毛细管参考链介导的构象分析法在HLA-DRB1等位基因分型中的应用

目的：探讨应用参考链构象分析法对HLA-DRB1等位基因分型的准确性及实用性。方法：应用毛细管参考链介导的构象分析法建立31个等位基因的标准迁移率，对50例样本进行分型，并与SBT法检测结果进行比较。结果：50例样本中47／50与测序法测得的等位基因一致，以DRB1^*08032、DRB1^*09012为参考链无法检测出DRB1^*1101、DRB1^*1403。结论：毛细管参考链介导的构象分析法具有准确性高、分辨率高、成本低、高通量的特点，值得在HLA分型中应用推广。     

HLA-DRB1基因分型新方法的建立

目的改进以测序为基础(sequencing based typing,SBT)的HLA-DRB1基因分型方法,从而降低其分型成本和工作量。方法根据序列比对结果将DRB1基因分为6个簇(cluster),并设计6对簇特异引物(cluster specific primer,CSP),依据其对应的等位基因簇在人群中的频率高低,利用巢式PCR和CSPs渐进式地扩增,PCR产物纯化后进行测序分型。我们将此方法命名为以频率为基础的CSP-SBT法(Frequency based-CSP-SBT,FB-CSP-SBT)。结果用FB-CSP-SBT法对224个中国南方汉族冠心病患者临床样本进行HLA-DRB1等位基因分型,总共鉴定出31个等位基因型,覆盖了所有的HLA-DRB1等位基因谱系。其中,4个在人群中频率最高的簇依次为DR52(47.99%,包含DRB1*03、DRB1*08、DRB1*11、DRB1*12、DRB1*13和DRB1*14等6个DRB1等位基因谱系)、DR15(19.20%,包括DRB1*15和DRB1*16)、DR79(18.53%,包括DRB1*07和DRB1*09)和DR04(12.72%),占整个人群的98%以上。观察到的杂合性(heterozygosity)为0.9107,与前人报道的HLA-DRB1基因位点的杂合性相似,基因型分布符合Hardy-Weinberg平衡(P=0.3517)。对于每个样本,利用此方法对DRB1基因进行测序分型比传统的SBT至少减少6～8个PCR反应,同时还减少了测序反应的数目。结论用FB-CSP-SBT法可以准确地对HLA-DRB1基因进行分型,比传统的SBT法减少了工作量并降低了分型成本。     

DNA测序鉴定新等位基因HLA-DRB1*1609

目的 鉴定HLA新等位基因DRB1＊1609。方法 应用分子克隆和DNA测序的技术测定HLA新等位基因的核苷酸序列，进行HLA等位基因序列比对分析和新等位基因的血清学分型及家系分析。结果 新等位基因DRB1第二外显子（exon2，Ex2）序列与所有已知的HLA等位基因序列均不相同，与同源性最高的HLA-DRB1＊160101相比，第127位碱基由A→T，引起相应编码第47位氨基酸由酪氨酸Tyr（Y）→苯丙氨酸Phe（F）。血清学分型表明抗原特异性为DR16。家系分析提示该志愿者DRB1＊1609等位基因遗传自母亲。结论 DNA测序表明被测标本含有HLA-DRB1新等位基因，被WHOHLA因子命名委员会正式命名为HLA-DRB1＊1609。     

HLA-DRB1*1218新等位基因克隆测序鉴定及内含子序列分析

目的 鉴定中国人群人类白细胞抗原(human leukocyte antigen,HLA)DRB1基因,分析新等位基因第1和2内含子序列信息.方法 采用聚合酶链反应-序列特异寡核苷酸探针反向杂交法(polymerase chain reaction-sequence specific oligonucleotide probes,PCR-SSOP)对广东地区随机正常人群进行HLA常规基因分型,发现1个与HLA-DRB1*120201相近的未知基因,对先证者DNA应用组特异性引物扩增HLA-DRB1位点第2外显子,PCR产物经克隆到质粒载体中以获得单链,对克隆所得产物进行HLA-DRB1基因的第2外显子及第1和第2内含子双向测序分析.并与DRB1*120201基因序列的第2外显子和DRB1*03010101等位基因内含子相比较.结果 发现该个体的一个HLA-DRB1*080302基因被确认,而另一个HLA-DRB1基因为新等位基因,其序列被GenBank接受(编号为FJ481086).新等位基因与最相近的DRB1*120201相比,在第2外显子上有1个核苷酸的不同,即第262位G→C(密码子59 GAG→CAG,氨基酸59 Glu→Gln).DRB1*1218与DRB1*03010101等位基因第2内含子序列完全相同,而与DRB1*03010101等位基因第1内含子序列相比较有12个碱基不同.结论 发现并鉴定一个新的HLA等位基因,经世界卫生组织HLA因子命名委员会正式命名为HLA-DRB1*1218.     

应用完整外显子2/3序列解决HLA-DRB1座位基因分型的歧义结果

背景：人类白细胞抗原基因测序分型中,当等位基因的差异碱基位于测序范围之外或不同等位基因对的杂合序列相同时,无法得到清晰的结果。 目的：通过完整外显子2/3序列的测定,解决常规HLA-DRB1基因分型中的高比例歧义结果。 方法：初次分型采用常规的测序方法检测320份样本的HLA-DRB1外显子2第一高变区以外的序列,测序反应设置codon86。后期采用一次性扩增外显子2/3,测序反应针对外显子2设置组特异性引物：DRB1*04/07/09为一组,其它基因家族为一组,设置conden86,对初次分型后为歧义结果的样本重新分型。 结果与结论：初次分型有180份样本为歧义结果,占总样本数的56.25 %。其中A类为差异碱基位于测序范围之外,共114例;B类为等位基因对的杂合序列相同,共17例;C类为两种情况同时存在,有49例。3种类别的歧义等位基因数分别为119个、34个、98个,占等位基因总数的33.06%、9.44 %、27.22%。完整外显子2/3序列的测定使歧义结果比例从56.25%下降到14.37%,其中A类103例、B类8例、C类23例样本的等位基因得到确认。此次研究中发现了一个新等位基因,与跟它最相近的等位基因DRB1*110101相比,其外显子3的第381位碱基G>T,导致第98位氨基酸AAG(赖氨酸 Lys)>AAT(天冬酰氨 Asn)。序列已提交Genbank,编号HM807583,2010-08被世界卫生组织HLA因子命名委员会命名为HLA-DRB1*1197(编号HWS10010999)。提示,完整外显子2/3序列的测定能大幅降低歧义分型结果的比例。     

汉族系统性红斑狼疮患者存在DRB1*1504等位基因

<正>我们使用聚合酶链反应结合顺序持异的寡核苷酸（PCR/SSO）探针杂交的方法对DR2阳性的系统性红斑狼疮（SLE）汉族患者（24例）和正常对照组（26例）作组特异性扩增和班点杂交,发现SLE患者中1例样本具有不同于指定的DRB1*1501,1502,1503,1601和1602等位基因独特的杂交格局。该样本与探针DRB8603杂交阳性,与DRB8601阴性,它的反应格局类似于DRB1*1501,而DRB1*1501与探针DRB7011杂交也为阳性,但该样本与DRB7011杂交则为阴性。探针DRB7011的核苷酸顺序是GAC ATC CTG GAG CAG GCG相应于DR15（2）第二外显子66-72位氨基酸编码顺序。该样本的杂交格局与已在我国彝族和傣族正常人群阳性细胞中发现的等位基因DRB1*504完全相同,这提示我国汉族人群中也存在DRB1*1504等位基因。     

中国人群中一个新的HLA-DRB4等位基因(DRB4·NC)的发现及比较分析

目的 :对人群进行HLA DRB的分型及多态性研究 ,发现未曾报道过的HLA DRB等位基因。方法 :用HLA DRB通用引物扩增该个体所有DRB等位基因的第二外显子 ,并对扩增产物进行克隆 ,通过双脱氧法进行DNA测序。结果 :发现一个新的HLA DRB核苷酸序列。结论 :通过与已发表的序列及Genbank已收载的序列比较 ,显示该序列属于HLA DRB4家族的新等位基因 ,我们暂时称它为DRB4 NC。该序列已被Genbank收载 (登录号为AF2 0 75 48)。     

HLA基因多态性与溃疡性结肠炎遗传易感关系的研究

目的:研究HLA-DRB1等位基因多态性与我国汉族溃疡性结肠炎遗传易感的相关性,并分析其与疾病临床分型的相关性。方法:应用基因芯片技术分析了本地区汉族溃疡性结肠炎60例患者和健康对照者DRB1的基因分型,采用Fisher’s精确概率法比较了两组各位点等位基因频率分布的差异。结果:溃疡性结肠炎患者DR2和DRB1*15基因表达频率分别为45%和41.7%,较对照组(23.3%和21.7%)明显升高,OR分别为2.688和2.582(均P<0.05)。慢性持续型UC的DRB1*15等位基因频率较相应其他型升高更为显著(P<0.05)。结论:DR2或DRB1*15等位基因可能是我国汉族人群UC的易感基因。HLA-DR基因多态性与UC的临床分型密切相关。     

新的HLA-DRB1等位基因DRB1*1212的核苷酸序列分析

目的验证一个新的HLA等位基因HLA—DRB1＊1212的序列。方法采用盐析法抽提样本基因组DNA，利用HLA—DRB1组特异性引物PCR扩增先证者HLA—DRB1等位基因的第2外显子，PCR产物经割胶回收后进行测序分析，通过聚合酶链反应-序列特异性寡核苷酸探针方法验证测序发现突变点。结果先证者有两个HLA—DRB1等位基因，其中一个为HLA—DRB1＊090102，另一个HLA—DRB1等位基因，经BLAST验证为新的等位基因，新的等位基因序列已递交GenBank（AY899825）。与最接近的DRB1＊120101等位基因序列相比，新的等位基因仅在第2外显子上有1个核苷酸不同，即第199位A→C，导致第67位氨基酸Ile—Leu。结论该等化基因为新的HLA—DRB1等位基因，被世界卫生组织HLA因子命名委员会正式命名为HLA-DRB1＊1212。     

HLA-DRB1新等位基因DRB1*1610的发现

目的 对HLA新的等位基因HLA-DRB1*1610的分析.方法 采用商用DNA试剂盒抽提样本基因组DNA,利用HLA-DRB1组特异性引物PCR扩增先证者HLA-DRB1基因的第2外显子,PCR产物经割胶回收后进行测序分析.结果 先证者有两个HLA-DRB1等位基因,其中一个为HLA-DRB1*1202,另一个HLA-DRB1等位基因经BLAST验证为新的等位基因,新的等位基因序列已递交GenBank(DQ192647).与最接近的DRB1*160201等位基因序列相比,新的等位基因仅在第2外显子上有1个核苷酸不同,即第227位A→T,导致第47位氨基酸Tyr→Phe.结论 该等位基因为新的HLA-DRB1等位基因,被世界卫生组织HLA因子命名委员会正式命名为HLA-DRB1*1610.     

Reference strand mediated conformation analysis resolves HLA-DRB1 typing ambiguities when matching for unrelated bone marrow transplantation

We show here the use of reference strand mediated conformation analysis (RSCA) to unambiguously resolve the HLA-DRB1 typing of two individuals which were selected as potential unrelated donors for bone marrow transplantation (BMT). In the first case, both sequence-specific primer (SSP) amplification and sequence-specific oligonucleotide probing (SSO), routinely used in different tissue typing laboratories gave, for the two unrelated donors, the same ambiguous typing of HLA-DRB1*04011+*0403 or DRB1*0407+*0413. In this case sequence-based typing (SBT) was not the method of choice to resolve the situation, due to the sequence ambiguities of these two given combinations. RSCA of both samples, using homozygous typing cells (HTCs) for DRB1*04011, *0403 and *0407 as internal controls, gave the unambiguous result that both donors were HLA-DRB1*04011+*0403. In the second case, a donor was typed as DRB1*1102+1103 by SSP, while SSO excluded the DRB1*1102 allele. The patient was unambiguously typed as DRB1*1101+1103 by both techniques. RSCA, using DNA from reference cell lines as internal controls, gave the unambiguous typing that the donor was DRB1*1103 homozygous.     

Discovery of HLA-DRB1*0331 in a Taiwanese marrow donor and the importance of sequence-based typing in a rare or previously unrecognized allele

We describe here a novel HLA-DRB1* allele, DRB1*0331, observed from a Taiwanese bone marrow donor using DNA sequence-based typing (SBT) method. The 'new' allele differs from DRB1*0306 and DRB1*0325 by one nucleotide at positions 196 and 227, respectively. Nucleotide mutations caused amino acid substitutions from N to Y at codon 37 and from F to Y at codon 47, as compared with amino acid sequence encoded by the DRB1*030101 allele. The donor was first typed as DRB1*0403/0406/0439/0441/0446/0451/0452 (NMDP code DRB1*04XX) and DRB1*0304/0323/0325 (NMDP code DRB1*03APDA) by sequence-specific oligonucleotide (SSO) typing kit. Subsequent typing of the donor by high-resolution sequence-specific primer (SSP) protocol indicated DRB1*0403 and DRB1*0306. The anomalous result of DRB1*03 was resolved by SBT and recognized as DRB1*0331. We concluded that SSP or SSO alone may mistype a precedent unrecognized allele and that two different typing techniques or SBT may have to be employed to safe guard true HLA typing when rare alleles are encountered at the first time.     

High-resolution HLA typing for the DRB3/4/5 genes by sequence-based typing

The high degree of polymorphism of the HLA genes at the nucleotide sequence level has proven sequence-based typing a major typing strategy. For DRB1 the allelic variability is predominantly present in the second exon and by DNA sequencing of exon 2 all hitherto known DRB1 alleles can be detected. For the associated genes DRB3, DRB4 and DRB5 the situation is slightly different. Allelic differences are not limited to exon 2 and the sequence of exon 3 and sometimes exon 4 is needed for complete subtyping. Oligonucleotides to amplify the exons needed for subtyping of DRB3, DRB4 and DRB5 were designed. Gene-specific products were generated to make simultaneous detection of alleles in heterozygous combinations possible. In this way 238 individuals were fully typed for their DRB3, 4 and 5 subtypes. Additional samples were typed for only one of the genes. All samples had been previously typed by PCR-SSP. Concordant typing results were obtained for all individuals tested. The DRB3 alleles typed for included *0101, *0201, *0202 and *0301, for DRB4 they were *01011, *0102 and *0103 and for DRB5 *0101, *0102, *0103, *0105, *0201, *0202 and *0203. All alleles were easily detected by the protocol described except for DRB5*0201. Sequencing of exon 3 and 4 of the DRB5*0201 allele showed this allele to be a sequencing error and the sequences obtained were identical to the exon 2, 3 and 4 sequences of DRB5*0202. Two new alleles were identified in the samples studied, DRB4*0105 and DRB3*0207. Sequence based typing has been recognized as a valuable tool for HLA typing of DRB1, DQB1 and DPB1 since several years. It is shown to be a superior typing method as well in the detection of the different DRB3, 4 and 5 subtypes.     

New DR5 sequences: a novelDRB1*11122 allele identified in Paiwan tribe members of Taiwan and a corrected sequence for the DRB1*1201 allele

We report herein the identification of a new DRB1 allele using sequence-based typing (SBT). This novel allele, HLA-DRB1*11122, was found in an aboriginal individual (SWP71) from the Paiwan tribe in the southern part of Taiwan. This individual was typed by SBT method as having an HLA genotype of HLA-A*24021/24021, HLA-B*4001/4002, HLA-DRB1*11122/15011, HLA-DRB3*0202, and HLA-DRB5*01011. This new allele differs from DRB1*1112 in the polymorphic exon 2 only at codon 34 (CAA-->CAG; both specify glutamine) and from DRB1*1110 in the exon 2 sequence only at codon 32 (CAT-->TAT; H32T). The most likely candidate allele which is found in the aboriginal populations of Taiwan and which may mutate into this new allele is DRB1*11011. DRB1*11122 allele differs from DRB1*11011 allele in the polymorphic exon 2 at both codon 34 (CAA-->CAG) and codon 37 (TAC-->TTC; T37F). This novel HLA-DRB1*11122 allele was also found in another aboriginal individual (SWP90) from the same Paiwan tribe. This SWP90 individual was typed by SBT method as having an HLA genotype of HLA-A*24021/24021, HLA-B*4002/5502, HLA-DRB1*11122/1201, and HLA-DRB3*01011/0202. However, the original DRB1*1201 sequence from HERLUFF was found to be erroneously reported and the corrected sequence from SWP90 is now presented herein.     

河南省骨髓库汉族捐献者HLA-A、B、DR高分辨基因多态性调查分析

背景：2009年开始,中华骨髓库加大HLA高分检测的力度,可缩短配型检索周期,提高配型成功率。 目的：统计分析河南省骨髓捐献者HLA-A、B、DRB1高分辨基因多态性。 方法：河南省汉族造血干细胞志愿捐献者血样3 874人份,志愿捐献静脉血,EDTA抗凝。采用SSO HD 荧光微珠流式高分辨HLA-A、B、DRB1基因分型检测方法,对3 874份骨髓捐献志愿者血样进行高分辨分型检测,用PCR-SSP高分辨检测、SBT检测解决存在的模棱两可问题。等位基因计数法计算等位基因的基因频率。 结果与结论：共检出A 34个,B 84个,DRB1 50个,A位点基因频率处于前5位的有A*0201(0.160 9)、 A*1101(0.162 7)、 A*2402(0.160 2)、A*3001(0.080 8)、 A*3303(0.078 9);B位点处于前5位的是B*1302(0.077 7)、B*4001(0.072 2)、B*5101(0.062 8)、B*4601(0.061 2)和B*0702(0.050 7);DRB1位点处于前5位的是DRB1*1501(0.146 9)、DRB1*0901(0.131 8)、DRB1*0701(0.121 1)、DRB1*1202(0.061 2)、DRB1*0405(0.058 2)。     

High-resolution HLA typing for the DQB1 gene by sequence-based typing

Abstract: The ideal high-resolution typing strategy for polymorphic genes is sequence-based typing. SBT of genomic DNA has been developed for the HLA class H genes DRB1, DRB3/4/5 and DPB1. For the DQB1 gene the sequence-based typing method was shown to cause a number of problems. To resolve those problems, different primers to amplify and sequence exon 2 of DQB1 were designed and tested. With several primer combinations, preferential amplification was observed in individuals heterozygous for DQB1*02/*03 and DQB1*02/*04. The preference was for DQB1*02 in many instances but could also be demonstrated for DQB1*03 or *04 and resulted occasionally in allelic drop-out. The best primer combination was selected and successfully used to type individuals heterozygous for DQB1*02, *03 and*04. To distinguish DQB1*0201 and *0202, primers for amplification and sequencing of exon 3 were developed and correct subtyping was obtained. The ambiguous typing DQB1*0301/*0302 and DQB1*0303/*0304 was resolved by allele-specifk amplification and sequencing. A total of 258 individuals were fully typed for their DQB1 subtypes. All samples had been previously typed by PCR-SSP and serology. Concordant typing results were obtained for all individuals tested. The DQB1 alleles detected included *0501, *0502, *0503, *0601, *0602, *0603, *0604, *0609, *0201, *0202, *0301, *0302, *0303, *0304, *0401 and *0402. Sequence-based typing of the DQB1 gene proved a reliable typing strategy for assignment of the different DQB1 alleles after intensive selection of primers and test conditions.     

Identification of a novel HLA-Cw*08 variant allele, Cw*0824

A novel HLA-C allele, Cw*0824, which was identified from an individual of the Han Chinese, differs from Cw*080101 at codon 222 (GAG > AAG ) in exon 4, which results in an amino acid change Glu222Lys.
In recent years, many human leukocyte antigen (HLA)-C alleles have been identified. Up to date, 23 different Cw*08 alleles have been identified according to the IMGT/HLA Database release 2.25.2 May 2009 (1) . Here, we describe the identification of the novel allele HLA-Cw*0824 that was found during routine high resolution sequence-based typing (SBT) of a Chinese stem cell voluntary donor. The HLA alleles of the donor were typed as A*11, 24; B*15, 46; and DRB1*09, 12.     

Two novel alleles HLA‐DRB1*11:150 and HLA‐DRB1*14:145 identified in Saudi individuals

Two new HLA‐ DRB1 alleles were identified by sequence‐based typing method (SBT) in 1100 participants in the Saudi Stem Cell Donor Registry. HLA‐DRB1*11:150 differs from HLA‐DRB1*11:01:01G by a single C to A substitution at nucleotide position 5580 in exon 2, resulting in an amino acid change from alanine to glutamic acid at position 74. HLA‐DRB1*14:145 differs from HLA‐DRB1*14:04 by a C to G substitution at nucleotide position 5511 in exon 2, resulting in an amino acid change from threonine to arginine at position 51.     

Evaluation of Ion Torrent sequencing technology for rapid clinical human leucocyte antigen typing

The development of techniques to define the human leucocyte antigen (HLA) region has proven to be challenging due to its high level of polymorphism. Within a clinical laboratory, a technique for high‐resolution HLA typing, which is rapid and cost effective is essential. NGS has provided a rapid, high‐resolution HLA typing solution, which has reduced the number of HLA ambiguities seen with other typing methods. In this study, the One Lambda NXType NGS kit was tested on the Ion Torrent PGM platform. A total of 362 registry donors from four ethnic populations (Europeans, South Asians, Africans and Chinese) were NGS HLA typed across 9‐loci (HLA‐A, ‐B, ‐C, ‐DRB1,‐DRB345 ‐DQB1 and ‐DPB1). Concordance rates of 91%–98% were obtained (for HLA‐A, ‐B, ‐C, ‐DRB1, ‐DQB1 and ‐DPB1) when compared to historical PCR‐SSO HLA types, and the identification of uncommon alleles such as A*24:07:01 and C*04:82 were observed. A turnaround time of four days was achieved for typing 44 samples. However, some limitations were observed; primer locations did not allow all ambiguities to be resolved for HLA Class II where Exon I and IV amplification are needed (HLA‐DRB1*04:07:01/04:92, HLA‐DRB1*09:01:02/*09:21 and HLA‐DRB1*12:01:01/*12:10). This study has demonstrated high‐resolution typing by NGS can be achieved in an acceptable turnaround time for a clinical laboratory; however, the Ion Torrent workflow has some technical limitations that should be addressed.     

New HLA haplotype frequency reference standards: high-resolution and large sample typing of HLA DR-DQ haplotypes in a sample of European Americans

A collaborative study involving a large sample of European Americans was typed for the histocompatibility loci of the HLA DR-DQ region and subjected to intensive typing validation measures in order to accurately determine haplotype composition and frequency. The resulting tables have immediate application to HLA typing and allogeneic transplantation. The loci within the DR-DQ region are especially valuable for such an undertaking because of their tight linkage and high linkage disequilibrium. The 3798 haplotypes, derived from 1899 unrelated individuals, had a total of 75 distinct DRB1-DQA1-DQB1 haplotypes. The frequency distribution of the haplotypes was right skewed with haplotypes occurring at a frequency of less than 1% numbering 59 and yet constituting less than 12% of the total sample. Given DRB1 typing, it was possible to infer the exact DQA1 and DQB1 composition of a haplotype with high confidence (>90% likelihood) in 21 of the 35 high-resolution DRB1 alleles present in the sample. Of the DRB1 alleles without high reliability for DQ haplotype inference, only *0401, *0701 and *1302 were common, the remaining 11 DRB1 alleles constituting less than 5% of the total sample. This approach failed for the 13 serologically equivalent DR alleles in which only 33% of DQ haplotypes could be reliably inferred. The 36 DQA1-DQB1 haplotypes present in the total sample conformed to the known pattern of permissible heterodimers. Four DQA1-DQB1 haplotypes, all rare, are reported here for the first time. The haplotype frequency tables are suitable as a reference standard for HLA typing of the DR and DQ loci in European Americans.