焦磷酸测序技术分析单核苷酸多态性在法医学中的应用

单核苷酸多态性（SNP）是新一代的法医学遗传标记,有望成为法医实践中解决高度降解检材及特殊案件DNA鉴定的重要工具。近年来涌现出许多高通量的SNP分析方法,如引物延伸结合时间飞行质谱分析法、微测序法、SNP lex以及焦磷酸测序法等。本文重点对焦磷酸测序技术的原理、步骤及其在法医学中的应用进展进行简要的综述。     

遗传标记微单倍型在法医学中的研究进展

微单倍型作为一种新型的法医学遗传标记,在国际法医学界已经引起了越来越多的关注。微单倍型是在较短片段内(例如200bp),包含2个或以上个SNP,具有单倍型多态性的序列。相较于STR,微单倍型突变率低,在混合斑鉴定中具有一定优势;与SNP相比较,微单倍型的多态性更高。选择含有祖先信息特征的微单倍型,在种群分析鉴定中具有应用价值。本文就微单倍型的演变,分型方法,命名及群体特征等方面作一综述。     

中国内蒙古地区蒙古族群体13个SNPs遗传多态性

单核苷酸多态性（SNP）是一种具有高度稳定性的遗传学标记。在基因多态性研究、基因图谱构建、疾病诊断、预防和药物筛选中具有重要作用。本文采用荧光标记片段长度差异等位基因特异性复合扩增技术,对内蒙古地区242名无血缘关系蒙古族个体13个SNP进行调查,并评价其法医学应用价值。     

采用Pyrosequencing和Pooling技术对SNP位点多态性分析

目的建立基于pyrosequencing和Pooling技术进行SNP位点的法医学多态性分析技术。方法对50名无关个体样本建立一适合pyrosequencing检测的组池;采用PyroMark Assay Design 2.0软件进行SNP位点等位基因定量分析的引物设计;对组池样本PCR产物进行焦磷酸测序检测。结果检测的3个SNP位点多态性良好,其中位点rs220028与以往人群调查后频率数据无显著差异。结论采用pyrosequencing和Pooling技术对SNP位点进行多态性分析,适合于位点的初筛及大规模群体调查。该技术准确可靠,方便快捷。     

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。     

采用Pyrosequencing和Pooling技术对SNP位点多态性分析

目的 建立基于pyrosequencing和Pooling技术进行SNP位点的法医学多态性分析技术.方法 对50名无关个体样本建立一适合pyrosequencing检测的组池;采用PyroMark Assay Design 2.0软件进行SNP位点等位基因定量分析的引物设计;对组池样本PCR产物进行焦磷酸测序检测.结果 检测的3个SNP位点多态性良好,其中位点rs220028与以往人群调查后频率数据无显著差异.结论 采用pyrosequencing和Pooling技术对SNP位点进行多态性分析,适合于位点的初筛及大规模群体调查.该技术准确可靠,方便快捷.     

焦磷酸测序在法医学中的应用及其评价

利用高灵敏度、全自动化的方法对微量和痕量样本的DNA分型一直是法医学工作的重点与难点。焦磷酸测序技术具有实时监测、高通量、无需胶检测和荧光标记、定量性能好、结果准确和可自动化的优势。本文就焦磷酸测序化学反应测序的原理、流程及其在法医学SNP分型、建立标准化分型体系、大规模人群数据库建设及与其他常用分型技术的比较做一综述。     

焦磷酸测序在法医学中的应用及其评价

利用高灵敏度、全自动化的方法对微量和痕量样本的DNA分型一直是法医学工作的重点与难点.焦磷酸测序技术具有实时监测、高通量、无需胶检测和荧光标记、定量性能好、结果准确和可自动化的优势.本文就焦磷酸测序化学反应测序的原理、流程及其在法医学SNP分型、建立标准化分型体系、大规模人群数据库建设及与其他常用分型技术的比较做一综述.     

焦磷酸测序在法医学中的应用及其评价

利用高灵敏度、全自动化的方法对微量和痕量样本的DNA分型一直是法医学工作的重点与难点.焦磷酸测序技术具有实时监测、高通量、无需胶检测和荧光标记、定量性能好、结果准确和可自动化的优势.本文就焦磷酸测序化学反应测序的原理、流程及其在法医学SNP分型、建立标准化分型体系、大规模人群数据库建设及与其他常用分型技术的比较做一综述.     

焦磷酸测序在法医学中的应用及其评价

利用高灵敏度、全自动化的方法对微量和痕量样本的DNA分型一直是法医学工作的重点与难点.焦磷酸测序技术具有实时监测、高通量、无需胶检测和荧光标记、定量性能好、结果准确和可自动化的优势.本文就焦磷酸测序化学反应测序的原理、流程及其在法医学SNP分型、建立标准化分型体系、大规模人群数据库建设及与其他常用分型技术的比较做一综述.     

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。     

荧光标记复合扩增毛细管电泳法在SNP分型中的应用

目的采用荧光标记复合扩增毛细管电泳法，对辽南地区汉族人群13个SNP进行等位基因频率调查，并评价其法医学应用价值。方法选择13个双等位基因SNP，应用荧光标记片段长度差异等位基因特异性复合扩增SNP分型方法，对辽南地区汉族人群进行群体调查。结果每个SNP纯合子为单一产物峰，杂合子则为长度不同的两个产物峰。不同位点扩增产物长度不同，根据产物长度和产物峰数量进行SNP分型，其结果与直接测序完全一致。同时获得辽南地区汉族人群13个SNP等位基因频率。结论采用荧光标记复合扩增毛细管电泳法进行SNP分型，方法简单实用，在法医学个人识别领域具有较高的应用。     

SNPs in forensic genetics: a review on SNP typing methodologies

There is an increasing interest in single nucleotide polymorphism (SNP) typing in the forensic field, not only for the usefulness of SNPs for defining Y chromosome or mtDNA haplogroups or for analyzing the geographical origin of samples, but also for the potential applications of autosomal SNPs. The interest of forensic researchers in autosomal SNPs has been attracted due to the potential advantages in paternity testing because of the low mutation rates and specially in the analysis of degraded samples by use of short amplicons. New SNP genotyping methods, chemistries and platforms are continuously being developed and it is often difficult to be keeping up to date and to decide on the best technology options available. This review offers to the reader a state of the art of SNP genotyping technologies with the advantages and disadvantages of the different chemistries and platforms for different forensic requirements.     

法医SNP复合检测体系的构建及应用

目的构建48-SNP位点复合检测体系,用于个体识别、性别鉴定、ABO基因分型。方法采集225份无关个体样本(血斑及口腔拭子),18份案例样本(不同组织及体液斑),选择43个常染色体位点、4个ABO基因位点和1个性别鉴定位点,根据单碱基延伸技术通过GenomeLabTMSNPstream基因分型系统进行SNP分型;并检测体系灵敏度、同一个体不同组织同一性及模拟腐败检材。结果 48-SNP体系分型结果与测序结果的一致性为100%,最小DNA检出量为0.25ng,不同组织来源样本检测同一性很好;利用该体系检测225名无关汉族个体,所有位点均符合Hardy-Weinberg平衡,整个系统的随机匹配概率为9.4×10-18,累积非父排除率(CEP)为0.999 788,累积个体识别率大于0.999 999 999 999 999 99。结论本文48-SNP体系能同时进行个体识别、ABO基因分型和性别鉴定,可以作为现有STR检验体系的补充。     

SNP genotyping by multiplex amplification and microarrays assay for forensic application

OBJECTIVE: Research on the application feasibility of SNP genotyping for forensic identification by microarrays. METHODS: Oligonucleotide microarrays which could detect 34 different SNPs were used. After hybridization and washing, the arrays were scanned and fluorescence intensities analyzed using Microarray software. Population studies on 34 SNP loci were carried out in a sample of 109 unrelated Chinese Han individuals using oligonucleotide microarrays for genotype detection. The method was also applied to cases. RESULTS: According to the results of population studies, no deviations from Hardy-Weinberg equilibrium could be found. Among the 34 loci, 3 SNPs were low informative, 4 were medium informative and 27 were high informative. The combination discrimination power (CDP) of the 31 optimal polymorphic SNPs was 0.9999999999979. The matching probability was 2.13 x 10(-12). The average exclusion probability in paternity testing for duos was 0.9609. The average exclusion probability in paternity testing for trios was 0.9970. CONCLUSION: The data and case application demonstrated that SNP typing by oligonucleotide probe microarrays was a useful technique for paternity testing and individual identification. Combined with the 28 SNPs loci distributed on HLA-DRB1 and ABO genes, the combination discrimination power (CDP) was 0.9999999999999910. The matching probability was 9.02 x 10(-15). The average exclusion probabilities in duos and in trios were 0.9894 and 0.9992, respectively. It may be concluded that the 59 SNPs loci yield the same power in forensic identification as CODIS STRs currently used.     

MtSNP typing before mtDNA sequencing: Why do it?

Analysis of control mitochondrial DNA (mtDNA) hypervariable regions is sometimes the only available method to study hair evidence in forensic casework although being a laborious technique. Nowadays there is a huge interest in new genetic markers such as single nucleotide polymorphisms (SNPs) to type degraded forensic samples. For that purpose, a 10-Plex mitochondrial SNP for haplogroup typing, chosen from several SNP studies and useful to study the most common populations in our laboratory was applied in forensic casework. Hair shafts from three forensic cases with different ethnic backgrounds were studied with mtDNA sequencing and compared with mitochondrial SNPs (mtSNPs) study. Coding mtSNP typing prior to sequencing can allow for a rapid screening in forensic casework, which is emphasized in the first two cases. Moreover, in cases in which mtDNA sequencing fails, mtSNPs can still be detected. This 10 SNP loci multiplex provides a less expensive and simpler method for mitochondrial typing compared to control region mtDNA sequencing, especially when used as a fast screening method.     

二代测序技术在法医学中的应用

随着二代测序技术的快速发展,其高通量和低成本在生命科学领域应用广泛,测序的通量更高,测序时间和成本不断下降,使得其被广泛应用于微生物研究、古DNA研究、临床诊断、法医学研究等。本文阐述了二代测序技术平台及其遗传标记在法医学中的应用,包括STR分型、SNP分型、HLA基因型预测以及在降解检材中的应用等。     

A new 39-plex analysis method for SNPs including 15 blood group loci

A novel 39-plex typing system for single nucleotide polymorphisms (SNPs) has been developed. This multiplex approach has the advantage of being able to type 38 autosomal SNPs and one sex-discriminating base exchange site on the X and Y chromosomes rapidly and simultaneously. The SNP loci on the autosomes, which we examined, contain 15 loci distributed on blood type genes: three on RhCE, two each on Km and Gc, and one each on Duffy, AcP1, Tf, MN, GPT, EsD, PI, and Kidd genes. Thirty-seven genomic DNA fragments containing a total of 38 SNPs and one sex-discriminating site were amplified in one multiplex PCR reaction. Following the reaction, single nucleotide primer extension reaction was performed by dividing these SNP loci into five groups. The SNP type of each of the 39 loci was determined at one time by capillary electrophoresis using the newly designed multi-injection method. The combined PD (power of discrimination) of this typing system was (1-1.1) x 10(-14), and the MEC (mean exclusion chance) was 0.9990. We applied this system to forensic cases, including 16 paternity testing cases (13 non-exclusion and three exclusion cases) and one personal identification case. For the paternity testing cases, the highest Essen-M?ller's W-value was 0.9999995. The pM (matching probability) of the personal identification case was 2.22 x 10(-17). These data showed that this system was an excellent tool for use in forensic cases of paternity testing and personal identification.     

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.     

Internal validation of 29 autosomal SNP multiplex using a ABI 310 genetic analyser

In the last few years genetic identification and paternity testing have begun to make increasing use of autosomal SNP (Single Nucleotide Polymorphism) typing as a supplement or alternative to STR analysis. With the improvement in detection technology SNP analysis is likely to be easier and more sensitive, with the generation of new methods and multiplex systems for a growing array of SNP markers. SNPforID consortium developed 52 SNP PCR multiplex for human identification purposes detected with 23 plex and 29 plex single base extension reactions (Auto1 and 2 respectively). In this study, internal validation for the 29 SNPs of Auto2 was carried out by performing a 29 plex PCR and single base extension reaction on control samples and previously analyzed forensic casework and subsequent detection with an AB 310 Genetic Analyzer. We tested the accuracy, precision, sensitivity and reproducibility of the Auto2 multiplex with this instrument in our laboratory. We used 9947A control DNA samples of the AmpF?STR Identifiler™ kit to test the validation parameters together with non-probative DNA samples from whole blood and buccal swab samples of 29 healthy donors from different parts of Istanbul. Good results were obtained but interpretation of the peak patterns obtained on the AB 310 requires care and thorough optimization before they can be readily compard to those obtained from multiple capillary AB 31xx Analyzers. We succesfully optimized and validated the SNPforID Auto2 multiplex system for identification analyses in our laboratory.