2 participation and the mechanisms that generate polymorphism at the HLA-B locus, intron 1 and 2 sequences from the HLA-B35, -B5, -B16 and -B15 groups of alleles were obtained. A group-specific intronic polymorphism was found: namely, B ^* 5301 shows intron 1 and 2 sequences identical to those found in all B35 alleles studied. On the other hand, B ^* 5101 and B ^* 52012 show the same intron 1 and 2 sequences and their intron 1 is the same as that found in the B35 group. This suggests that B5 and B35 groups of alleles may have arisen from a common ancestor. All known B16 alleles show the same introns 1 and 2, with the exception of B ^* 39061 and B ^* 39062, and all B15 alleles also bear the same introns 1 and 2, with the exception of B ^* 1522. Variability at intron 1 is more restricted than at intron 2, and the use of intron 1 for HLA-B allele phylogenetic analysis is better for grouping alleles of a postulated common origin. In conclusion, there is a remarkable conservation of intronic sequences within related HLA-B alleles, which probably reflects a common origin and perhaps a selective force avoiding DNA changes. Intronic sequences are also potentially useful to design DNA typing strategies. Received: 11 March 1997 / Revised: 29 May 1997     

Polymorphisms in the TNF gene cluster and MHC serotypes in the West of Scotland

 We examined the distribution of polymorphic elements within the tumor necrosis factor (TNF) gene cluster in 105 unrelated individuals and determined their relationship to class I and class II major histocompatibility complex (MHC) antigens, and to the highly polymorphic microsatellites TNFa and TNFb. The data demonstrate the contribution of elements within the TNF cluster to two extended haplotypes which are recognized to straddle the MHC. The A1.B8.DR3 haplotype appears to contain the TNF alleles TNFa2, TNFb3, LT.Nco-1.B ^* 1, and TNF-308.2, while the A3.B7.DR2 haplotype is associated with the TNF alleles TNFa11, TNFb6, TNFc1, LT.Nco-1.B ^* 2, LT.AspH1.1, TNF-308.1, and TNFe1. The presence of other extended associations which covered smaller parts of the MHC was also suggested. In most cases, the associations described here were in keeping with previously described extended haplotypes which dominate the structure of the MHC, but these did not always match completely. Taken together, these data suggest that the structure of the TNF locus is well integrated into the rest of the MHC but that important ethnic differences may exist. Received: 12 June 1996 / Revised: 27 September 1996     

An approach to mapping haplotype-specific recombination sites in human MHC class III

Studies of the major histocompatibility complex (MHC) in mouse indicate that the recombination sites are not randomly distributed and their occurrence is haplotype-dependent. No data concerning haplotype-specific recombination sites in human are available due to the low number of informative families. To investigate haplotype-specific recombination sites in human MHC, we here describe an approach based on identification of recombinant haplotypes derived from one conserved haplotype at the population level. The recombination sites were mapped by comparing polymorphic markers between the recombinant and assumed original haplotypes. We tested this approach on the extended haplotype HLA A3; B47; Bf ^* F; C4A ^* 1; C4B ^* Q0; DR7, which is most suitable for this analysis. First, it carries a number of rare markers, and second, the haplotype, albeit rare in the general population, is frequent in patients with 21-hydroxylase (21OH) defect. We observed recombinants derived from this haplotype in patients with 21OH defect. All these haplotypes had the centromeric part (from Bf to DR) identical to the original haplotype, but they differed in HLA A and B. We therefore assumed that they underwent recombinations in the segment that separates the Bf and HLA B genes. Polymorphic markers indicated that all break points mapped to two segments near the TNF locus. This approach makes possible the mapping of preferential recombination sites in different haplotypes.     

Major histocompatibility complex and alveolar epithelial apoptosis in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic disease characterized by fibroblast expansion, and tissue remodeling. It is considered a multifactorial disease but the possible involved genes are largely unknown. Interestingly, studies regarding the possible role of major histocompatibility complex (MHC) are scanty and show contradictory results. In this study, we evaluated the polymorphisms of the MHC, locus HLA-B, -DRB1, and -DQB1 in a cohort of 75 IPF patients and 95 controls by using PCR and hybridization with sequence-specific oligonucleotide probes. In addition, we examined the effect of bronchoalveolar lavage (BAL) from IPF patients with different MHC haplotypes on alveolar epithelial growth rate by WST-1 cell viability assay and on epithelial apoptosis by flow cytometry and by cleaved caspase-3 in cell homogenates. Three haplotypes were significantly increased in IPF: (1) HLA-B*15-DRB1*0101-DQB1*0501 (OR=10.72, CI=1.43–459.6; pC=0.011); (2) HLA-B*52-DRB1*1402-DQB1*0301 (OR=4.42, CI=1.21–24.1; pC=0.024); and (3) HLA-B*35-DRB1*0407-DQB1*0302 (OR=4.73, CI=1.53–19.5; pC=0.005). BAL from patients with the later haplotype significantly reduced epithelial growth rate (∼30%) and caused epithelial cell apoptosis assayed by cleaved caspase-3 (351.7±16.5 pg/10⁶ cells versus 264±24 from controls, and 274±36.8 and 256.5±10.7 from the other haplotypes; P<0.05), and DNA breaks labeling by flow cytometry (23.7±6.9% versus 3.1±0.7% from controls, and 6.5±0.6% and 7.6±1.2% from the other two haplotypes; P<0.01). These findings suggest that some MHC polymorphisms confer susceptibility to IPF, which might be related with the induction of epithelial cell apoptosis, a critical process in the development of the disease.     

Immunofixation for C2 typing: C2 allotypes in Spaniards in relation to HLA,Bf and C4

Summary C2 typing is performed by immunofixation with anti-C2 antiserum instead of by a hemolytic overlay. This method gives sharp band definition, is less cumbersome than the hemolytic overlay, gel files are easily made, and it also enables one to describe putative new nonhemolytic variants. C2 allele frequencies were studied in a sample of the normal Spanish population and were found to be similar to other Caucasoids. HLA-Bw62,-Cw3, and-DR4 were significantly associated with C2 B. Concordantly, the only C2^*B extended HLA haplotype found in family material was Bw62-Cw3-Bw6-(DR4)-Bf^*S-C2^*B-C4A^*3 B^*2-(GLO^*1). C4A^*4 B^*2 and C4A^*4 B^*4 are not found within the same haplotype together with C2^*B and Bw62 or Bw22 respectively, nor do other C2^*B haplotypes occur with common HLA-B alleles. These results may favour the hypothesis that the Bw62-C2^*B haplotype is produced by one mutation arising in the Bw62-C2^*C haplotype and that subsequent crossovers can explain other C2^*B haplotypes (including Bw22-C2^*B).     

High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program

Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20^th, 31^st, and 81^sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68^th, 79^th, and 95^th haplotypes), one was predominant in the South and Southwest China regions (the 18^th haplotype), one was relatively common in the Northeast and North China regions (the 94^th haplotype), and one was common in the Northeast, North and Northwest China (the 40^th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis studies.     

The Ap-Bp blood groups of baboons

Four isoimmunized baboons each produced isoantibodies defining a number of blood factors of baboon blood of which two, A^p and B^p, have been most intensively studied. The two blood factors determine the A^P-B^P blood group system which, judging from its serological behavior, may be the baboon analogue of the human M-N system and the chimpanzee V-A-B system. Tests for A^P-B^P types of 592 baboons showed striking differences in the distributions of the four types among the four sub-species, Papio cynocephalus, Papio anubis, Papio ursinus (South Africa) and Papio papio (Senegal). The baboon A^P-B^P types could also be demonstrated by tests on the red cells of geladas (Theropithecus gelada). If one assumes inheritance by multiple allelic genes, then the existence of only a single gene O^p need be invoked for Papio ursinus, three alleles O^p, A^p and B^p for Papio cynocephalus and Papio anubis, but four alleles for Papio papio including an allele, very frequent in that subspecies, which determines an agglutinogen having both blood factors A^p and B^p.     

Mhc-DRB diversity of the chimpanzee (Pan troglodytes)

Fifty-four chimpanzee Patr-DRB and five human HLA-DRB second exons were cloned and sequenced from thirty-five chimpanzees and four B-cell lines and compared with known Mhc-DRB sequences of these two species. Equivalents of the HLA-DRB1 ^* 02,-DRB1 ^* 03, -DRB1 ^* 07 allelic lineages and the HLA-DRB3,-DRB4, -DRB5, -DRB6, and -DRB7 loci were all found in the chimpanzee. In addition, two chimpanzee Patr-DRB lineages (Patr-DRBX and -DRBY) were found for which no human counterparts have been described. None of the Patr-DRB sequences is identical to known HLA-DRB sequences. The Patr-DRB1 ^* 0702 and HLA-DRB1 ^* 0701 alleles are the most similar sequences in a comparison between the two species and differ by only two nucleotides out of 246 sequences. Equivalents of the HLA-DRB1 ^* 01,-DRB1 ^* 04, and -DRB1 ^* 09 alleles were not found in our sample of chimpanzees. A per locus comparison of the number of Patr-DRB alleles with the HLA-DRB alleles shows that the Patr-DRB3, -DRB4, -DRB5, and -DRB6 locus are, thus far, more polymorphic than ther human homologs. The polymorphism of the Patr-DRB1 locus seems to be less extensive than that reported for the HLA-DRB1 locus. Nevertheless, the Patr-DRB1 locus seems to be the most polymorphic of the Patr-DRB loci. Phylogenetic analyses indicate that the HLA-DRB1 ^* 09 allele may have originated from a recombination between a Mhc-DRB5 allele and the DRB1 allele of a Mhc-DR7 haplotype. Although recombination seems to increase the diversity of the Patr-DRB alleles, its contribution to the generation of Patr-DRB variation is probably low. Hence, most Patr-DRB diversity presumably accumulated via recurrent point mutations. Finally, two distinct PAtr-DRB haplotypes are deduced, one of which (the chimpanzee equivalent of the HLA-Dr7 haplotype) is probably older than 6–8 million years.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide database and have been assigned the accession numbers Mg6074-Mg6132. Correspondence to: M. Kenter.     

A new<Emphasis Type="Italic"> DR7-DQ8</Emphasis> haplotype resulting from a recombination between the<Emphasis Type="Italic"> DQA1</Emphasis> and<Emphasis Type="Italic"> DQB1</Emphasis> loci in a leukemic patient of Caucasoid origin

Meiotic recombinations within the HLA-DR/DQ subregion are seldomly observed. However the high number of unusual DRB1-DQB1 allelic combinations underline the importance of crossover in shaping the class II haplotypic diversity. We present here the first report of a DQA1-DQB1 recombination event in a leukemic patient as detected by complete class II molecular typing of the family, including analysis of the DQCAR microsatellite. The recombination that occurred on the maternal chromosomes led to the unusual DR7-DQ8 haplotype characterized by the DRB1*0701-DRB4*01030102N-DQA1*0201-DQB1*0302 alleles. Because the patient had no HLA-identical sibling donor, a search for an unrelated hematopoietic stem cell donor was initiated. Out of three potential donors, only one HLA-A/-B/-C/DRB1-compatible but DQB1-mismatched donor could be identified.     

Haplotypes of the BoLA‐A,Bf, CYP21 and DQB loci in Angus cattle

Abstract

The genetic diversity of bovine major histocompatibility complex (BoLA) haplotypes within the Angus breed was studied. Four BoLA loci were chosen for our study; BoLA‐A, complement factor B (Bf), cytochrome P450 steroid 21‐hydroxylase (CYP21) and BoLA‐DQB. Polymorphism of BoLA‐A products was determined by serology. Alleles of the Bf, CYP21 and BoLA‐DQB loci were distinguished by restriction fragment length polymorphism (RFLP) analysis. Thirteen different haplotypes were identified, eleven of which were confirmed by segregation analysis in a paternal half‐sibling family of Angus cattle (n=9 offspring). These thirteen haplotypes were comprised of 9 BoLA‐A alleles and a “blank”, two Bf alleles detected with TaqI, two CYP21 alleles detected with PstI, and eight DQB alleles detected with Taql and PvuII. Two haplotypes containing the supertypic BoLA‐URAA specificity were clearly differentiated by Bf and DQB typing. Two haplotypes distinguished by the BoLA‐A alleles w2 and w3, shared the same DQB?2 allele. Nine and four haplotypes carried the Bf?1 and Bf?2 alleles, respectively. Three haplotypes carried CYP21?A and ten contained CYP21?B. Linkage between BoLA‐A and the CYP21 locus, both previously mapped to chromosome 23 by synteny mapping, was confirmed by segregation analysis. These results demonstrate that extended BoLA haplotypes are useful for studying genetic diversity within a breed.