Resolution of HLA class I sequence-based typing ambiguities by group-specific sequencing primers.

The increasing demand for allele-level human leukocyte antigen (HLA) typing has led the sequence-based typing (SBT) to become the preferred method. In turn, the steady increase in the number of HLA alleles driven by the adoption of SBT as the ultimate typing method leads to the ever increasing number of cis/trans ambiguities. Over the last few years, additional sequencing with the commercially available group-specific sequencing primers (GSSPs) has replaced sequence-specific primer-polymerase chain reaction and group-specific amplification as the means of resolving cis/trans ambiguities in many laboratories. Here we summarize our 3-year experience in designing and utilizing GSSPs for resolution of HLA class I ambiguities. The panel of GSSPs used in our laboratory includes 14 primers for HLA-A, 18 for HLA-B, and 13 primers for HLA-C. The panel resolves 99.9% of all ambiguities.

New HLA-C alleles identified in minority populations.

Twenty new human leukocyte antigen C alleles identified in 2200 minority individuals characterized by sequence-based typing.

The recombinant HLA-B*5518 allele supports the evidence of conserved haplotype association of rare alleles.

Allelic polymorphism of the major histocompatibility complex arises mostly from gene recombination. Intralocus gene recombination usually involves short fragments of DNA leading most commonly to single-nucleotide substitutions and rarely involves large fragments. Here, we report a new recombinant human leukocyte antigen (HLA)-B*5518 allele that has arisen via recombination of a large fragment of DNA spanning more than 70 nucleotides. During routine HLA typing of potential volunteer donors for the National Marrow Donor Program((R)), a new HLA-B allele was identified in two donors from Guam. The allele, B*5518, appears to be a product of recombination between B*5502 and B*40. Exons 1, 3, and 4 of the new allele belong to B*5502, whereas part of exon 2 belongs to one of B*40 alleles. Introns 1 and 2 appear to belong to B*55, suggesting that the recombination event may have occurred within the homologous parts of exon 2.

HLA-Cw*1214 allele arisen via recombination between HLA-Cw*070201 and HLA-Cw*120201.

Allelic polymorphism of the major histocompatibility complex arises mostly from gene conversion. Intralocus gene conversion usually involves limited fragments of DNA, whereas recombination involving large fragments of DNA is considered to be a rare event. During routine sequencing-based typing of donors for the National Marrow Donor Program, a new HLA-C allele was identified in a Caucasian donor. The allele, HLA-Cw*1214, proved to be the product of recombination between HLA-Cw*070201 and HLA-Cw*120201. Exons 1, 2, the 3' end of exon 3 and exon 4 (with one mismatch) belong to HLA-Cw*120201, whereas part of exon 3 belongs to HLA-Cw*070201. Sequencing with primers based in exon 2 and exon 3 showed that intron 2 of the new allele also belonged completely to HLA-Cw*1202. The recombination event apparently occurred within exon 3 with the first point of recombination somewhere between codons 92 and 134 and the second one between codons 157 and 181.

Error rate for HLA-B antigen assignment by serology: implications for proficiency testing and utilization of DNA-based typing methods.

Until recently, the majority of HLA class I typing has been performed by serology. Expensive commercial typing trays are frequently used for testing non-Caucasian subjects and new strategies using DNA-based methods have been adopted for improving clinical histocompatibility testing results and adapted as supplements in proficiency testing. A double-blind comparison of the typing of HLA-B specificities in 40 samples was carried out between serology and two polymerase chain reaction (PCR) methods, PCR amplification with sequence-specific primers (PCR-SSP) and PCR amplification and subsequent hybridization with sequence-specific oligonucleotide probes (PCR-SSOP). The results demonstrated 22.5% misassignments of HLA-B antigens by serology. There was complete concordance between the results obtained with the two PCR based typing methods. A second panel of 20 donor samples with incomplete or ambiguous serologic results was analyzed by PCR-SSP and SSOP Both PCR methods identified correctly the HLA-B antigens. Our results suggest that more accurate typing results can be achieved by complementing serologic testing with DNA-based typing techniques. The level of resolution for HLA-B antigen assignment can be obtained by this combination of serology and limited DNA-based typing is equivalent to the HLA-B specificities defined by the WHO-HLA Committee. This level of resolution cannot routinely be achieved in clinical histocompatibility testing or in proficiency testing using serologic reagents only.

Comparison of HLA-A antigen typing by serology with two polymerase chain reaction based DNA typing methods: implications for proficiency testing.

Serology has been routinely used for class I HLA typing for the selection of donors for allotransplantation. However, serology is not adequate for the assignment of all class I specificities especially when testing non-Caucasians subjects and it is necessary to adopt new strategies for routine testing. At the present time the extent of incorrect serologic HLA-A assignments in clinical testing is not known. The polymerase chain reaction (PCR) based techniques have become useful standard clinical typing methods of HLA class II alleles but most laboratories still use serology for class I typing. In this report we have compared two PCR based techniques, PCR amplification with sequence-specific primers (PCR-SSP) and PCR amplification and subsequent hybridization with sequence-specific oligonucleotide probes (PCR-SSOP), for the assignment of HLA-A specificities in 56 blood samples from patients and families serologically typed for HLA-A. This side-by-side comparison of PCR methods showed 100% correlation between them. However, serology showed 7.1% misassignments and, in an additional panel of 19 cells where serology produced equivocal results, the PCR-SSP and SSOP methods identified the correct HLA-A specificity. Our results emphasize the need to complement routine serologic testing of HLA specificities with a small number of primers designed to test HLA-A34, A36, A43, A66, A74 and A80, that are not detected with high precision by serology. We concluded that the PCR-SSP and -SSOP methods can be used in routine HLA-A typing of patients and donors for transplantation with a greater precision than serology.

HLA-DQA1 and MLC among HLA (generic)-identical unrelated individuals.

We modified a previously published PCR-RFLP for DQA1 typing (1) and examined the predictive value of HLA-DQA1 in mixed lymphocyte cultures (MLC) among matched (HLA generic types) pairs of unrelated individuals. There were 61/102 (60%) pairs with positive MLC, one-third of which could be predicted by DQA1* typing alone. DQA1 matching and MLC reactions were classified into 3 groups: 1) DQA1 mismatches showing positive MLC: 19/102 (19%); 2) DQA1 matches showing negative MLC: 41/102 (40%); 3) DQA1 identical showing positive MLC: 42/102 (41%). Five different HLA haplotypes that result from non-random association of HLA generic types (high delta haplotypes) were overrepresented in the individuals tested. One of these haplotypes carrying HLA-B7, DR2 was found associated with three different DQA1 alleles (*0201, *0103, *0102). The remaining four high delta haplotypes were associated with one DQA1 allele in all independent examples tested: HLA-A1, B8, DR3 with DQA1*0501; HLA-A26, B38, DR4 with DQA1*0301; HLA-A2, Bw62, DR4 with DQA1*0301 and HLA-A1, Bw57, DR7 with DQA1*0201. Forty per cent of the negative MLC were explained in part by the excessive number of individuals carrying two of these four haplotypes, which probably carry determinants in linkage disequilibrium with HLA. Nineteen per cent of HLA-identical (generic types) unrelated pairs show positive MLC reactions and all of them are DQA1* mismatched, suggesting that DQA1* allele typing should be used to screen samples prior to performing MLC.

HLA-DPB1 allele mismatches between unrelated HLA-A,B,C,DR (generic) DQA1-identical unrelated individuals with unreactive MLC.

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.

HLA-DQ RFLP variants of five HLA-DQw2-bearing major histocompatibility complex extended haplotypes.

We have analyzed genomic DNA in a large number of independent examples of five HLA-DQw2-bearing extended haplotypes for their associated subtypes by restriction fragment length polymorphism (RFLP) using DRB, DQA, and DQB probes after Taq I and Pst I digestion and Southern blotting. In addition to three previously described HLA-DQw2 subtypes, DQw2a, DQw2b, and DQw2c, we observed a fourth subtype, HLA-DQw2d, characterized by 5.8 kilobase (kb) DRB/Taq I, 2.4, 2.3, and 1.8 kb DQB/Taq I, and 8.0 and 2.3 kb DQA/Pst I fragments. All 22 independent examples of the extended haplotype [HLA-B8, SC01, DR3] carried DQw2a and all 11 independent examples of [HLA-B18, F1C30, DR3] carried DQw2b. In addition, all independent examples (21 and 4, respectively) of two DR7-carrying extended haplotypes, [HLA-B44, FC31, DR7] and [HLA-Bw47, FC91,0,DR7], carried DQw2c and all independent examples of [HLA-Bw57, SC61, DR7] carried DQw2d. Our results show that the DNA in the DR/DQ region of extended haplotypes is relatively fixed and that different DQw2 subtypes characterize different DQw2-bearing extended haplotypes.

Characterization of HLA-Bw73 by serology and one-dimensional isoelectric focusing patterns.

The HLA-Bw73 antigen has been characterized by antisera in the Ninth International Histocompatibility Workshop. The International Workshop antibodies 9w245, 9w246, and 9w247 detected HLA-B7 and one or more antigens of this group (HLA-B40, Bw22, Bw42, or Bw48) in addition to HLA-Bw73. We have serologically characterized three additional antibodies, in two family studies, which contain anti-Bw73 (two of the antisera also contain anti-B7 activity). We have performed absorption studies with the three antisera, which indicate that anti-Bw73 activity is removed by HLA-B7 positive lymphocytes in two of the antisera and that, in one case, anti-B7 activity is removed by HLA-Bw73 positive HLA-B7 negative lymphocytes. The third antiserum is cytotoxicity negative absorption positive for HLA-B7. Neither HLA-B27 positive nor HLA-B8 positive lymphocytes removed any antibody activity. Using one-dimensional isoelectric focusing, unique bands have been characterized for over 30 Caucasian allotypes, including HLA-B7 and HLA-B27. Lymphocytes from two families carrying the HLA-Bw73 antigen were analyzed by isoelectric focusing. These two families show that HLA-Bw73 has a band migrating in the gel very close to HLA-B35 but distant from the cross-reactive group HLA-B7. These studies indicate that HLA antigens which share common epitopes (including those recently characterized, such as HLA-Bw73 and HLA-B7), can be distinguished serologically and by isoelectric focusing.

Unrelated individuals matched for MHC extended haplotypes and HLA-identical siblings show comparable responses in mixed lymphocyte culture.

Extended haplotypes are specific HLA B, HLA DR, BF, C2, C4A, and C4B combinations in significant linkage disequilibrium in chromosomes of unrelated individuals. The possibility that matching unrelated individuals for extended haplotypes may match for the genes that cause mixed lymphocyte reactivity was tested. 22 of 26 unrelated extended-haplotype-matched subjects had similar mixed lymphocyte reactivity to HLA-identical siblings.

HLA antigens of insulin-dependent diabetics. I. PLT colonies detecting Dw10 and a new class II determinant distinct from HLA-D, DR, MB(DC), MT, and SB.

We describe three human proliferating T cell colonies, derived from mixed leukocyte culture with a non-diabetic individual (DR3 + 4) as the source of responding cells and an insulin-dependent diabetic patient (also DR3 + 4) as the source of stimulating cells. One colony detects HLA-Dw10 or a closely related antigen, and two detect an antigen that we call BO1 (Boston 1). BO1 is found so far on cells of all persons with DR5, about half of those with DRw6, and a particular subset of those with DR3. Among DR3-positive subjects, BO1 is positively correlated with HLA-B18 and BfF1, and negatively correlated with HLA-B8. These findings suggest that BO1 occurs in linkage disequilibrium with DR5, DRw6, and the haplotype B18, BfF1, DR3, the latter being common in southern Europe and reported previously to be a marker for insulin-dependent diabetes. In limited testing (21 subjects), BO1 was completely included in the supertypic specificity MT2, BO1 is a Class II HLA antigen, as demonstrated by blocking with monoclonal antibodies, but is distinct from all known antigens of the DR, MB(DC), MT, and SB series. It could be located on the same polypeptide chain as one or more of these antigen groups, however, particularly DR and/or MT.

Linkage disequilibrium of HLA-SB1 with the HLA-A1, B8, DR3, SCO1 and of HLA-SB4 with the HLA-A26, Bw38, Dw10, DR4, SC21 extended haplotypes.

Homozygous typing cells from 13 normal HLA-A1, B8, Dw3, DR3 and five normal HLA-A26, Bw38, Dw10, DR4 individuals were typed for the following markers: HLA-SB, MB, MT; complement proteins BF, C2, C4A, C4B; and GLO. Ninety-one percent of A1, B8, Dw3, DR3 homozygous individuals (HI) tested were homozygous for BF*S, C2*C, C4A*QO, and C4B*1 (SCO1 complotype), which indicates that the SCO1 complotype is in linkage disequilibrium with the A1, B8, DR3 haplotype in randomly selected normal populations. Sixty-seven percent of HLA-A1, B8, Dw3, DR3, SCO1 positive HI also expressed SB1; since the frequency of SB1 in random Caucasian populations is 11.2%, this finding indicates that SB1 is in linkage disequilibrium with the A1, B8, DR3, SCO1 extended haplotype. All HI with the A26, Bw38, Dw10, DR4 haplotype were homozygous for both SC21 and SB4, suggesting that SC21 and SB4 should be included in the A26, Bw38, Dw10, DR4 extended haplotype. On the other hand, neither of the GLO markers were found in association with either haplotype. The results of this study indicate that HLA-SB is included in some extended haplotypes and may be important in these markers for diseases such as insulin-dependent diabetes mellitus. This study also demonstrated an apparent influence of HLA-SB on primary mixed lymphocyte culture (MLC) responses. The mean relative response of primary MLCs between individuals matched for HLA-A, B, D, DR, MB and MT but not SB was 40% of that for the MLCs with mismatched HLA-D, significantly higher than the MLCs matched for all HLA and complotypes.

Extended MHC haplotypes in 21-hydroxylase-deficiency congenital adrenal hyperplasia: shared genotypes in unrelated patients.

HLA, complement, and glyoxalase I alleles were studied in 29 families in which at least one member has classical 21-hydroxylase-deficiency congenital adrenal hyperplasia. A rare complement allele, C4B*31, was found in over 20% of the haplotypes defined in these families and was always part of the complement haplotype BF*F, C2*C, C4A*Q0, C4B*31 (abbreviated FCO,31). The haplotype containing this rare set of complement alleles always carried the rare HLA allele, HLA-Bw47, usually carried HLA-A3, and almost always had the alleles HLA-Cw6, HLA-DR7, and the glyoxalase I (GLO) allele GLO1. Thus over 20% of the haplotypes in the population studied contained all or almost all of the rare extended haplotype HLA-(A3), Bw47, Cw6,DR7, FCO,31, GLO 1. 3 other haplotypes were each found twice in unrelated patients concordant for their disease phenotype and ethnic background. Extended MHC haplotypes may be markers for different genetic mutations causing 21-hydroxylase deficiency.