中国4个群体VDR基因2号外显子的SNP基因座遗传多态性

目的 调查中国北方汉族、维吾尔族、藏族和哈萨克族群体维生素D受体基因2号外显子SNP基因座的遗传多态性和群体差别。方法 应用PCR-RFLPs和DNA序列分析技术对271例个体的DNA样品进行分型。结果等位基因ACG的频率最高,分布在0.57～0.72之间。藏族与维吾尔族基因型ACG/ATG的频率超过0.5,汉族基因型ACG/ATG与ACG/ACG的频率均为0.3976;哈萨克族基因型ACG/ACG的频率达到0.5769。DP值与EPP值在4个群体中均超过0.56和0.16。基因型分布符合Hardy-Weinberg平衡,并在4个群体间有一定程度差异。结论 维生素D受体基因2号外显子SNP基因座具有较高的多态性,并具有一定的群体差别。     

个体识别SNPs位点组合筛选与法医学应用价值初探

目的筛选用于包括中国主要民族在内的多个群体个体识别的SNPs位点组合体系。方法以Kidd实验室筛选的86个SNPs位点、欧洲SNPforID组织构建的52-plex SNPs复合检测体系为基础,收集和整理这些位点在HapMap数据库中11个人群的分型数据,计算各位点杂合度和Fst值,筛选杂合度〉0.4,Fst值〈0.06,并在研究人群中处于Hardy-Weinberg和连锁平衡的位点组合。针对这些位点,采用MassARRAY分子阵列技术对自行收集的8个人群（尼日利亚人、坦桑尼亚查加人、印度人、丹麦人、俄罗斯汉特人、中国汉族、藏族、维吾尔族）308份样本进行分型,统计群体遗传学参数。结果按本文标准共筛选出66个SNPs位点,均符合Hardy-Weinberg平衡,之间互不连锁,平均杂合度和Fst值分别为0.475、0.014。在本文收集的8个人群中的随机匹配概率在1.45E-24~4.72E-27之间,累积非父排除率为0.999 995 608~0.999 997 876之间。结论本文筛选的SNPs组合系统具有较强的个体识别能力,可用于本文调查的HapMap数据库中11个人群和本文收集的8个人群的个体识别鉴定。     

Genome‐wide Screen for Individual Identification SNPs (IISNPs) and the Confirmation of Six of Them in Han Chinese with Pyrosequencing Technology*

Abstract: Single nucleotide polymorphisms (SNPs) offer promise to forensic DNA analysts, but it remains uncertain whether a panel of individual identification SNPs can be as informative as the Combined DNA Index System short tandem repeats. Based on the highly accurate and publicly available HapMap SNP database (r21a) and a minor allele frequency cutoff of ≥0.45, we completed a genome‐wide screen through 3,905,819 SNPs with internally modified computer programs and identified 1439 SNPs with high heterozygosity and low F_st values among four populations (Utah Caucasian, Han Chinese, Tokyo Japanese, and Nigerian Yoruba). Using pyrosequencing technology, we studied six loci in a relatively large group of samples to determine whether these loci were as informative as the HapMap data suggest. These SNPs performed as expected in the Han Chinese in terms of heterozygosity and F_st. The 1439 identified SNPs should provide a comprehensive and reliable set of loci for identity and relationship testing.     

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。     

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。     

基于38-plex InDels的青海地区三个族群遗传推断

目的 基于38-plex InDels族群推断体系研究青海地区汉族、回族及撒拉族的族群成分与遗传结构.方法 使用38-plex InDels复合扩增体系检测3个族群的220份样本并获取InDels位点分型,利用主成分分析、STRUCTURE聚类分析及系统发育树综合分析族群之间的遗传关系,使用族群推断软件DAA v1.0...     

48个X-SNP位点的筛选及法医学应用价值分析

目的对筛选出的48个X-SNP位点进行遗传学分析,评价其法医学应用价值。方法根据NCBI和Hap-Map网站提供的位点信息筛选出48个高信息量X-SNP位点,利用SNPlexTMSystem技术平台进行分型检测,通过中国华东地区汉族人群200个无关个体的调查建立遗传学资料,对48个X-SNP位点的遗传多态性进行研究分析,并进行连锁不平衡检验。结果除rs6527549外,筛选出的48个X-SNP位点在中国华东汉族人群中具有高信息量,多态信息含量均在0.32以上,个体识别率在女性群体和男性群体分别为0.56和0.40以上,非父排除率在二联体和三联体中分别为0.20和0.32以上。检验发现,部分位点存在连锁不平衡现象。结论本实验选取的48个X-SNP位点分型结果稳定,重复性好,在法医生物学研究中具有较高的应用价值,适于开展大规模的高通量检测。     

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.     

Evaluation of skin-related variants in African ancestry populations and their role in personal identification

Pigment-related genetic variants point out their role in personal identification as they can be considered predictors suitable for Forensic DNA Phenotyping (FDP) and mounting evidence suggest also their bio-geographic inferential power for gaining information about the individual geographical origin. As they could be regarded as AIMs (Ancestry Informative Markers) they are powerful tools for inferring genetic composition of admixed population. Despite the huge range of skin tones across our species, little is known about genetic basis in global population and particularly our knowledge is less precise for those showing a complex historical and genomic background. The current research aims to explore the allelic status in several SNPs mapped in selected genes known to be involved in skin pigmentation: OCA2, HERC2, SLC45A2, SLC24A5 and two intergenic regions between BEND7/PRPF18 and EIF2S2/ASIP. The genetic evaluation has been performed on selected African and African derived populations: Fon, Dendi, Bariba and Berba communities from Benin, and Afroecuadorians. Data integration has been made up merging genotypic results with available information from major biological data warehouse as Phase 3–1000 Genomes Project or International HapMap Project in order to obtain a selected populations panel useful for their use as inferential model training set to test the likelihood of correct assignment to geographically differentiated human groups. The proposed variants panel seems to properly interpret the geographic variation and some new interesting evidence could be pointed out in African mixed populations, that seem to be differentially distributed if the total panel is considered. Understanding human pigmentation architecture can provide fundamental insight into genetic interaction of complex traits and the relationship between environmental adaptation and population history. In addition, the results support the use of phenotypic inference along with bio-geographical ancestry information as valid auxiliary tools in personal identification.     

中国南方两汉族群体的19个STR基因座的特征分析

目的获得南方汉族群体的基因多态性信息,分析16个东亚各人群的族源关系。方法 2018年3~7月收集贵州省和江西省汉族群体中健康且无亲缘关系的720份个体血液样本,其中贵州省407份,江西省313份。使用短串联重复序列(STR)试剂盒扩增检测样本,获得法医学参数;通过文献获取湖北汉族,湖南汉族,四川汉族,重庆汉族,贵州布依族、侗族和苗族,云南白族、彝族、哈尼族和纳西族,广西壮族以及日本和韩国共14个人群的法医学参数,采用Arlequin v3.5遗传软件计算16个东亚人群(本研究的贵州汉族、江西汉族以及文献获得的14个人群)之间的相对遗传距离(Fst),采用SPSS 21.0统计学软件进行多维尺度分析(MDS)和主成分分析(PCA),MEGA6软件绘制系统进化树。结果在贵州汉族人群中,累积个人识别率为1-3.3080×10-23,累积非父排除率为1-3.1792×10-8。在江西汉族人群中,累积个人识别率为1-5.4721×10-23,累积非父排除率为1-1.6544×10-8。少数民族(贵州布依族、贵州侗族、贵州苗族、广西壮族、云南哈尼族和云南纳西族)与汉族群体间存在明显的遗传距离。日本人群与汉族群体的遗传距离最大,韩国人群与汉族群体具有较近的遗传距离。进化树结果表明贵州汉族、江西汉族群体与其他汉族群体聚集在一起,未见明显区别。结论 14个基因座在贵州、广西人群中遗传多态性较好,少数民族与汉族之间、日本与汉族之间的遗传差异明显,而汉族人群内部遗传差异不明显。     

GENETIC PORTRAIT OF THE PUNJABI POPULATION FROM PAKISTAN USING THE PRECISION ID ANCESTRY PANEL

Prediction of geographical ancestry using genetic markers has a great potential in forensic genetics and may be used as an investigative lead in crime casework or missing person identification. Exploration of AIMs in Pakistan is interesting due to the distinct subpopulations with multidirectional ancestry from different groups. In the current study, 87 individuals from the Punjabi population from Pakistan were investigated using the Precision ID Ancestry Panel (Thermo Fisher Scientific) to assess whether it was possible to diff ;erentiate Punjabi individuals from other populations. With this panel, it is revealed that Punjabis are admixed and cannot be distinguished from other populations in South Central Asia and the Middle East.     

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.     

27个常染色体AIM-SNP的筛选和验证

目的构建27个常染色体AIM-SNP组合用于未知个体种族来源推断。方法通过对Hap Map数据库中描述祖先遗传信息标记的908个AIMs位点(非洲、欧洲、东亚人群)筛选,选出27个AIMs位点组合,利用相关软件同时与数据库908个AIMs不同子集合的分析进行对比,验证其推断祖先来源的可行性。结果应用本研究27个AIMs的SNP多态性分析方法可以正确推断未知样品祖先起源,估算祖先成分比例。结论本研究建立的常染色体27个AIMs的SNP多态性分析方法可准确推断来自于欧洲、非洲、东亚3大祖先血统个体的祖先来源,是SNP多态性分析用于个体种族来源推断的一种有效方法,在法医实践中可以用于DNA检验中未知DNA供者洲际人群祖先来源推断。     

Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African-American, and Hispanic samples

189 samples from 3 different U.S. sample groups Caucasian (74), African American (71) and Hispanic (44) were typed for 70 autosomal genetic markers. These 70 markers are bi-allelic (C/T) short nucleotide polymorphisms (SNPs). For each sample, the 70 SNP markers were typed in 11 unique 6-plexes and a single 4-plex PCR. A total of 10 of the 210 tests (70 loci x 3 populations) for Hardy-Weinberg equilibrium indicated a statistically significant result. In order to evaluate the minimum number of SNP loci needed to distinguish all 189 samples from one another, we ranked the loci according to their levels of observed heterozygosity and p-values obtained upon testing for Hardy-Weinberg equilibrium. The top 12 loci according to these ranking criteria were tabulated along with the number of unique genotypes observed when combining subsequent SNP markers. The 12 selected SNPs possessed an observed heterozygosity of >0.45 in all three populations examined and thus would be expected to exhibit more differences between samples. All of the 189 samples in this study were individualized with a subset of 12 SNP loci. However, it is likely that the addition of more than 12 SNP loci will be required to resolve larger sets of unrelated individuals from one another. By way of comparison, in these same 189 individuals all but one pair is resolved from one another with three of the traditional short tandem repeat (STR) loci possessing the highest heterozygosity values (D2S1338, D18S51, and FGA) run with the Identifiler kit. The final pair of unrelated samples could be resolved with the combination of 4 STR loci: D2S1338, D18S51, FGA, and VWA.     

Frequency assessment of SNPs for forensic identification in different populations

Allele frequencies for 16 previously described autosomal SNPs were tested in 1020 unrelated individuals originating from three different continents (Africa, Asia and Europe). The populations analyzed included Africans from Benin Gulf (180), Asians from Mongolia (160) and Europeans from Italy (680).     

华东汉族人群乙醇代谢酶相关SNP位点的多态性

目的对ADH2、ADH3、ALDH2和CYP2E1基因的40个SNP位点进行群体遗传学分析,得到多态性信息。方法利用PCR和质谱技术平台对SNP位点进行分型检测,通过对中国华东地区汉族人群199个无关个体的调查,统计分析40个SNP位点的等位基因分布频率。结果 40个SNP位点中,rs698、rs2241894（ADH3基因座）,rs13306164、rs671（ALDH2基因座）和rs28371746、rs2515641（CYP2E1基因座）的小等位基因分布频率（MAF）均大于1%,其它SNP位点的MAF均小于1%。结论 ADH2、ADH3、ALDH2和CYP2E1基因的40个SNP位点中,6个位点（rs698、rs2241894、rs13306164、rs671、rs28371746和rs2515641）在华东汉族人群中具有多态性。     

Investigator Argus X-12试剂盒在华东汉族人群中的法医学应用评估

目的 调查Investigator Argus X-12试剂盒中所包含的12个X-STR基因座在华东汉族人群中的遗传学数据,考察其法医学应用价值.方法 应用Investigator Argus X-12试剂盒对华东地区309名汉族无关个体进行X-STR基因座分型检测,统计分析12个X-STR基因座的频率数据、群体遗传学...     

Tri-allelic SNP markers enable analysis of mixed and degraded DNA samples

For the analysis of degraded DNA in disaster victim identification (DVI) and criminal investigations, single nucleotide polymorphisms (SNPs) have been recognized as promising markers mainly because they can be analyzed in short sized amplicons. Most SNPs are bi-allelic and are thereby ineffective to detect mixtures, which may lead to incorrect genotyping. We developed an algorithm to find non-binary (i.e. tri-allelic or tetra-allelic) SNPs in the NCBI dbSNP database. We selected 31 potential tri-allelic SNPs with a minor allele frequency of at least 10%. The tri-allelic nature was confirmed for 15 SNPs residing on 14 different chromosomes. Multiplex SNaPshot™ assays were developed, and the allele frequencies of 16 SNPs were determined among 153 Dutch and 111 Netherlands Antilles reference samples. Using these multiplex SNP assays, the presence of a mixture of two DNA samples in a ratio up to 1:8 could be recognized reliably. Furthermore, we compared the genotyping efficiency of the tri-allelic SNP markers and short tandem repeat (STR) markers by analyzing artificially degraded DNA and DNA from 30 approximately 500-year-old bone and molar samples. In both types of degraded DNA samples, the larger sized STR amplicons failed to amplify whereas the tri-allelic SNP markers still provided valuable information. In conclusion, tri-allelic SNP markers are suited for the analysis of degraded DNA and enable the detection of a second DNA source in a sample.     

Update of aims population data and test with the genogeographer admixture module

Individuals from Slovenia, Greece, Albania, and Eritrea were typed with the Precision ID Ancestry Panel and included among GenoGeographer’s nine reference populations (Sub-Saharan Africa, Horn of Africa, North Africa, Middle East, Europe, South/Central Asia, East Asia, and East and West Greenland). We tested the performance of GenoGeographer with the Admixture Module on AIM profiles of 3548 individuals assumed to belong to one of the reference populations. A total of 3387 (95.5 %) profiles were assigned to one or more of the reference populations, either a single population or an admixture of two or more populations, while 161 (4.5 %) profiles were not assigned to any reference population or admixtures thereof. For 1486 AIM profiles with no reference population of origin in GenoGeographer, the rejection rate was more than 70 % for AIM profiles from North and South America and less than 20 % for those from Central, North, and Northeast Asia.