与先天性长 QT 综合征 (LQTS) 相关的功能性和单体型标记 SNPs 的硅学研究。

IF 3.5 Q1 EDUCATION & EDUCATIONAL RESEARCH
Genomic medicine Pub Date : 2008-12-01 Epub Date: 2009-02-12 DOI:10.1007/s11568-009-9027-3
C Sudandiradoss, Rao Sethumadhavan
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引用次数: 0

摘要

单核苷酸多态性(SNPs)在了解许多复杂人类疾病的遗传基础方面发挥着重要作用。如何识别疾病相关基因中的功能性 SNPs 仍是一项重大挑战。本综述分析了可改变 KCNQ1、KCNH2、SCN5A、KCNE1 和 KCNE2 等基因的表达和功能的遗传变异,以及这些基因在先天性长 QT 综合征(LQTS)发病中的潜在作用。在所有五个基因的总共 3,309 个 SNPs 中,27 个编码区的非同义 SNPs (nsSNPs) 和 44 个 5' 和 3' 非翻译区 (UTR) 的 SNPs 被鉴定为功能显著。SIFT 和 PolyPhen 程序用于分析 nsSNPs 和 FastSNP;UTR 扫描程序用于计算 5' 和 3' 非翻译区的 SNPs。在所选的 5 个基因中,KCNQ1 的单倍型块数量最多,有 26 个单倍型块和 6 个具有完全连锁不平衡值的标记 SNP。SCN5A 基因有 10 个单倍型区块和 4 个标记 SNP。KCNE1 和 KCNE2 基因都只有一个单倍型区块和四个标记 SNP。KCNH2 基因有四个单倍型区块和两个标记 SNP。此外,本综述还报告了所选基因的拷贝数变异(CNV)、表达序列标签(EST)和基因组调查序列(GSS)。这些计算方法与早先报道的有关 LQTS 的实验研究结果非常吻合。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
In silico investigations on functional and haplotype tag SNPs associated with congenital long QT syndromes (LQTSs).

Single-nucleotide polymorphisms (SNPs) play a major role in the understanding of the genetic basis of many complex human diseases. It is still a major challenge to identify the functional SNPs in disease-related genes. In this review, the genetic variation that can alter the expression and the function of the genes, namely KCNQ1, KCNH2, SCN5A, KCNE1 and KCNE2, with the potential role for the development of congenital long QT syndrome (LQTS) was analyzed. Of the total of 3,309 SNPs in all five genes, 27 non-synonymous SNPs (nsSNPs) in the coding region and 44 SNPs in the 5' and 3' un-translated regions (UTR) were identified as functionally significant. SIFT and PolyPhen programs were used to analyze the nsSNPs and FastSNP; UTR scan programs were used to compute SNPs in the 5' and 3' untranslated regions. Of the five selected genes, KCNQ1 has the highest number of 26 haplotype blocks and 6 tag SNPs with a complete linkage disequilibrium value. The gene SCN5A has ten haplotype blocks and four tag SNPs. Both KCNE1 and KCNE2 genes have only one haplotype block and four tag SNPs. Four haplotype blocks and two tag SNPs were obtained for KCNH2 gene. Also, this review reports the copy number variations (CNVs), expressed sequence tags (ESTs) and genome survey sequences (GSS) of the selected genes. These computational methods are in good agreement with experimental works reported earlier concerning LQTS.

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