PCR／SSCP技术在检测HLA基因点突变中的应用

聚合酶链反应－单链构象多态性（ＰＣＲ／ＳＳＣＰ）是根据核苷酸序列不同的单链ＤＮＡ，可形成不同构象，从而在不含变性剂的聚丙烯酰胺凝胶中泳动速度不同的原理，分离鉴定等长ＤＮＡ单链的方法，本文应用ＰＣＲ／ＳＳＣＰ方法检测了６０例无亲属关系个体白细胞抗原Ⅱ类基因（ＨＬＡ－ＤＱＡ１）５－上游调控区的等位基因多态性，并以ＰＣＲ直接测序证明每种ＳＳＣＰ带型都与不同位置单个碱基取代相关联。     

上海地区汉族人HLA—DQA1启动子多态性以及QAP,DQA1单元型 …

目的：分析上海地区汉族人ＨＬＡ－ＤＱＡ１启动子（ＱＡＰ）多态性,以及ＱＡＰ与ＤＱＡ１的连锁关系。方法：采用ＰＣＲＲＦＬＰ分析ＤＱＡ１等位基因多态性;采用ＰＣＲ－ＳＳＯ检测ＱＡＰ多态性。结果：在９６个个体中检测到９种ＤＱＡ１启动子（ＱＡＰ）等位基因。ＱＡＰ与ＤＱＡ１之间有３种连锁格局：①ＱＡＰ与ＤＱＡ１存在一对一关系;②一种ＱＡＰ可与不同的ＤＱＡ１组成多种单元型;③一种ＤＱＡ１等位基因可受到多种类型     

维吾尔族人群抗原处理相关转运体（TAP）基因多态性及与类风湿...

目的：探讨新疆维吾尔族人群抗原处理相关转运体（ＴＡＰ）基因多态性及与类风湿关节炎（ＲＡ）的相关性。方法：采用ＰＣＲ－ＡＲＭＳ，－ＲＦＬＰ，－ＳＳＯＰ检测ＲＡ患者３９例及健康献血者４１例ＴＡＰ１－３３３和６３７位，ＴＡＰ２－３７９、５６５、６５１、６６５、６８７等位氨基酸等位基因多态性。结果：健康维吾尔族人群ＴＡＰ１－３３３位和６３７位等位基因基因型分别以Ｉ和Ｄ为主，表现型以Ｉ和Ｄ为主，表现型主要为     

HLA－DPB131个等位基因的PCR－RFLP高分辨分型

本文报道建立了一种基于ＰＣＲ－ＲＦＬＰ技术的ＨＬＡ－ＤＰＢ１分型方法。经计算机分析而选出１０个限制性内切酶，在３１个ＤＰＢ１等位基因组成的４９６个ＤＰＢ１基因型中，可唯一性分辨４８４个。用于确定ＤＰＢ１基因型的３３个多态性酶切片段有２９个在８种纯合／杂合子分型细胞ＤＮＡ的ＤＰＢ１分型中得到验证。经研究来自十个家系２３人的ＤＰＢ１等位基因分布，证实在等位基因和杂合性多态片段的分布上均符合孟德尔分离律。与目前其他ＰＣＲ－ＲＦＬＰ和ＰＣＲ－ＳＳＯＤＰＢ１分型系统比较，本分型系统在分辨的ＤＰＢ１等位基因数目和唯一性反应格局率方面居于领先，特别适用于异基因骨髓移植供者的选择。     

早衰蛋白-1基因内含子多态性与Alzheimer's病的关系

为探讨早衰蛋白－１（ＰＳ－１）基因多态性与Ａｌｚｈｅｉｍｅｒ’ｓ病（ＡＤ０的关系,用聚合酶链反应－限制性片段长度多态性（ＰＣＲ－ＲＦＬＰ）方法检测５１例散发性ＡＤ患者ＰＳ－１外显子８的３‘端内含子基因型,其中４０例晚发性ＡＤ患者,同时检测８７６例健康对照者ＰＳＤ－１基因型。结果发现散发性ＡＤ组１／１基因型和１等位基因频率分别为０．５１０和０．６９６,显著高于对照组的０．２９９和０．５２２;晚发性Ａ     

用PCR—RFLP方法调查上海汉族人群中HLA—DP多态性

用聚合酶链反应－限制性内切酶片段长度多态性（ＰＣＲ－ＲＦＬＰ）技术对１５０名上海地区健康汉族人所作的ＨＬＡ－ＤＰ分型，结果在本群体中共检出２种ＤＰＡ１和１２种ＤＰＢ１等位基因。ＤＰＡ１０１和ＤＰＡ１０２频率分别为３１％和６９％。在ＤＰＢ１等位基因中，以ＤＰＢ１０５０１（３８．６７％），０２０１（１７．３３％），０４０２（１１．６７％）和０４０１（１０．６７％）最为常见。对不同人种中ＨＬＡ－ＤＰ分布特点加以比较，并对ＰＣＲ－ＲＦＬＰ技术在ＨＬＡ－ＤＰ分型应用中的优点进行了讨论。     

Wilson病家系ATP7B基因第18外显子突变及多态

目的：检测中国人Ｗｉｌｓｏｎ病（ＷＤ）基因的第１８外显子（ｅｘｏｎ１８）突变及多态。方法：应用多聚酶链反应－单链构象多态性（ＰＣＲ－ＳＳＣＰ）技术，分析１６个ＷＤ家系５４例个体和１８例正常人ＡＴＰ７Ｂ基因ｅｘｏｎ１８分子结构改变。结果：在ＷＤ家系中发现有３种单链构象，其中１种为正常构象，１种为突变，另１种可能为正常ＤＮＡ多态；１７例ＷＤ患者及其３７例一级亲属中分别检出突变者１０例和１１例，突变率分别为２９．４％和１４．９％。其中一级亲属检出的突变者中有３例经血清铜氧化酶及眼科Ｋ－Ｆ环检查证实为ＷＤ症状前患者。结论：ｅｘｏｎ１８是中国人ＷＤ基因突变热点之一，大多数ＷＤ患者为复合杂合子；应用ＰＣＲ－ＳＳＣＰ技术分析ｅｘ－ｏｎ１８是一种有效的ＷＤ基因筛选方法，也可为无家族史的ＷＤ可疑者提供诊疗依据     

用PCR—RFLP方法检测动脉硬化性脑梗死患者的载脂蛋白E基因多态性分布

目的 研究动脉硬化性脑梗死（ＡＣＩ）患者中的载脂蛋白Ｅ（ＡｐｏＥ）基因的分布。方法 利用聚合酶链式反应（ＰＣＲ）技术扩增ＡｐｏＥ基因含编码１１２位和１５８位氨基酸的片段，并用限制性片段长度多态性（ＲＦＬＰ）技术对ＡＣＩ患者和相应健康对照的ＡｐｏＥ基因进行分型，从而进行ＡＣＩ与ＡｐｏＥ等位基因多态性的关联分析。结果 ＡＣＩ患者中ＡｐｏＥ等位基因ε４占２８．３０％，明显高于正常人对照组的７．６４％，而等位基因ε３则占５７．５５％，低于正常人对照组的８４．１２％，均有极显著性差异（ｐ〈０．０１）。结论 ＰＣＲ－ＲＦＬＰ是一种快速有效的ＡｐｏＥ基因分型方法，ε４可能为ＡＣＩ的易感因子，而ε３则为保护因子。     

用于研究DLA－DRB1基因分型的寡核苷酸引物对的选择

我们用ＰＣＲ－ＲＦＬＰ法研究ＤＬＡⅡ类基因。为寻找合适的引物，用四对不同的引物：ＤＬＡ－ＤＲ－ＳＰ／Ｓｔｏｐ，ＤＬＡ－ＤＲ－ＳＰ／Ｐ３，ＨＬＡ－ＤＲＢ－ＧＨ４６／５０及ＨＤＡ－ＤＲＢ－ＡＭＰ－Ａ／Ｂ进行了一系列扩增。只有引物对ＨＬＡ－ＤＲＢ－ＡＭＰ－Ａ／Ｂ获得了满意的结果。其类似核苷酸序列在ＤＬＡ－ＤＲＢｃＤＮＡ的核苷酸序列内被发现，特异性也为Ｓｏｕｔｈｅｒｎｂｌｏｔ杂交分析所证实。内切酶ＨａｅⅢ和ＨｉｎｆⅠ酶解后显示出ＤＬＡ－ＤⅡ类基因高度的多态性和等位基因特异的多态性带型。揭示该引物对是目前用ＰＣＲ－ＲＦＬＰ法研究ＤＬＡ－ＤＲＢ１基因较理想的、实用的引物。     

T细胞识别HLA—DRB1＊0901分子显示TCR BV基因取用的高 …

目的 分析ＤＲ９纯合细胞刺激下ＤＲ９阴性正常人ＴＣＲ ＢＶ基因片段的取用格局,确定和分离出ＤＲ９关联性疾病中的自身反应性Ｔ细胞史隆。方法 常规方法获取ＰＢＭＣ经ＰＣＲ－ＳＳＯ和ＰＣＲ－ＲＦＬＰ ＤＮＡ分型,确定ＤＲ、ＤＱ、ＤＰ等位基因后,进行单向混合淋巴细胞培养,抽提总ＲＮＡ并合成北一链ｃＤＮＡ,定量ＰＣＲ检测２２种ＴＣＲ ＢＶ 基因片段的取用格局。结果 Ｔ细胞对ＤＲ９分子的识别和扩增具有寡克隆笥     

Three new DP alleles identified in a study of 800 unrelated bone marrow donor-recipient pairs

HLA-DP genotyping of 800 unrelated donor-recipient pairs in phase 5 of a retrospective analysis of unrelated bone marrow transplantation, sponsored by the National Marrow Donor Program (NMDP), has identified two new DPB1 alleles (DPB1*8701 and DBP1*8801) and one new DPA1 (DPA1*0108) allele. Sequencing confirmed that all three of these new alleles represent novel combinations of previously described sequence motifs, reinforcing the notion that "gene conversion-like" events play an important role in generating HLA allelic diversity. The identification of these new alleles brings the total number of DPA1 alleles to 20 and the total number of DPB1 alleles to 94.     

Polymerase chain reaction--single-strand conformation polymorphism analysis of polymorphism in DPA1 and DPB1 genes: a simple, economical, and rapid method for histocompatibility testing.

A new technical trial was carried out to detect polymorphism in HLA-DP genes, based on the diversity in electrophoretic mobility of single-stranded DNA (single-strand conformation polymorphism, SSCP). Genomic DNAs from 31 cell lines homozygous for 2 and 14 different DPA1 and DPB1 alleles, respectively, and from peripheral blood cells of a normal individual homozygous for another DPB1 allele were subjected to polymerase chain reaction (PCR) to amplify the polymorphic exon 2 of DPA1 or DPB1 genes. The PCR samples were denatured by heating in the presence of formamide to obtain single-stranded DNA, electrophoresed in a neutral polyacrylamide gel, and visualized by silver staining. Allelic differences were detected by the distinctive electrophoretic pattern of each single strand, depending on the sequence-specific conformation. Fifteen DPB1 alleles showed 11 distinct electrophoretic patterns, leaving four allelic combinations not distinguished. These four allelic combinations could be further distinguished by using another couple of primers in PCR, with which a part of the exon was amplified, and by subsequent SSCP analysis. The use of four pairs of primers in PCR allowed for discrimination of all the 15 DPB1 alleles tested. Two allelic differences in exon 2 of DPA1 gene could be clearly demonstrated. In addition, putative new alleles of DPA1 and DPB1 genes were detected by SSCP analyses. The PCR-SSCP analysis is simple and rapid, requires neither radioactive materials nor restriction enzymes, and is expected to be a useful tool for investigating the fine HLA-matching required for clinical transplantation of organs.     

DPB1 LOCUS PCR-RFLP TYPING OF THE FOURTH ASIA-OCEANIA HISTOCOMPATIBILITY WORKSHOP CELL PANEL REVEALS A NOVEL DPB1 ALLELE

DPB1 locus typing of the 155 cell 4AOHW panel was performed using a PCR-RFLP method. Ambiguity of allele assignment was resolved by amplification using sequence-specific primers. Of the 150 cells for which typings were achieved, three exhibited unusual restriction enzyme fragment patterns, suggesting the possibility of novel DPB1 alleles. Sequence analysis revealed one allele present in the currently reported 46, one novel allele (4AOHW/107) not present among the 46, and one from a non-human primate which is being investigated. Twenty-six (26) of the 34 10IHW cells have been studied previously by cDNA RFLP, and strong haplotypic associations have been demonstrated between DPA1 and DPB1 locus alleles. It is proposed that exploitation of intron polymorphisms marking haplotypes will be an integral part of future DPB 1 typing as a ‘first-pass’ stratification process to minimize the requirement for sequence-based methods to definitively assign DPB 1 alleles.     

Matching for HLA DPA1 and DPB1 alleles in unrelated bone marrow transplantation.

The impact of donor-recipient DPA1 and DPB1 matching was examined in 122 unrelated bone marrow transplant pairs. All pairs were serologically matched at the time of transplantation for HLA class I and II and a majority also DRB1 allele matched. Retrospective A, B, C, DRB1, DQA1, DQB1 in addition to DPA1 and DPB1 allele matching was performed by molecular techniques. The percentage of pairs that were allele matched was as follows; HLA-A = 91% (n = 80), HLA-B = 94% (n = 80), HLA-C = 78% (n = 80), HLA-DRB1 = 96% (n = 122), HLA-DQA1 = 99% (n = 80), HLA-DQB1 = 92% (n = 122). 92 recipient/donor pairs with informative clinical data were available for analysis. DPA1 identity (no incompatibility in either direction) was observed in 57% and DPA1 compatibility in 76% of pairs with no apparent beneficial effect of matching on patient survival or Graft Versus Host Disease (GVHD). DPB1 identity was observed in 11% and compatibility in 27% of pairs. A significant improvement in patient survival was observed in DPB1 matched compared to one DPB1 mismatch (p < 0.01) and combined one and two DPB1 mismatched transplants (p = 0.03). This beneficial effect remained when allele mismatches at HLA-A, B, C, DRB1, DQA1, DQB1 were excluded (p = 0.05, p = 0.03, respectively). There was a significant association of increased frequency of severe GVHD (grades III-IV) compared to mild GVHD (grades I-II) with DPB1 mismatched transplants compared to DPB1 matched transplants (p = 0.04). In DPB1 mismatched transplants an association between patient survival and matching for individual DPB1 polymorphic regions was not observed; however in the HLA-A, B, DRB1, DQA1, DQB1 allele matched transplants a non significant increase in the frequency of Grade IV GVHD was observed in recipients who were negative compared to those who were positive for DPB1 alleles coding for glutamic acid at position 69.     

Selection of unrelated bone marrow donors by PCR-SSP typing and subsequent nonradioactive sequence-based typing for HLA DRB1/3/4/5, DQB1, and DPB1 alleles

Abstract: HLA incompatibility between bone marrow recipients and unrelated donors is one of the main obstacles in bone marrow transplantation. HLA class I and generic class II DR and DQ typing is generally performed by serology. Precise subtyping of HLA class II genes, however, can only be achieved by molecular genetic methods. Here, the final selection of serologically pretyped unrelated bone marrow donors by confirmatory PCR-SSP (PCR-sequence-specific primers) typing and subsequent nucleic acid sequence analysis of the second exon of DRB1, DRB3, DRB4, DRB5, DQB1, and DPB1 alleles is presented. Serologically identical potential marrow donors and their corresponding recipients were analyzed for HLA-DRB identity by PCR-SSP analysis. After solid-phase single-strand separation, direct sequencing of the allele- or group-specific DRB amplified products was performed by applying fluorophor-labelled sequencing primers. Electrophoretically separated sequencing products were detected by means of an automated DNA sequencer. Group-specific amplification and sequencing of DQB1 alleles was carried out for all potential bone marrow donors and recipients, while only the final donor-recipient pair was analyzed for DPB1 alleles. Thus, the presented amplification strategy in combination with direct sequencing of PCR products allows matching of bone marrow transplant pairs with the highest degree of reliability for the assessment of HLA class II identity.     

DISCRIMINATION OF HUMAN HLA-DRB1 ALLELES BY PCR-SSCP (SINGLE-STRAND CONFORMATION POLYMORPHISM) METHOD

A single-strand conformation polymorphism (PCR-SSCP) method has been adopted for discrimination of human HLA-DRB1 alleles. This method enabled the detection of DN A polymorphisms including point mutations at a variety of positions in the DN A fragments of the HLA-DRB1 gene. A total of 27 HLA-DRB1 alleles from 172 healthy donors were analysed using a combination of PCR-SSCP with group-specific amplifications. Application of a small amount of amplified and denatured DNA to non-denaturing electrophoresis followed by silver staining resulted in distinct banding patterns. Samples possessing a single allele in each amplification group showed two-band patterns which correspond to the sense and antisense strands, while heterozygotes in the same group or a mixture of two single-type samples showed four-band patterns. All of the analysed alleles were discriminated in each DRB1 group. The method described here may be somewhat complicated for routine typing of HLA-DRB1 alleles. However, it is useful in the screening of ‘new’ alleles as well as the donor-recipient molecular matching of HLA class II genes for various purposes, e.g. selection of bone marrow transplant donors.     

Six new DPB1 alleles identified in a study of 1,302 unrelated bone marrow donor-recipient pairs

HLA-DPB1 typing (PCR-based SSOP) of 1,302 unrelated donor-recipient pairs by two independent laboratories for a study sponsored by the National Marrow Donor Program (Office of Naval Research Grant #N00014-93-1-0658) has led to the identification of six putative new DPB1 alleles. Four of the six alleles were detected as a result of unique probe hybridization patterns to amplicons generated using a generic primer pair and were detected by both laboratories. The sample carrying the fifth new allele was typed as DPB1^*0402,0801 using a generic amplification; however, SSOP analysis of the two individual alleles after allele-specific amplification typed the sample as DPB1^*0201,new. The sixth new allele was typed as ^*0301 by one laboratory but as new by the other laboratory. This allele appears to have a mutation in the first region of variability. The apparent discrepancy between the two laboratories can be explained by the use of overlapping but nonidentical probes for this region. The identification of six new alleles in this study brings the total number of DPB1 alleles to over 70, making it the second most polymorphic class II locus. These alleles are currently being sequenced.     

DP reactive antibody in a zero mismatch renal transplant pair

This study describes molecular basis for positive B-cell flow crossmatch in a zero mismatch (0MM) transplant pair. Our end-stage renal disease patient was B-cell flow crossmatch positive with a 0MM deceased donor. DNA from the donor and patient were further typed by a high-resolution method. The patient’s sera were tested for anti-HLA reactivity by single antigen bead using a Luminex platform. The patient and donor were found to be HLA identical except for a single DP allele MM (DPB1*0601). As there was no single antigen bead coated with DPB*0601, analysis of the amino acid residues of reactive and nonreactive DPB1 alleles was conducted. The results showed that all reactive alleles carried the amino acid D-E at residue 55 and 56 of DPB1. The MM allele DPB1*0601 also carries the DE 55-56 epitope. We conclude that positive B-cell flow crossmatch was likely the result of single MM in the DP locus.     

HLA-DPB1 typing by polymerase chain reaction amplification with sequence-specific primers

DPB1 is the second most polymorphic class II locus with currently 84 recognized alleles, i.e. DPB1*0101 to DPB1*8101. Most of the alleles have been described during the last few years using oligonucleotide and sequencing techniques and relatively little is known about the role and importance of the polymorphic residues as regards to the function of DP molecules. In the present study, polymerase chain reaction (PCR) primers were designed for identification of all the phenotypically different DPB1 alleles by PCR amplification with sequence-specific primers. Forty-eight standard genomic PCR reactions per sample were performed in order to achieve this resolution. Unique amplification patterns were obtained in 2983 of 3160 (94.4%) possible genotypes. The primers were combined so that only very rare genotypes gave rise to ambiguous patterns. Sixty-four Histocompatibility Workshop cell lines and 150 DNAs provided by the UCLA DNA exchange were investigated by the DPB1 primer set. All typing results were conclusive. Analysis of the distribution of DPB1 alleles was performed in 200 Caucasian samples, 100 African samples and 40 Oriental samples. The population study by the DPB1 PCR-SSP method showed a characteristic distribution of HLA-DPB1 alleles. Each ethnic group had one, or two, frequent DPB1 allele(s) and the frequency of homozygotes was high, suggesting that balancing selection does not appear to be affecting the evolution of the DPB1 locus.     

HLA-DP and susceptibility to insulin-dependent diabetes mellitus in Japanese

ABSTRACT: Human leukocyte antigen (HLA) genes are candidates for susceptibility genes in insulin-dependent diabetes mellitus (IDDM). Recently, the association of DR and DQ with IDDM has been reported, but the role of HLA-DP genes remains uncertain. To address the question, we analyzed the DPB1 gene of 20 Japanese IDDM patients and 30 control subjects using a combination of polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis (PCR-RFLP method). DPB1*0501 was the most frequent allele both in Japanese patients and control subjects. There was no appreciable association between IDDM and the DPB1 allele in Japanese. The absence of association between IDDM and DP, in spite of the known association between this disease and both DR and DQ, suggests that the HLA locus (loci) telomeric to DP encodes susceptibility to IDDM.