单核苷酸多态性及其检测方法

单核苷酸多态性（single nucleotide polymorphisms，SNPs），作为第三代遗传标记，已经广泛应用于基因作图、遗传性和遗传相关性疾病的诊断、群体遗传学、药学研究和法医学等领域。SNP的检测方法多种多样．本文简要介绍SNP的特点和几种检测方法。     

采用SNP分型方法对甲醛固定组织进行个体识别

目的通过对X染色体SNP遗传标记的检测,探讨甲醛固定组织块的DNA分型策略。方法提取甲醛固定组织块的DNA,在用SinofilerTM试剂盒、MiniFilerTM试剂盒检测未能获得分型结果的情形下,采用多重PCR和飞行质谱技术对X染色体上的51个SNP位点进行分型检测。结果对于常染色体STR、miniSTR分型失败的甲醛固定组织块,X-SNP分型获得成功。结论对于甲醛固定组织块等微量、降解的生物学检材,若常染色体STR基因座分型失败,可尝试进行SNP位点的分型,以获得更多的遗传信息。     

中国北方汉族群体TPH2基因5′和3′端SNP位点遗传多态性

目的调查中国北方汉族群体TPH2基因5′和3′端SNP位点遗传多态性并探讨其法医学应用价值。方法测序分析244例中国北方健康无关个体TPH2基因5′端905 bp和3′端1 104 bp两个靶片段的序列特征和6个SNP位点(rs4570625、rs11178997、rs11178998、rs41317118、rs17110747和rs41317114)的遗传多态性,应用Haploview v4.2软件进行统计分析。结果 244例中国北方汉族个体6个SNP位点基因型分布均符合Hardy-Weinberg平衡定律,在92922位点检测到1例C/T变异,TPH2基因5′端3个SNP位点(rs4570625、rs11178997和rs11178998)和3′端3个SNP位点(rs41317118、rs17110747和rs41317114)分别显示出高度连锁不平衡,获得了TPH2基因6个SNP位点的群体遗传学参数。结论中国北方汉族群体TPH2基因5′和3′端序列呈现出高度遗传多态性,可作为相关疾病关联分析的遗传学指标,同时可用于个体识别和亲权鉴定。     

SNPlex系统检测方法及在法医遗传学中的应用前景

被称为第三代遗传标记的SNP是近年来的研究热点,对SNP检验检测方法很多,例如引物延伸结合时间飞行质谱分析法,微矩阵基因分型法,SNPlex基因分型系统等,本文重点介绍的就是SNPlex基因分型系统,及其法医学应用前景.这种系统是利用DNA模板直接与等位基因特异探针和位点特异性探针结合,连接产物经扩增之后与特异探针杂交结合,最后通过毛细管电泳检测特异探针进行SNP分型.     

血小板同种抗原基因中9个单核苷酸多态性在广西地区壮族和汉族人群中的差异分析

目的检测血小板同种抗原基因中9个单核苷酸多态性在广西地区壮族和汉族人群中的差异。方法利用基于单碱基延伸的单核苷酸多态性（SNP）分型芯片,对广西壮族地区99例壮族个体和107例汉族个体的染色体基因组上10个SNP位点进行了分型,其中9个位于6个血小板同种抗原基因中,1个位于基因间区。此外,结合Hapmap计划第二期公布的四个人群的SNP分型数据,分析这六个人群的遗传结构。结果广西原住汉族人在等位基因频率上未检测到与当地壮族有显著性的差异位点,但在基因型频率上,rs630014和rs9441951两位点是显著差异的。广西壮族人与广西汉族、北京汉族人及日本东京人的遗传结构相近,但与祖先来自欧洲西部和北部的犹他州居民以及尼日利亚伊巴丹的约鲁巴人有显著差异的遗传成分存在。结论壮汉两族由于历史上的多次基因交流可能导致其遗传信息在很大程度上是相近的。     

SeqType~? P52人类祖先识别SNP检测试剂盒性能验证

目的评估基于高通量测序平台研发的SeqType~? P52人类祖先识别SNP检测试剂盒对中国5个民族的区分效能。方法基于高通量测序平台检测SeqType~? P52人类祖先识别SNP检测试剂盒,对来自中国汉族、藏族、蒙古族、维吾尔族、彝族共计350份样本进行检测和族群聚类分析。结果单个样本单个位点有效测序深度≥720×,平均检出率96%。藏族、蒙古族、维吾尔族、彝族4个民族和汉族的群体间等位基因频率差均值分别为0.20、0.05、0.24和0.11。在Structure 2.3.4 K=5模式下可以检测到汉族、藏族和维吾尔族比较独立的祖先成分,这与主成分分析(pricipal component analysis,PCA)结果相一致。对于彝族,其2/3拥有相对独立的与藏族人群接近的祖先成分,1/3成分和维吾尔族相似。蒙古族则拥有与汉族人群相似的祖先来源成分。结论本研究筛选并建立的52个祖先信息SNP位点复合检测体系能够有效地实现汉族、藏族、维吾尔族人群的成分构成和个体遗传成分的分析,对汉族、蒙古族、彝族3个民族区分能力还有待提高。SeqType~? P52人类祖先识别SNP检测试剂盒可以用于法医DNA部分案件中个体祖先的来源推断。     

31个SNP位点多重PCR扩增和芯片分型技术的建立及其法医学应用

目的对SNP基因分型芯片在个体识别中的应用价值进行研究。方法根据SNP不同等位基因的序列设计探针,制成分型芯片。采用4个复合PCR体系,用末端标记了Cy5的引物进行复合PCR扩增,产物与寡核苷酸探针进行杂交,根据杂交产生的荧光信号值确定样品在各SNP位点的基因型。将这一方法应用于109份样本的分型,根据基因型分布统计分析31个SNP位点的法医学应用价值。同时,进行家系调查和方法灵敏度分析。结果方法的灵敏度为1ng;所检测的31个SNP位点的累积个体识别率为0.9999999999979(偶合率为2.13×10-12),二联体亲子鉴定中累积非父排除率为0.9609,三联体亲子鉴定中累积非父排除率为0.9970。家系调查的结果表明,这些位点等位基因由亲代向子代的传递符合孟德尔遗传定律。结论上述31个SNP位点为中高信息量位点,适用于法医学个体识别,可作为当前STR系统的补充。     

中国回族人群SNP rs445251和rs1523537遗传多态性

由于单核苷酸（single nucleotide polymorphisms,SNP）具有广泛存在于基因组中,突变率低及扩增产物长度可小于100bp等优点,是法医实践中亲子鉴定和个人识别的重要遗传标记,也适合于高度降解检材的检测。     

单核苷酸多态性分析方法

SNP是第三代遗传标记,在法庭科学及其领域中具有重要作用。当前,已建立了许多SNP分析方法,本文介绍变性高压液相色谱法、时间飞行质谱熔解曲线法、熔解温度曲线法、等位基因特异扩增结合熔解曲线法、分子信号和TaqMan等新的SNP分析方法。     

SNP-STR遗传标记复合扩增体系的构建及法医学应用

目的筛选并构建与目前STR数据库兼容的SNP-STR遗传标记复合扩增体系,调查其在四川汉族群体中的遗传多态性,并探讨其在混合DNA样本分析中的应用价值。方法以现有商业试剂盒中使用的STR遗传标记为基础,筛选与STR遗传标记相邻的SNP位点并组成SNP-STR遗传标记。运用SNP等位基因设计特异性引物,构建基于等位基因特异性扩增的SNP-STR遗传标记复合扩增体系。调查该体系在四川汉族群体的遗传多态性,并评价不同位点数目的体系对两个体混合DNA样本的检测效能。结果筛选并构建了由13个SNP-STR遗传标记构成的等位基因特异性复合扩增体系。在四川汉族群体中,各位点杂合度为0.76～0.88,累积个体识别率达0.999 999 999 999 999 968。在对两个体混合DNA的分析中:单位点扩增时,混合样本的混合比例达到1 000∶1时依然可以检测到少量成分所特有的分型;多位点复合扩增时,混合比例最大可达500∶1;随着体系中位点数量的增加,对混合DNA中少量成分的检测效能降低。结论SNP-STR遗传标记较STR具有更高的多态性,其构成的复合扩增体系对混合样本的分析效能优于传统的STR复合扩增体系。     

单核苷酸多态性及其在法医学中的应用前景

单核苷酸多态性是人类基因组中最常见、分布最广泛的DNA多态性类型。随着人类基因组计划的迅猛发展,已有越来越多的单核苷酸多态性位点被发现,使其可以广泛应用于人类遗传性和遗传相关性疾病的诊断、群体遗传学的研究、药物的开发及应用等方面,同样在法医学也具有广阔的应用前景。本文综合介绍了单核苷酸多态性的一般特性及法医学应用前景,包括其应用的可行性、存在的问题及高通量自动化的检测方法。     

The Mediterranean basin: A population genetic study based on 25 X-chromosome SNPs

The X-chromosome has valuable characteristics for population genetic studies. In order to investigate the genetics of the human Mediterranean populations further, we developed a 25 X-chromosome SNP-multiplex typing system. The system was based on PCR multiplex amplification and subsequent multiplex single base extension with the SNaPshot reaction, capillary electrophoresis and multicolor fluorescence detection.We investigated 11 Mediterranean populations with the 25 X-chromosome SNPs. A high overall homogeneity was found among the Mediterranean populations except for Moroccans, who differed genetically from the rest of the populations in the Mediterranean area. This result supports the hypothesis of a low incidence of the south-north genetic interchange at the western shores of the Mediterranean basin. A low genetic distance was found between populations in the Middle East and the western part of the Mediterranean area most likely reflecting the strong effect of the Neolithic wave.A certain level of background linkage disequilibrium among the 25 SNPs on the X-chromosome in Ibiza and Cosenza was observed, possibly as a consequence of their demographic history.     

Y－染色体SNPs及其在法医学中的应用价值

随着人类基因组计划的迅猛发展,已有越来越多的Y染色体SNP位点被发现,在个人识别、家系谱的建立、疾病的预测与诊断方面,Y染色体单核苷酸多态性提供了非常有价值的遗传标记。同样在法医学中也有广阔的应用前景。本文综合介绍了SNP和Y-SNP的一般特性及在法医学中的应用价值。     

X染色体上高信息量SNP位点及其法医学价值

人类X染色体长154.8Mb,其上密布SNP位点,蕴涵着大量的信息。用于法医学鉴定的X-SNP标记多态性好、突变率低。本研究从Hapmap、NCBI的数据库中筛选了167个高信息量SNP位点,这些位点的等位基因在北京汉族人群中的分布频率均高于0.3,通过高通量、高灵敏度的检测方法可对各个X-SNP位点进行分型验证,通过正确的统计学分析可得到其法医学多态性参数。X-SNP位点具有一些常染色体遗传标记无法比拟的优点,作为常规STR基因座的补充,能用于解决特殊的亲子鉴定案,性别鉴定和混合斑鉴定。     

Mass spectrometry-based SNP genotyping as a potential tool for ancestry inference and human identification in Chinese Han and Uygur populations

Ancestry informative SNPs (AISNPs) are genetic variants that exhibit substantially different frequencies between populations from different geographical regions; thus, they can provide some valuable information regarding samples and be used in predicting an individual's ancestry origin. In this study, we selected the potentially best SNPs from our previous study with genome-wide high-density SNP data in mainland Chinese Uygur and Han populations and investigated the allele distribution patterns and genetic information of AISNPs with a mass spectrometry-based SNP genotyping panel. Mass spectrometry-based detection technology offers the opportunity to analyze forensic DNA samples and obtain SNP variants with accuracy and ease. The panel can distinguish and cluster Han and Uygur populations and is suitable for human identification and parentage testing in the two populations. Heatmap, PCA, and Structure analyses indicated that the ideal 64 AISNPs can collectively provide additional information on differences among populations from East Asia, South Asia, Europe and Africa. Additionally, the results proved that the Uygur population is the admixture of East Asia and Europe.     

Y-SNP typing of U.S. African American and Caucasian samples using allele-specific hybridization and primer extension

Multiplex analysis of genetic markers has become increasingly important in a number of fields, including DNA diagnostics and human identity testing. Two methods for examination of single nucleotide polymorphisms (SNPs) with a potential for a high degree of multiplex analysis of markers are primer extension with fluorescence detection, and allele-specific hybridization using flow cytometry. In this paper, we examined 50 different SNPs on the Y-chromosome using three primer extension multiplexes and five hybridization multiplex assays. For certain loci, the allele-specific hybridization method exhibited sizable background signal from the absent alternate allele. However, 100% concordance (>2000 alleles) was observed in ten markers that were typed using both methods. A total of 18 unique haplogroups out of a possible 45 were observed in a group of 229 U.S. African American and Caucasian males with the majority of samples being assigned into 2 of the 18 haplogroups.     

SNPs在个体识别与表型预测中的研究进展

单核苷酸多态性（single nucleotide polymorphism,SNP）作为第三代遗传标记,具有分布广泛、突变率低、遗传稳定及易于自动化高通量快速检测分析的特点。同时,因其扩增片段长度短、不存在复制滑动,所以利于腐败降解、痕量检材的检测。随着研究的深入,SNPs在法医学领域受到了广泛重视,与表型（ABO血型、色素沉积及颅面形态）相关的SNPs有望用于预测嫌疑人的基本特征,为案件侦破提供新的思路。本文对近年来SNPs在个体识别和表型预测的研究进行总结,介绍该领域的研究进展,为法医学工作者提供参考。     

Development of a genetic traceability test in pig based on single nucleotide polymorphism detection

In order to assure traceability along the meat transformation process, a powerful system is required. The administrative traceability shows limits that the use of genetic markers could overcome. The individual genomes contain sequence differences, basis of the genetic polymorphism of which the genetic markers are the witnesses. Among them, two classes seem to dominate on the traceability field: the microsatellites and the single nucleotide polymorphisms (SNP). The aim of this work was to develop a genetic traceability test in pig based on SNPs mainly located in 5' and 3' untranslated regions (UTRs). A set of 21 SNP markers including new SNPs identified in this study and SNPs previously described was selected. A genotyping assay was performed on 96 individuals representing the major crossbred of the pig population in Belgium. Results showed that all individuals tested presented a different genotype. This genotyping method might help the administrative system to guarantee the traceability of pork meat along the transformation process.     

Forensic typing of autosomal SNPs with a 29 SNP-multiplex—Results of a collaborative EDNAP exercise

We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised the exercise. A total of 11 European and one US forensic genetic laboratories tested a subset of a 52 SNP-multiplex PCR kit developed by the SNPforID consortium. The 52 SNP-multiplex kit amplifies 52 DNA fragments with 52 autosomal SNP loci in one multiplex PCR. The 52 SNPs are detected in two separate single base extension (SBE) multiplex reactions with 29 and 23 SNPs, respectively, using SNaPshot kit, capillary electrophoresis and multicolour fluorescence detection. For practical reasons, only the 29 SBE multiplex reaction was carried out by the participating laboratories. A total of 11 bloodstains on FTA cards including a sample of poor quality and a negative control were sent to the laboratories together with the essential reagents for the initial multiplex PCR and the multiplex SBE reaction. The total SNP locus dropout rate was 2.8% and more than 50% of the dropouts were observed with the poor quality sample. The overall rate of discrepant SNP allele assignments was 2.0%. Two laboratories reported 60% of all the discrepancies. Two laboratories reported all 29 SNP alleles in all 10 positive samples correctly. The results of the collaborative exercise were surprisingly good and demonstrate that SNP typing with SBE, capillary electrophoresis and multicolour detection methods can be developed for forensic genetics.