The new allele HLA-DRB114:54:01:04 in a Chinese family identified using next-generation sequencing
The new allele HLA-DRB114:54:01:04 in a Chinese family identified using next-generation sequencing
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使用下一代测序鉴定出一个中国家族的新等位基因 HLA-DRB114:54:01:04
作者：
Peng Dan;Li Haixia;Wang Zhiyuan;Wu Riga;Sun Hongyu
人类白细胞抗原系统是已知的人类基因组中最多态的区域，被认为是遗传学研究的范例。截至2018年4月，在IPD-IMGT/人类白细胞抗原数据库(http://www.)中共记录了2,165个人类白细胞抗原-DRB1等位基因虾。交流电。Uk/ipd/imgt/hla)。1在本文中，我们描述了一个新的等位基因DRB1*14：54：01：04的鉴定，该等位基因是在一个北方汉族家庭的人类白细胞抗原分型过程中发现的。在母亲和她的儿子身上都发现了这种新的等位基因。从外周血中提取基因组DNA，并使用Qubit dsDNA HS分析试剂盒(Thermo Fisher Science，Waltham，Massachusetts)进行定量。在Illumina MiSeq平台上，使用Tru-Sight人类白细胞抗原v2测序板(Illumina，Inc.，San Diego，California)扩增出人类白细胞抗原-DRB1基因的全长序列，并使用MiSeq试剂盒v2 Micro进行测序(300个循环，成对的末端150bp测序)。原始数据使用Tru-Sight HLAAssign 2.0软件(版本2.1)进行分析。0.943；Illumina)，具有默认设置。通过Sanger测序验证了序列差异。用ExTaqDNA聚合酶扩增获得单核苷酸多态的样本(Takara公司，大连，中国)。这些方法的细节已经在我们之前的研究中描述过了。2-4共获得13282个核苷酸序列。DRB1*14：54：01：04与DRB1*14：54：01：01有两个差异。新等位基因DRB1*14：54：01：04在第10 544位由DRB1*14：54：01：01转变为A，在第9068位有一个四核苷酸插入(TGAG)。这两种差异都存在于内含子2中，如图1所示。母亲的基因为HLAA*02：06：01：01，03：01：01：01；C*07：02：01：01，07：02：01：03；B*07：02：01，39：01：01G；DRB1*14：05：01，14：54：01：04；DQ A1*01：04：01G，01：04：01G；DQB1*05：02：01，05：03：01：02；DPA1*01：03：01：01，02：02：02；DPB1*02：01：02，05：01：01。
The HLA system is known to be the most polymorphic region of the human genome and is considered a paradigm for genetics studies. As of April 2018, a total of 2165 HLA-DRB1 alleles have been recorded in the IPD-IMGT/HLA database (http://www. ebi. ac. uk/ipd/imgt/hla). 1 In this article, we described the identification of a new allele DRB1* 14: 54: 01: 04, which was discovered during the HLA typing of a north Han Chinese family. This novel allele was identified in both the mother and her son. Genomic DNA was isolated from peripheral blood and quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, Massachusetts). The full-length sequence of the HLA-DRB1 gene was amplified using a Tru-Sight HLA v2 Sequencing Panel (Illumina, Inc., San Diego, California) and sequenced using a MiSeq Reagent Kit v2 Micro (300 cycles, paired-end 150-bp sequencing) on Illumina MiSeq platform. Raw data were analyzed using Tru-Sight HLA Assign 2.0 Software (version 2.1. 0.943; Illumina) with default settings. The sequence differences were validated by Sanger sequencing. All samples with the identified singlenucleotide polymorphism were amplified using ExTaq DNA polymerase (Takara Inc., Dalian, China). Details of the methods were described in our previous studies. 2–4 A total of 13 282 nt sequence was obtained. Two differences were identified in DRB1* 14: 54: 01: 04 when compared with DRB1* 14: 54: 01: 01. The new allele DRB1* 14: 54: 01: 04 has a G to A transition change from DRB1* 14: 54: 01: 01 at nucleotide 10 544 and a four-nucleotide insertion (TGAG) at nucleotide 9068. Both the differences exist in intron 2 and are illustrated in Figure 1. The genotype of the mother is HLAA* 02: 06: 01: 01, 03: 01: 01: 01; C* 07: 02: 01: 01, 07: 02: 01: 03; B* 07: 02: 01, 39: 01: 01G; DRB1* 14: 05: 01, 14: 54: 01: 04; DQ A1* 01: 04: 01G, 01: 04: 01G; DQB1* 05: 02: 01, 05: 03: 01: 02; DPA1* 01: 03: 01: 01, 02: 02: 02; DPB1* 02: 01: 02, 05: 01: 01.