Oligonucleotide-genotyping as a method of detecting the HLA-DR2 (DRw15)-Dw2, -DR2 (DRw15)-Dw12, -DR4-Dw15, and -DR4-D"KT2" haplotypes in the Japanese population

Genetic analysis of hydatidiform moles utilizing the oligonucleotide-DNA typing of the HLA-DRB gene

The genetic origin of hydatidiform moles was analysed utilizing HLA-DNA typing. Using HLA-DR type-specific oligonucleotide probes, the DRB types of seven moles were determined and compared with the parental DRB types to determine the paternal and/or maternal origin of the moles. In four cases, the molar tissues showed single DRB types of paternal origin, although in one, the molar DRB type was also possessed by the mother. These four moles were, therefore, considered to be androgenetic in origin. Chromosomal karyotyping was carried out for three of these cases and confirmed the DR-DNA typing results. Two moles demonstrated a DRB-type triplet, which strongly suggested triploidy. Although one mole showed a heterozygous DRB type, karyotyping indicated triploidy (69, XXX) and suggested that this mole was caused by dispermy-fertilization, in which both of the sperms had the same DRB type. Although the majority (about 80%) of partial hydatidiform moles have been reported to be triploid as a result of dispermy, four of the moles analysed in this study (cases 1, 2, 3 and 4), diagnosed as partial macroscopically and/or histopathologically, were found to be androgenetic in origin using karyotyping and DR-DNA typing. Therefore, HLA-DR DNA typing, combined in some cases with karyotyping, provides an accurate method for diagnosing androgenesis and triploidy in complete and partial hydatidiform moles.

Rapid DNA typing utilizing immobilized oligonucleotide probe and a nonradioactive detection system. Application to HLA-DR typing of the Japanese population

We established a rapid and simple method of HLA-DR genotyping, and applied it for analysis of the Japanese population. Our method includes rapid preparation of DNA samples from buccal mucosa, incorporation of biotin-dATP into DRB genes during amplification by the polymerase chain reaction, hybridization with sequence-specific oligonucleotide (SSO) probes immobilized on nylon membranes via poly (dT) tails, and detection of the hybridization signal as chemiluminescence. We carried out DR typing of 30 Japanese donors using 20 different immobilized SSO probes, and obtained unambiguous typing signals showing perfect correlation with their serologic DR types. The genotyping also enabled us to identify several DR types unique to the Japanese population, such as DRw12b (DRB1*1202), DRw14c (DRB1*1405), and serology blank type, DR'JX6' (DRB1*1403). The method presented here would be suitable for routine DR typing in tissue-typing laboratories.

Analysis of HLA-DR types of unexplained recurrent spontaneous aborters in the Japanese population by oligonucleotide-DNA typing

To examine whether unexplained recurrent spontaneous abortion (URSA), defined as 2 or more consecutive spontaneous abortions, is correlated with a particular DR type in the Japanese population, we determined the HLA-DR types of 82 primary aborters and 21 secondary aborters by DNA typing utilizing the polymerase chain reaction (PCR) and hybridization with sequence-specific oligonucleotides (SSOs). The DR gene frequencies of the patient group were compared with those of a normal group at three different levels of DR-definition (27, 13 and 11 DR types). At none of the three levels of comparison was any particular DR type with a frequency differing significantly between the patient and normal groups detected in Japanese URSA patients. Furthermore, we examined whether URSA was correlated with the degree of compatibility of HLA-DR antigen within patients and their husbands. Comparison of the DR compatibility between patients and normal couples was made in two different ways, i.e., comparison of the numbers of couples with mismatches and comparison of the average number of mismatches. For either of these two comparisons, we observed no difference in DR compatibility between patients and normal couples. Our results suggest that URSA is not correlated with any particular DR type and that the condition cannot be explained simply by DR compatibility between husband and wife.

Molecular characterization of a recombinant HLA-DR1/DR2 haplotype

Serologic analysis of two families identified an HLA-DR haplotype in which DR1 and DR2 cosegregated. DNA-RFLP analysis of these families with an HLA-DRB probe revealed a pattern of hybridization suggestive of a recombination between DR1 and DR15. Following amplification, cloning, and nucleotide sequencing of HLA-DRB-gene second-exon DNA sequences, three DRB amplification products associated with the novel haplotype were identified: these corresponded to DRB1*0101, DR2 pseudogene, and DRB5*0101. Clones representing the DRB1*1501 and DR1 pseudogenes were not identified: oligonucleotide typing with DRB1*1501-specific probes confirmed the absence of this gene within the DR1/DR2 haplotype. We postulate that the DR1/DR2 haplotype represents a recombinant between those of DR1-Dw1 and DR15-Dw2, and that the crossing-over may have been between the DRB1*0101 gene and the DR2 pseudogene. This is further supported by DNA-RFLP analysis with HLA-DQB and DQA CDNA probes, which revealed conserved linkage genes between the DQB1*0501, DQA1*0101, and DRB1*0101 genes.

HLA-DR gene frequencies in the Japanese population obtained by oligonucleotide genotyping

We determined HLA-DRB types of 375 randomly chosen healthy Japanese donors using a set of 29 different sequence-specific oligonucleotide (SSO) probes directed against various DRB alleles. Except for a few cases, these SSOs enabled us to identify 33 different DRB types including those detectable only by SSO genotyping. Gene frequencies were calculated for each of the DRB types identified. The "blank" frequency calculated by our SSO typing was essentially zero, in contrast to the considerably high "blank" frequencies reported at serological HLA-DR or cellular HLA-D workshops. This indicates that almost all of the DRB types in the Japanese population are positively detectable by our SSO typing. By comparing the gene frequencies for each of the DR types obtained by our SSO typing with those obtained by immunological typing at workshops, significant differences were observed for several of the DR types.

Modified PCR-RFLP method for HLA-DPB1 and -DQA1 genotyping

We previously developed a new technique for HLA class II genotyping by digestion of polymerase chain reaction-amplified genes with restriction endonucleases (PCR-RFLP method). This PCR-RFLP method is an efficient and convenient typing technique for class II alleles. However, small fragments or bands located close to each other on polyacrylamide gels sometimes prevent precise analysis of the RFLP bands. Furthermore, the restriction enzymes we have reported in the previous papers are not sufficient to identify the genotypes of all heterozygous individuals. Here, we report an improved PCR-RFLP method using some informative restriction enzymes which have either a single cleavage site or, alternatively, no cleavage site in the amplified DNA region, depending on the HLA alleles, making reading of RFLP band patterns much easier. Each second exon of the HLA-DQA1 or -DPB1 gene was selectively amplified from genomic DNAs of 70 HLA-homozygous B-cell lines and 100 healthy Japanese by PCR. Amplified DNAs were digested with restriction endonucleases and then subjected to electrophoresis assaying simply for cutting, or no cutting, of the DNA. ApaLI, HphI, BsaJI, FokI, MboII and Mn1I can discriminate eight alleles of the DQA1 gene. Similarly 19 alleles of the DPB1 gene can be discriminated with Bsp1286I, FokI, DdeI, BsaJI, BssHII, Cfr13I, RsaI, EcoNI, and AvaII enzymes. This modified PCR-RFLP method can be successfully applied to heterozygotes. Thus, the method is technically simpler and more practical for routine HLA typing work than our previous PCR-RFLP method.

HLA-DQB1 genotyping by a modified PCR-RFLP method combined with group-specific primers

We previously reported a simple technique for HLA-DQB genotyping by digestion of polymerase chain reaction-amplified genes with restriction endonucleases (PCR-RFLP method). However, this method has some problems in that some heterozygotes cannot be discriminated from each other. Furthermore, concomitantly amplified product derived from the DQB2 gene by the primers used previously also obstructs precise DQB1 genotyping. To resolve these problems, we have developed two different pairs of specific primers for selective amplification of the DQB1 gene and also used restriction endonucleases which have either a single cleavage site or, alternatively, no cleavage site in the amplified DNA region, depending on the HLA-DQB1 alleles, making reading of RFLP band patterns much easier. The second exon of the DQB1 gene was selectively amplified by DQw1 group-specific primers and/or DQw2,3,4 group-specific primers using genomic DNAs from 70 HLA-homozygous B-cell lines and 50 healthy Japanese. Of the seven DQw1-associated DQB1 alleles, six alleles could be defined by digestion of 6 restriction enzymes, although DQB1*0602 and DQB1*0603 could not be discriminated from each other because of unavailability of suitable enzymes. Similarly, all of the six DQw2,3,4-associated DQB1 alleles could be defined by digestion of 5 restriction enzymes. Using this modified PCR-RFLP method, complete DQB1 genotyping of all heterozygotes is possible except for discrimination between DQB1*0602 and 0603. Thus this method is simpler and more practical for a routine DNA typing than the PCR-SSO method or our previous PCR-RFLP method.

Discrimination between HLA-DR1 (DRB1*0101) and DR'Br' (DRB1*0103) using sequence-specific oligonucleotide probes

Serological identification of the HLA-DQw1(w5)-associated or HLA-DQw3(w7)-associated DR'Br' (DRB1*0103) allele cannot be accomplished in the presence of a second DQw1(w5)-positive or DQw3(w7)-positive haplotype, respectively. DNA-restriction fragment length polymorphism (RFLP) analysis assists in identification of DR'Br', though not in the presence of DR1. We describe an alternative or complementary method for identification of DR'Br' using two oligonucleotide probes which target HLA-DRB1 gene HV3 regions.

Sequence analysis and oligonucleotide genotyping of HLA-DR"JX6", a DR"blank" haplotype found in the Japanese population

We analyzed one of the HLA-DR"blank" haplotypes found in the Japanese population using serologic studies, sequence determination, and genotyping with sequence-specific oligonucleotide (SSO) probes. The DR"blank" haplotype, designated DR"JX6", segregated in a family in association with the DRw52 and the DQw7 specificities. The cDNA and genomic DNA of the DRB1 gene originating from the DR"JX6" haplotype were amplified enzymatically and sequenced after cloning into a plasmid vector. The amino acid sequence of the first domain in the DR beta 1 chain of the DR"JX6" haplotype was different from those of other DR haplotypes sequenced so far, but in the first hypervariable region, the sequence was identical to those of the DRw11, DRw13, DRw14, and DRw17 haplotypes. SSO probes were synthesized on the basis of the DR"JX6" haplotype sequence as well as known sequences of the DRB1, DRB3, and DRB4 genes of other DR haplotypes. These SSO probes were used for the genotyping of Japanese donors whose DRB genes were amplified enzymatically and found to show a hybridization profile that was consistent with the results of serologic studies on the DR"JX6" haplotype.

Two distinct subtypes of the HLA-DRw12 haplotypes in the Japanese population detected by nucleotide sequence analysis and oligonucleotide genotyping

We determined the DNA sequence of the enzymatically amplified second exon of the DRB1 gene of the Drw12 haplotypes derived from three Japanese donors and found two distinct subtypes of the DRw12 haplotype. The two subtypes, designated DRw12a and DRw12b, had single-base substitutions that predicted one amino acid change at residue number 67. The sequence of the DRw12a and DRw12b subtypes differed from those of the other DR haplotypes, but in the first hypervariable region of the DRB1 gene the sequences were identical to those of the DRw8(Dw8.1) and DRw8(Dw8.3) haplotypes. The DRw12a and DRw12b subtypes were detected in a wide range of Japanese donors by genotyping with sequence-specific oligonucleotide probes synthesized according to the DNA sequences of the two subtypes. Results of this study demonstrated that the DRw12 haplotypes in the Japanese population are genetically diverse, as many other DR haplotypes are.