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.

Typing of HLA-B*15 alleles using sequence-specific primers.

We have developed a DNA based typing method to detect 38 known B*15 alleles using sequence-specific primers (PCR-SSP). This method involves 38 primers and 39 PCR-SSP reactions with results that can be obtained in 3 hours. The method is easy, fast and suitable for clinical typing for bone marrow and organ transplantation. We have typed 106 HLA-B15 samples using this method. For homozygous HLA-B15 samples, some B*15 allele combinations need to be resolved by additional PCR reactions not included in this article. The method allows the detection of potential new alleles requiring sequencing for confirmation, and it is useful to resolve unusual serological reaction patterns for different HLA-B15 serological specificities. In addition, it could be used to resolve ambiguous PCR-SSOP typing results and for recognition of mismatches in serologically matched unrelated individuals.

Analysis of HLA-A and -B serologic typing of bone marrow registry donors using polymerase chain reaction with sequence-specific oligonucleotide probes and DNA sequencing.

Unrelated volunteer donors (69) recruited by the National Marrow Donor Program were HLA typed by DNA-based methods for both the HLA-A and -B loci. Each donor had been previously typed by serology by at least two independent laboratories. Of the 69 samples, all serologic laboratories were in concordance for HLA-A in 62 typed samples and for HLA-B in 48 typed samples. Of the serologically concordant samples, 5 samples typed for HLA-A and 7 samples typed for HLA-B received DNA and serology types differing in their level of resolution. One sample typed for HLA-A and 3 samples typed for HLA-B by DNA methods gave different results from their serologic assignments. Of the samples exhibiting disparities among the different serologic typing laboratories, the DNA-defined types of 7 samples typed for HLA-A and 18 samples typed for HLA-B were consistent with at least one of the serologic assignments. The DNA types for the remaining 3 HLA-B typed samples did not agree with the serologic assignments and their alleles were subsequently sequenced. One of these sequences was a previously undefined allele, B*1537. Sharing of polymorphic sequences among HLA allelic products creates difficulties for consistent serologic assignments of some types complicating the process of identifying potential donors from bone marrow registries. Thus, the use of DNA-based typing techniques for characterization of donor class I types should allow a more consistent definition of types and should speed the donor selection process.

Accurate typing of HLA-A antigens and analysis of serological deficiencies.

We are reporting the results of HLA-A typing by PCR-SSOP complemented by PCR-SSP of samples obtained from the National Marrow Donor Program (NMDP). These samples were a representative group from 2486 tested in duplicate by serology. A total of 390 samples gave HLA-A discrepant results. Comparing the molecular typing results of 238 samples (samples with available DNA) with the serological typing results, 54 homozygotes and 184 heterozygotes produced a total of 422 assignments by molecular methods. We found assignment discrepancies in 147/422 (35%) in laboratory 1 and 144/422 (34%) in laboratory 2 (a combined group of 4 NMDP laboratories; laboratory 1 is not included). The serological discrepancies found were of 3 categories: a) false negatives, b) incomplete typing (discrepancies due to the level of resolution within a cross-reactive or CREG group) and c) false positives. Major problems were identified using serology for typing HLA-A antigens: a) inability to identify all WHO-recognized specificities, more frequently in non-Caucasians or in HLA-A specificities known to be found more frequently in non-Caucasians for laboratory 1 and incorrect assignments of A19 specificities in laboratory 2, b) incorrect assignments in cells with poor viability and c) false-positive assignments in homozygotes. We propose a possible strategy to type HLA-A specificities with two steps: a) a minimum of serology for typing specificities for common CREG groups: A1, A2, A3, A11, A9, A10, A28, A19. However, a given laboratory can determine the level of serological assignments needed as a first step. And b) molecular methods to identify splits: A23, A24, A29, A30, A31, A32, A33, A34, A36, A66, A74 and A80. The technique described is useful for large-scale bone marrow donor typings for cells with poor viability, and for resolving ambiguous results including false-positive assignments of homozygous cells.

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.

New HLA-DR haplotypes containing the DRB6 pseudogene.

An unexpected probe reaction pattern was observed in two samples during HLA-DR typing by PCR-Sequence Specific Oligonucleotide Probes. In order to confirm the unusual typings, samples were analyzed by PCR-Sequence Specific Primers, cloning, and nucleotide sequencing of the second exon of the HLA-DRB-genes. The confirmed DR, DQ phenotype for one sample was DRB1*0701, DRB4*01, DRB5*0101, DRB6*0201, DQB*0602, DQB1*0202. The phenotype of other sample was DRB1*1602, DRB1*1302, DRB3*0301, DRB6*0101, DQB1*0501, DQB1*0502. The first sample has the novel combination of DRB1*0701 with DRB5*0101 and DRB6*0201. The second sample has either DRB6*0101 together with DRB1*1602 in absence of any DRB5 allele or DRB6*0101 together with DRB1*1302, DRB3*0301. We postulate that the most likely haplotype in sample #1 is DRB1*0701; DRB5*0101, DRB1*0602 which could have arisen from gene conversion. The most likely haplotype in sample #2, DRB1*1602, DRB6*0101, DQB1*0502 would have arisen from an homologous recombination event.

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.

Unrelated donor matching for bone marrow transplantation.

We found that in our laboratory the MLC was interpretable in most cases, in spite of patient disease state and shipping blood from unrelated donors over great distances. Our data clearly show that DRB1 allele typing was a good predictor of MLC reactivity and we believe that MLC testing in DRB1 allele mismatched unrelated pairs is not informative. However, our data suggest that MLC testing in DRB1 allele matched unrelated pairs is informative, because many such pairs produced weak but significant allostimulation. These weak MLC reactions may guide improvements in matching unrelated donors for BMT. For example, our MLC data suggest that it is important to match unrelated donors at DRB3 alleles for BMT.

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.

Complotypes in individuals of African origin: frequencies and possible extended MHC haplotypes.

We analyzed the frequency distribution of 106 complotypes [four allele sets of the major histocompatibility complex (MHC) genes for the complement proteins factor B, C2, C4A, and C4B] from 32 Black families residing in Boston and Washington, DC. Twenty-five different complotypes were identified, among which there were four complotypes that had not been previously observed in our large database of complotypes compiled from family studies of Boston Caucasians and that are, presumably, unique to individuals of African origin. These four African-derived complotypes are FC(1,90)0, FC63, S1C2, 17, and SC(3,2,90)0. The frequencies of two of these four unique Black complotypes, FC(1,90)0 and FC63, were increased significantly when compared to Caucasians (pcorr less than 0.00042, pcorr = 0.00294, respectively). The complotype FC(1,90)0 was in positive linkage disequilibrium with HLA-DR3 haplotypes containing the B locus antigens Bw42, Bw52, Bw53, and Bw58, while FC63 was associated with HLA-Bw70, -DR5. These findings demonstrate the extensive polymorphism of complotypes in Blacks, and also suggest that it may be possible to define unique extended haplotypes of African origin.

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.

Effects of frequent and sustained plateletapheresis on peripheral blood mononuclear cell populations and lymphocyte functions of normal volunteer donors.

Per procedure, plateletapheresis may remove 2 X 10(9) to 3 X 10(9) white cells from the peripheral blood of a normal donor. To investigate the effects of frequent and sustained plateletapheresis, multiple peripheral blood tests were performed on 25 volunteer donors undergoing plateletapheresis an average of 72 times over periods of up to 8 years, and results were compared with 25 age- and sex-matched controls who had not undergone apheresis. In donors, significant decreases were observed in: 1) both absolute number and percentage of T4+ cells; 2) absolute number of both T8+ cells and Leu-7+ cells; 3) T4/T8 ratio; 4) responses to both pokeweed mitogen and alloantigens; and 5) IgG levels. Significant increases were observed in percentages of both B cells and monocytes, and responses to both phytohemagglutinin and Concanavalin A. Plateletapheresis removes a large number of T4 and T8 cells, a moderate number of B cells, and a smaller number of monocytes and Leu-7 cells. The results suggest that during vigorous plateletapheresis the replenishment to peripheral blood per month was less than 1.83 X 10(9) and 0.93 X 10(9) for T4 cells and T8 cells, respectively, greater than 0.27 X 10(9) and 0.62 X 10(9) for B cells and monocytes, respectively, and approximately 0.39 X 10(9) for Leu-7 cells. Although no clinical effect was noted, these data suggest that frequent and sustained non-lymphocyte sparing plateletapheresis is associated with changes in laboratory findings related to the immune system.

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.