基于生物信息学的SNP候选位点搜寻方法

单核苷酸多态性(Single Nucleotide Polymorphism,SNP)是人类基因组中最常见的遗传多态,在遗传学研究的很多方面具有重要的作用。它的搜寻正受到广泛关注。近年来,国际上出现了一种基于生物信息学的发掘SNP新方法。本文对该方法的两种策略及其各自所存在的问题作一介绍。 Abstract：Single Nucleotide Polymorphism (SNP), the most common form of human genetic variation, represents a valuable resources for a variety of genetic research. There is considerable interest in the discovery of it. Recently, a new method based on bioinfomatics has been developed for the discovery of SNP. In this paper, the two strategy of this method and their respective problem are discussed.     

强直性肌营养不良症DMPK基因CTG重复序列与Alu±1kb单倍型研究

强直性肌营养不良(myotonic dystrophy,DM)是由于DMPK基因3′非翻译区CTG重复序列异常扩展所致的、主要累及神经肌肉系统的常染色体显性遗传病。在该基因的第8内含子中还存在一个Alu重复序列的1kb插入/缺失多态性,即Alu±1kb多态性。为了帮助阐明汉族人群中DM突变的起源,并为解释DM在不同群体中发病率的差异提供更多依据,本文从300例已知CTG拷贝数的正常汉族群体中随机挑选60例,首先通过PCR扩增确定其Alu±1kb多态性,然后对Alu±1kb和CTG双杂合的标本,采用长PCR方法先行扩增含Alu±1kb和CTG重复序列的DNA片段,再分别对含Alu(＋)和Alu(－)的DNA片段中的CTG拷贝数进行常规PCR分析,以确定二位点的单倍型。结果表明60例正常人中二位点间呈连锁不平衡。其单倍型为:（CTG）5均与Alu(＋)连锁;多数(CTG)11～14与Alu(－)连锁;在两个(CTG)≥19的等位基因中一个与Alu(＋)连锁,另一个与Alu(－)连锁。各民族相关资料的比较提示,汉族人群中(CTG)11～14与非洲黑人的起源可能不同;(CTG)19～30/Alu－1kb在汉族人群中的频率远比欧洲人群的高;(CTG)19～30/Alu－1kb与(CTG)19～30/Alu＋1kb在汉族人群中是以一定比例共存的;(CTG)19～30在不同民族间的起源不尽相同;如果从(CTG)5到(CTG)19～30的假设成立的话,则很可能是一个较为复杂的过程。 Abstract：Myotonic dystrophy(DM),an autosomal dominant disease of the neuromascular system,is caused by expansion of the CTG repeats in the 3＇untranslated region of the DMPK gene.In the eighth intron of this gene,there is another polymorphism－the insertion/deletion of 1kb Alu repeat(Alu±1kb).In order to help elucidate the origin of DM mutation in Chinese Han patients,and explain the difference of incidence of DM in different populations,60 normal Han individuals were randomly chosen from 300 Chinese,whose CTG copy number had been previously ascertained.The polymorphism of Alu±1kb of the 60 cases were firstly analyzed by in vitro amplification;then the 22 cases in which both sites were heterozygous were analyzed as following:the fragments containing both Alu±1kb and CTG repeat sequence were first amplified by long PCR method;and then the CTG copy numbers were analyzed in the Alu(＋)and Alu(－)alleles.In the 60 cases studied,a remarkable linkage disequilibrium between CTG triplet repeats and Alu±1kb were observed.All the(CTG)5 alleles were linked with Alu(＋),and most of the(CTG）11－14 alleles were linked with Alu(－);one of the two alleles of(CTG）≥19 was linked with Alu(＋),the other was linked with Alu(－).This suggests that the origin of(CTG)11－14 in Chinese Han may be different from that of African Blacks;the frequency of (CTG)19－30 /Alu－1kb in Chinese Han might be much higher than that in Europeans Caucasians.The(CTG)19－30/Alu－1kb and(CTG)19－30/Alu＋1kb coexist in Chinese Han in some proportion;the origin of (CTG)19－30 in different population may be different;if the hypothesis of(CTG)5 to(CTG)19－30 is true,then the progress should have been a relatively complicated process.     

中国羌族人群强直性肌营养不良症基因CTG重复序列多态性研究

强直性肌营养不良症是由于MT-PK基因3'非编码区CTG三核苷酸重复序列的过度扩展所致。正常人群中CTG的拷贝数为5-30,而患者在50以上,且具民族差异。目前尚无我国羌族人群的有关资料。为了解中国羌族人群该基因3'UT R CTG三核苷重复序列的分布情况,作者采用PCR、聚丙烯酰胺凝胶电泳、银染和测序等技术,对60例正常羌族人的CTG重复序列进行了分析。共发现8种等位基因,其中CTG拷贝数为5的等位基因最为常见,占30 .83%,其余依次为13拷贝(22.5%)、12(19.17%)、11(15.83%)、14(5.83%)和15(4.17%);拷贝数大于15的等位基因极少,仅检测到一例,为27拷贝;CT G拷贝数在6-10之间的等位基因也很少,仅发现一例为9拷贝,而该等位基因在其它人群尚无报道。60名个体中共发现纯合子18例,其中9例为5/5,2例为11/11,2例为12/12,4例13/13和1例为15/15,杂合率为70%。本系统的多态信息量(PIC)为0.77。羌族和汉族人群该位点的多态性无显著差异。 Abstract:Myotonic dystrophy is associated with an increased number of CTG repeats in the 3’UTR of the myotonic protein kinase gene(MT-PK) located on chromosome 19q13.3.The triplet repeats region of the gene of 60 healthy Qiang subjects from Sichuan province was analyzed by polymerase chain reaction and polyacrylamide gel electrophoresis.A total of 8 alleles were found ranging in size from 5 to 27copies with the most common allele of 5 copies(30.83%).The other major alleles were 11,12 and 13 copies with frequency of 15.83%,19.17% and 22.5%,respectively.An allele of 9 copies was found in a Qiang individual which has never been reported before in other populations.Only 5.83% of alleles were longer than 14 copies and one longer than 15 copies.Heterozygote frequency in this population was 70%.The CTG repeats is highly informative with a PIC value of 0.77.There is no significant difference between Qiang and Han population in the distribution of the CTG allele frequencies.