GoKinD研究中HLA-DQA1的高分辨率基因分型及新等位基因HLA-DQA1040102、HLA-DQA10402和HLA-DQA1*0404的鉴定。

High-resolution genotyping of HLA-DQA1 in the GoKinD study and identification of novel alleles HLA-DQA1040102, HLA-DQA10402 and HLA-DQA1*0404.

作者信息

Cordovado S K, Hancock L N, Simone A E, Hendrix M, Mueller P W

机构信息

Division of Laboratory Sciences, Molecular Biology Branch, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, Atlanta, GA 30341, USA.

出版信息

Tissue Antigens. 2005 May;65(5):448-58. doi: 10.1111/j.1399-0039.2005.00389.x.

DOI:10.1111/j.1399-0039.2005.00389.x

PMID:15853899

Abstract

In order to achieve high-resolution HLA-DQA1 genotyping, it is necessary to identify polymorphisms in exons 1, 2 and 3. We present a high-resolution sequence-based typing (SBT) strategy for genotyping exons 1, 2 and 3 of the polymorphic HLA-DQA1 locus. This method is an improvement upon previously presented methods, because it utilizes the minimum number of SSP-PCR assays to obtain clear DNA sequence in both the forward and reverse directions of all three exons. All known HLA-DQA1 alleles are resolved with the exception of HLA-DQA1010101 and HLA-DQA1010102 for which the distinguishing polymorphism is located in exon 4 and does not result in an amino acid change. This method has enabled our laboratory to identify three new HLA-DQA1 alleles - HLA-DQA1040102, HLA- DQA10402 and HLA-DQA10404 - in the Genetics of Kidneys in Diabetes (GoKinD) study population. Additionally, we present single-allele amplification methods, which identify the coding sequences of HLA-DQA1 exons 1, 2, 3, intron 2 and 300 bp of the HLA-DQA1 promoter (QAP). This study, also describes the QAP for most of the known HLA-DQA1 alleles, three HLA-DQA2 promoter sequences and the intron 2 sequences for HLA-DQA1040101, HLA-DQA1040102, HLA-DQA10402 and HLA-DQA1*0404.

摘要

为了实现高分辨率的HLA - DQA1基因分型，有必要鉴定外显子1、2和3中的多态性。我们提出了一种基于序列的高分辨率分型（SBT）策略，用于对多态性HLA - DQA1基因座的外显子1、2和3进行基因分型。该方法是对先前提出的方法的改进，因为它利用最少数量的序列特异性引物 - 聚合酶链反应（SSP - PCR）检测，在所有三个外显子的正向和反向都获得清晰的DNA序列。除了HLA - DQA1010101和HLA - DQA1010102外，所有已知的HLA - DQA1等位基因都能得到区分，其区别性多态性位于外显子4中，且不会导致氨基酸变化。该方法使我们实验室能够在糖尿病肾脏遗传学（GoKinD）研究人群中鉴定出三个新的HLA - DQA1等位基因——HLA - DQA1040102、HLA - DQA10402和HLA - DQA10404。此外，我们还提出了单等位基因扩增方法，该方法可鉴定HLA - DQA1外显子1、2、3、内含子2以及HLA - DQA1启动子（QAP）的300 bp的编码序列。本研究还描述了大多数已知HLA - DQA1等位基因的QAP、三个HLA - DQA2启动子序列以及HLA - DQA1040101、HLA - DQA1040102、HLA - DQA10402和HLA - DQA1*0404的内含子2序列。