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。     

大规模平行测序技术在STR遗传标记检测中的应用进展

近年来,越来越多的法医遗传学实验室着手应用大规模平行测序（massively parallel sequencing,MPS）技术,即二代测序（next-generation sequencing,NGS）技术,检测包括短串联重复序列（short tandem repeat,STR）和单核苷酸多态性（single nucleotide polymorphism,SNP）在内的常用法医学遗传标记,以及线粒体DNA(mitochondrial DNA,mtDNA)控制区或全序列和信使RNA(messenger RNA,mRNA)等,用于个体识别、亲缘关系鉴定、祖源推断和体液识别等法医学实践。其中,STR作为法医遗传学中使用范围最广的遗传标记,目前主要应用毛细管电泳（capillary electrophoresis,CE）平台检测。与该平台相比,MPS技术具有能够同时检测大量遗传标记、多样本并行检测、测得序列多态性使STR具有更高的分辨能力和系统效能等优势。然而,MPS检测技术花费较大,尚未有统一的使用规范,以及存在如何整合MPS-STR数据与现存CE-STR数据库等难题。本文总结了法医遗...     

等位基因特异性PCR技术及其法医学应用

等位基因特异性PCR（allele-specific polymerase chain reaction,AS-PCR）是一种基于等位基因特异性引物引导的PCR技术,可以有效地分析单核苷酸多态性（SNP）,包括碱基的转换、颠换以及插入/缺失多态性,在疾病研究、分子诊断以及法医物证学研究中具有很好的应用价值.本文系统地综述了AS-PCR技术的原理、检测手段、改进方法及在常染色体、Y染色体和线粒体SNP等领域的研究成果,探讨其法医学应用价值.     

湖南平江地区汉族人群(客家人)20个STR基因座的遗传多态性CSCD

短串联重复序列（STR）分型检验是当前法医DNA检验的重要技术之一,被广泛应用于法医学个体识别和亲缘关系鉴定.湖南平江地区东南部是“客姓人”（客家人）的聚居地,本研究对该地区汉族人群（客家人）20个STR基因座进行遗传多态性分析,为法医学研究提供遗传学基础数据。     

GRIN1基因-855G／C和-1140G／A位点遗传多态性

谷氨酸（glutamate．Glu）是哺乳动物脑内重要的兴奋性神经递质．Glu通过作用其受体发挥着重要的生物学功能。Glu受体基因存在单核苷酸多态性（single nueleotide polymorphism．SNP）,为探讨其在法医学中的应用价值．本研究调查了Glu受体基因之一GRIN1启动子区域-855G／C与-1140G／A2个SNP位点在中国北方汉族群体中的频率分布。     

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。     

法医SNP系谱推断技术研究进展

法医SNP系谱推断技术是利用基因组中的高密度SNP数据，基于血缘同源片段长度分析等算法，推断远亲缘关系的一种新型侦查技术手段。与传统STR亲缘关系鉴定方法相比，法医SNP系谱推断技术可以分析更远的亲缘关系，且可以在社会公共DNA数据库中进行家族关系搜索，应用场景更为广阔，包括犯罪嫌疑人查找、受害者的身源鉴定、失踪人口寻找等。本文就法医SNP系谱推断技术的遗传学原理、高密度SNP分型技术、常用的推断算法以及在低质量DNA中的应用等方面的研究进展进行阐述，以期为该技术应用时选择合适的检测技术和亲缘关系分析算法提供思路。     

CCK受体基因多态性及与部分精神疾病症状的相关性

胆囊收缩素(CCK)不仅存在于消化系统,而且还广泛存在于中枢及外周神经系统,并以神经递质的形式通过其受体(CCK-R)发挥着重要的生理作用。CCK-R有两种类型,CCK-AR和CCK-BR。CCK-R基因具有遗传多态性,并通过影响或改变CCK对中枢神经系统的作用强度而与酒精中毒、精神分裂症、恐慌症等人类精神疾病密切相关。CCK-R基因遗传多态性的研究可能为法医学个人识别与亲权鉴定新提供新的遗传标记及为司法精神病鉴定提供参考性遗传学指标。     

第一届“两岸法医学术交流论坛”将在台北市召开

1．会议专题：（1）法医制度与法规（2）法医病理学（3）法医毒物学（4）法医生物学（含DNA鉴定）（5）临床法医学（6）其它：牙科法医学、精神法医学等     

新一代遗传标记——InDel研究进展

法医DNA分型经历了三代遗传标记的研究,短串联重复序列(short tandem repeat,STR)作为比较成熟的工具已被广泛运用于法医生物学鉴定中。进一步对人类基因组的探索,先后发现了单核苷酸多态性(single nucleotide polymorphism,SNP)、插入/缺失(Insertion/Deletion,InDel)等一系列遗传标记,而其中InDel作为新型的遗传标记,基本兼具各类遗传标记的优点,受到包括医学分子生物学和法医生物学在内各领域的广泛关注。本文就InDel的研究历史与相应的成果进行简单总结与回顾,以时间轴与研究目的为主要的分类指标,重点关注以多个InDel联合作为遗传标记的多重扩增系统(常染色体或X染色体)在法医生物学及人类学研究中的进展,并对今后该领域研究的方向与暨待解决的问题进行了综述。     

Polymorphisms of the cholecystokinin gene promoter region in suicide victims in Japan

Cholecystokinin (CCK), a neurotransmitter in the central nervous system (CNS), co-exists in a large portion of A10 dopamine neurons to exert some effect on dopamine behavior. The aim of this study was to determine whether any association exists between the genotype of CCK gene promoter regions (-45C/T and -196G/A) and suicidal behavior. Genotypes and allele frequencies of CCK -45C/T and -196G/A were analyzed using polymerase chain reaction (PCR) followed by single-strand conformational polymorphism (SSCP) analysis on the genomic DNA from selected suicide victims (N=154) and from control subjects (N=328). Statistical analysis was performed using the Mantel-Haesnzel chi2-test and multiple logistic regression analysis with distinction of gender. An association between CCK -196G/A polymorphism and suicidal behavior in Japanese males was confirmed by statistical analysis (Odds ratio: 3.462, 95% CI: 1.128-10.626, P=0.038 by multiple logistic regression analysis). However, a significant association between CCK -196G/A polymorphism and suicidal behavior was not discovered in females. The polymorphism of the CCK gene promoter region was found to represent a susceptibility factor for suicidal behavior in Japanese males.     

谷氨酸受体基因单核苷酸多态性与精神分裂症的关联

谷氨酸是人类神经系统中重要的兴奋性神经递质,通过与受体结合发挥生物学作用.当编码受体的基因异常时,可能导致精神疾病发生.本文通过回顾相关研究,发现诸如GRIN1、GRIN2B、GRM3等受体基因上的rs11146020、366C/G、rs1468412与精神分裂症相关联;同时也存在矛盾的研究结果,表明精神分裂症可能为多因素、多位点、多基因复杂遗传疾病.部分位点如GRIN2B上的366C/G、2664C/T,GRIK2上的rs1408766(C/T)的遗传多态性较好,可能成为法医学个人识别与亲权鉴定的新指标.该领域研究在司法精神病的鉴定工作中可能具有潜在的意义.     

Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing

The development of new methodologies for high-throughput SNP analysis is one of the most stimulating areas in genetic research. Here, we describe a rapid and robust assay to simultaneously genotype 17 mitochondrial DNA (mtDNA) coding region SNPs by minisequencing using SNaPshot. SNaPshot is a methodology based on a single base extension of an unlabeled oligonucleotide with labeled dideoxy terminators. The set of SNPs implemented in this multiplexed SNaPshot reaction allow us to allocate common mitochondrial West Eurasian haplotypes into their corresponding branch in the mtDNA skeleton, with special focus on those haplogroups lacking unambiguous diagnostic positions in the first and second hypervariable regions (HVS-I/II; by far, the most common segments analyzed by sequencing). Particularly interesting is the set of SNPs that subdivide haplogroup H; the most frequent haplogroup in Europe (40-50%) and one of the most poorly characterized phylogenetically in the HVS-I/II region. In addition, the polymorphic positions selected for this multiplex reaction increase considerably the discrimination power of current mitochondrial analysis in the forensic field and can also be used as a rapid screening tool prior to full sequencing analysis. The method has been validated in a sample of 266 individuals and shows high accuracy and robustness avoiding both the use of alternative time-consuming classical strategies (i.e. RFLP typing) and the need for high quantities of DNA template.     

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.     

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。     

基于二代测序平台的90个常染色体SNP分型研究

目的基于二代测序平台进行90个常染色体SNP位点分型,调查其在中国广东汉族人群中的多态性,评估其法医学应用价值。方法采集100例中国广东汉族无关个体外周血样,采用Auto Mate Express TM提取样本DNA,使用HID-Ion Ampli Seq?Identity Panel分型体系复合扩增90个SNP位点制备文库,Ion One Touch?2进行乳化PCR,Ion PGM?平台进行测序,Torrent_Suite_v4.4.2软件及HID_SNP_Genotyper_v4.3.1插件进行数据分析,计算常用法医学参数并与该群体Goldeneye TM 20A体系的检测效能进行比较。结果经Bonferroni法校正后,90个常染色体SNP位点分布均符合Hardy-Weinberg平衡,不存在连锁不平衡现象。各位点平均杂合度(Ho)为0.423,平均个体识别力(DP)为0.560,平均多态信息含量(PIC)为0.329。90个SNP体系的累积个体识别率(CDP)为(1-1.20×10~(-33)),大于20A体系;三联体累积非父排除率(CPE_(tri))为0.999 999 911,二联体累积非父排除率(CPE_(duo))为0.999 882,均小于20A。结论 90个常染色体SNP检测体系可独立应用于法医个体识别和三联体亲子鉴定,并辅助进行二联体亲子鉴定。     

常染色体21个SNPs多态性分型方法研究

目的建立常染色体21个SNPs的多态性分型方法。方法采用荧光标记公用引物和等位基因特异性引物原理设计SNP复合扩增引物体系,对45个备选SNP位点筛选,选出21个及性别Amelogenin构成复合扩增体系。PCR产物经3130XL型电泳仪电泳分离,GeneMaperTM3.0数据分析软件分析结果。同时随机选取6份样品,使用测序方法对SNP分型并进行测序验证。结果应用本研究建立的复合扩增体系扩增样品,产物经毛细管电泳后,每个SNPs均可正确判定基因型。随机选取6份样品SNPs位点测序结果显示,荧光标记SNPs复合扩增分型与直接测序结果完全一致。结论本研究建立的荧光标记公有引物特异性片段常染色体21个SNPs复合扩增方法是SNP多态性分析的一种有效方法,并有助于解决SNP分型识别能力、效率、通量和高成本的问题。     

Forensic Identification Using a Multiplex Assay of 47 SNPs*

Abstract: As a powerful alternative to short tandem repeat (STR) profiling, we have developed a novel panel of 47 single nucleotide polymorphisms (SNPs) for DNA profiling and ABO genotyping. We selected 42 of the 47 SNPs from a panel of 86 markers that were previously validated as universal individual identification markers and identified five additional SNPs including one gender marker and four ABO loci. Match probability of the 42 validated SNPs was found to be 9.5 × 10^?18 in Han Chinese. SNP analysis correctly assessed a panel of historical cases, including both paternity identifications in trios and individual identifications. In addition, while STR profiling of degraded DNA provided information for 11 loci of 16 potential markers with low peak intensities, SNPstream^® genotyping was sufficient to identify all 47 SNPs. In summary, SNP analysis is equally effective as STR profiling, but appears more suited for individual identification than STR profiling in cases where DNA may be degraded.     

The use of the LightCycler for the detection of Y chromosome SNPs

A novel methodology based on PCR monitoring on-line with fluorescent formats using the LightCycler for Y chromosome SNP typing is proposed. The main advantages of the system are the time necessary for the analysis (which is around 20 min), the robustness and the accuracy of the method and especially its sensitivity, which permits the detection of the male component in male-female mixtures up to 1:300 for some of the SNPs.Singleplexes of four different SNPs (M9, sY81, SRY-1532 and SRY-2627) as well as two duplexes (M9 and sY81 on the one hand and SRY-1532 and SRY-2627 on the other) were efficiently implemented. A simultaneous amplification and analysis of the four SNPs is also possible. It seems difficult with the current methodology to implement more than a quadruplex.