基于38-plex InDels的西北地区人群遗传推断研究

目的基于38-plex InDels族群推断体系对中国西北地区新疆汉族、兰州汉族、兰州东乡族、兰州撒拉族、兰州裕固族5个族群的群体遗传结构和族群成分进行研究,评估该体系的推断效能。方法使用38-plex InDels体系检验西北地区5个族群共165份样本并获取InDel位点分型,使用Structure聚类分析、主成分分析及系统发育树综合分析族群间遗传关系,使用族群推断软件(DNA Ancestry Analyzer, DAA)对样本的族群来源进行推断,通过与已知样本信息以及27-plex SNPs族群推断体系检测结果的对比,分析38-plex InDels体系的推断效能。结果 Structure聚类分析和主成分分析显示5个族群的主要祖先成分均为东亚(占88%以上);系统发育树显示新疆汉族、兰州汉族、东乡族、撒拉族、裕固族均聚集到东亚一支,且兰州东乡族、撒拉族、裕固族遗传关系较近;两种族群推断体系检测结果一致性为95.15%(157/165)。结论新疆汉族、兰州汉族、东乡族、撒拉族、裕固族均为东亚族群,兰州东乡族、撒拉族、裕固族遗传关系更近。使用38-plex InDels族群推断体系研究西北地区5个族群的群体遗传结构和遗传关系,结果可供实践应用。     

基于27-plex SNPs的四川地区四个族群遗传推断研究

目的基于27-plex SNPs族群推断体系对四川地区汉族、藏族、羌族及彝族四个族群遗传结构及成分进行研究。方法使用27-plex SNPs试剂检验四个族群1054份样本并获取SNPs位点分型,利用主成分分析、聚类分析及系统发育树综合分析族群间遗传关系,使用族群推断软件(DNA Ancestry Analyzer,DAA)推断样本的族群来源并统计推断结果的准确性。结果系统发育树显示四川汉族、藏族、羌族、彝族和其他东亚族群共同聚为一支;主成分分析和聚类分析结果显示四川汉族、藏族、羌族及彝族主要祖先成分均为东亚。除1例样本祖先来源不排除东亚或混合族群外,其余1053份样本均来源于东亚。结论四川地区汉族、藏族、羌族和彝族均为典型的东亚族群,藏族、彝族和羌族的遗传关系较近。使用27-plex SNPs族群推断系统对四川汉族、藏族、羌族和彝族进行遗传推断,结果可靠。     

基于27-plex SNPs的内蒙古地区4个人群的族源推断研究

目的基于27-plex SNPs族群推断体系对内蒙古地区汉族、蒙古族、鄂温克族及达翰尔族的遗传结构及族群成分进行研究。方法使用27-plex SNPs试剂盒检验四个人群的989份样本并获取SNPs位点分型,利用STRUCTURE聚类分析、主成分分析及系统发育树综合分析人群之间的遗传关系,使用族群推断软件DAA v1.0(DNA Ancestry Analyzer,DAA)对族群来源进行推断,通过与已知样本信息对比,推断结果的准确性。结果 STRUCTURE聚类分析和主成分分析结果显示调查的四个民族主要族群成分均为东亚(占92%以上);系统发育树显示四个民族与其他东亚族群的亲缘关系较近,聚为一支;除27份样本祖先来源被归为混合族群或不排除混合族群外,其余样本祖先来源均为东亚,推断准确率达97.27%。结论内蒙古地区汉族、蒙古族、达翰尔族及温克族均为东亚族群,蒙古族、达翰尔族及鄂温克族3个少数民族的遗传关系更近。使用27-plex SNPs族群推断系统对内蒙古地区汉族、蒙古族、达翰尔族及鄂温克族进行遗传推断,结果可靠。     

两种DNA族群推断技术在一组家系样本中的比较

目的使用课题组构建的27-plex SNPs和38-plex InDels两套族群推断体系,检测一组维族与回族通婚家系样本,通过两种体系间的相互印证,以获得更可靠的种族分析结果。方法分别利用两套检测体系,对来自一维族—回族通婚家系的三代成员共16份样本进行检测,推断其族源信息。结果 16份样本在两种体系下的推断结果与样本的实际来源信息基本一致,该家族成员的遗传成分呈现出欧亚混合特征。结论本实验室构建的两种不同遗传标记的族群推断体系可以有效区分洲际人群的祖先来源,通过两种体系的相互印证,可为案件的侦查提供更为准确的科学线索和依据,同时38-plex InDels体系具有操作步骤简单,检测时间短,可以直接扩增等优势。     

27-plex SNPs复合扩增检测体系构建与应用评价

目的建立27个常染色体SNPs复合检测体系,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(非洲、欧洲、东亚)的遗传标记信息分析,选出27个SNPs位点,构建27个SNPs复合扩增体系;采用该体系对17个不同祖先人群的1 164份样本进行测试,得到的分型数据和在Hap Map数据库查询到的11个相关人群的数据;采用据聚类分析方法(K=3)进行祖先成分和匹配率计算,分析推算样品9947A的祖先来源,并进行体系性能验证。结果该体系可以进行单一和混合人群的种族来源和种族成分推断,来自新疆的人群遗传成分呈现在欧洲与东亚祖先之间连续分布,样品9947A祖先成分和匹配率与相关文献分析结果一致。浓度最低为0.1ng/μL时27个等位基因均可正确判型。结论本文构建的27-plex SNPs复合体系可以精确推断非洲、欧洲、东亚血统的个体祖先起源,且对欧亚混合人群(欧洲/东亚)有较好的推断能力,可在相关研究和实践中选择使用。     

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。     

基于AIM-InDels位点复合扩增体系检测乌鲁木齐蒙古族祖先信息

目的基于课题组前期构建的用于祖先信息推断的39个AIM-InDels位点复合扩增检测体系,探索乌鲁木齐地区蒙古族的遗传背景和遗传结构。方法采集乌鲁木齐市蒙古族145名健康无关个体血样进行基因分型,以千人基因组计划数据库中三个洲际(东亚、欧洲和非洲)的17个群体作为参考人群,研究乌鲁木齐蒙古族的祖先信息构成。应用多种群体遗传学和生物信息学分析方法,进行配对群体间的Fst值与DA值比较分析、PCA分析、系统发育树的构建。应用Strucutre等软件分析乌鲁木齐蒙古族的祖先信息成分比例。结果乌鲁木齐蒙古族在不同洲际群体的祖先信息成分占比为89∶7∶3(东亚∶欧洲∶非洲)。相对于其他洲际群体,乌鲁木齐蒙古族与东亚群体有较小的Fst值与DA值,PCA分析中其与东亚群体形成聚类,系统发育树中亦与东亚群体在同一个分支。结论乌鲁木齐蒙古族与东亚人群有着较近的遗传关系,其东亚祖先成分比例约为89%。     

高原适应基因中藏族祖先信息位点的研究

目的基于高原适应基因上的SNPs位点筛选出藏族祖先信息位点。方法本研究利用Mass ARRAY?基因分型系统对183份藏族个体在EGLN1和EPAS1基因上的87个SNPs位点进行分型检测,结合千人数据库中26个世界人群2504份样本的分型数据,进行群体间差异分析,筛选出藏族特异性高的位点作为藏族祖先信息位点(Ancestry informative SNPs,AISNPs),并通过群体间遗传结构对筛选出的位点进行分析评估。结果在87个高原适应基因SNPs位点中,有23个位点在藏族群体中的频率分布具有特异性,可作为藏族AISNPs。STRUCTURE聚类分析结果表明:在K=2时,藏族人群具有与其他26个人群不同的遗传主成分。结论本研究筛选出的23个藏族祖先信息位点可合并到现有的祖先推断体系中,进一步增加针对东亚亚人群的分辨率,也可为相关案件提供侦破线索。     

东亚人群族源推断SNP Panel分析

目的研发东亚人群中具有较高个体识别率及族源分析能力的SNP Panal。方法以耶鲁大学共计170个SNP Panel(简称170 SNP Panel)为基础,收集其在东亚人群中的检测数据,计算SNP位点的遗传学参数,结合热图分析结果筛选出适合东亚人群的SNP位点,并检测部分藏族及汉族人群样本,运用STRUCTURE软件、主成分分析、热图分析等方法分析其用于族源推断的可能性。结果筛选出45个SNP组成的Panel(简称45 SNP Panel),其中SNP位点的遗传学参数平均值优于170 SNP Panel,与170 SNP Panel达到相同的族源分析及推断能力。而在遗传学参数上,在东亚人群中45 SNP Panel优于170 SNP Panel,体现了其潜在的重要法医学应用价值。     

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。     

Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs

Tests that infer the ancestral origin of a DNA sample have considerable potential in the development of forensic tools that can help to guide crime investigation. We have developed a single-tube 34-plex SNP assay for the assignment of ancestral origin by choosing ancestry-informative markers (AIMs) exhibiting highly contrasting allele frequency distributions between the three major population-groups. To predict ancestral origin from the profiles obtained, a classification algorithm was developed based on maximum likelihood. Sampling of two populations each from African, European and East Asian groups provided training sets for the algorithm and this was tested using the CEPH Human Genome Diversity Panel. We detected negligible theoretical and practical error for assignments to one of the three groups analyzed with consistently high classification probabilities, even when using reduced subsets of SNPs. This study shows that by choosing SNPs exhibiting marked allele frequency differences between population-groups a practical forensic test for assigning the most likely ancestry can be achieved from a single multiplexed assay.     

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。     

中国青海藏族、汉族mtDNA控制区遗传多态性

目的研究中国青海藏族、汉族mtDNA控制区遗传多态性。方法收集69份青海藏族和青海汉族无关人群外周血样本，对其mtDNA控制区进行序列分析，计算多个多态性指标。结合其他民族mtDNA遗传资料，根据Nei法计算包括青海藏族和汉族群体在内的11个群体之间的Fst和Rst遗传距离．进行聚类分析，绘制系统发生树。结果在青海藏族和汉族群体mtDNA控制区中分别发现56和59个多态性位点。Rst遗传距离显示青海藏族人群与各人群之间遗传距离均较远（P〈0．05）；青海汉族人群与西安汉族、蒙古族、长沙汉族等人群之间距离较近（P〉0．05）。结论我国青海藏族和汉族人群mtDNA具有相对独特的遗传特征，其遗传多态性和个体识别力较高，可用于民族起源、迁徙、法医学个体识别等领域研究。     

Inferring recent human phylogenies using forensic STR technology

STR loci are characterized by extremely high mutation rates and thus, high levels of length polymorphism both within and among populations. In addition, much of the observed variation is believed to be nearly selectively neutral. Because of these features, STRs are ideal markers for genetic mapping, intra-species phylogenetic reconstructions and forensic analysis. In the present study, we investigate the application of five STR loci (CS1PO, TH01, TPOX, FGA and vWA) routinely used in forensic analysis for delineating the phylogenetic relationships of 10 human populations representing the three major racial groups (African-Caribbean, Croatian from the island of Hvar, East Asian, Han Chinese, Italian, Japanese, Portuguese, UK Caucasian, US Caucasian and Zimbabwe). The resulting tree topology exhibited strong geographic and racial partitioning consistent with that obtained with mtDNA haplotypes, Y-chromosome markers, SNPs, PAIs (polymorphic Alu insertions) as well as classic genetic polymorphisms. These findings suggest that forensic STR loci may be particularly powerful tools and provide the necessary fine resolution for the reconstruction of recent human evolutionary history.     

The SNPforID 34-plex—Its ability to infer level of admixture in individuals

Forensic scientists use genetic individualization markers to include or exclude persons of interest in investigations. However, when there are no suspects due to absence of database matches or eye-witness information, prediction of biogeographical ancestry can be a valuable investigative tool. The SNPforID 34-plex uses 34 autosomal markers to predict ancestry from three geographic regions, Africa, Europe and East Asia. However, its ability to identify levels of admixture within individuals is unclear. We tested the 34-plex assay in 56 individuals from 15 families with varying levels of self-declared Asian/European admixed ancestry. STRUCTURE 2.3.4 was used for population structure analysis and cluster information provided inferences on levels of admixture. Chi-square tests were performed to evaluate the ability of the SNPforID 34-plex to predict level of admixture. The average/SD Asian and European contribution for individuals self-declared as first generation since admixture was 0.46/0.13 and 0.54/0.13, respectively. As expected, the average European contribution increased for individuals of 1/4, 1/8 and 1/16 Asian/European ancestries – 0.78/0.13, 0.89/0.05 and 0.91/0.03, respectively. There were no significant differences between observed and expected average contribution from each ancestry. However, individual outliers were observed, which could have been misclassified if analyzed separately. These results suggest the 34-plex can be a reliable tool to predict levels of admixture; however caution is required when an individual sample is investigated. A larger number of markers, combined with increased sample sizes comprising varying levels of admixture of different biogeographical ancestries, are required to enhance the ability to predict an individual's level of biogeographical ancestry.     

The polymorphisms of 12 X-STR loci in six ethnic populations in China

To explore the genetic polymorphisms of 12 X-STR loci for Guangdong Han population and other five minor ethnic populations (Tibetan, Mongolian, Korean, Uighur and Hui) in China, 1298 samples from unrelated individuals of these 6 ethnic populations were amplified with Investigator™ Argus X-12 multiplex PCR system. 238 alleles were observed totally, which included 66 off-ladder alleles. All the loci showed no difference in sex-related allele frequency. The combined discrimination power (CDP) was ranged from 0.999999996 to 0.999999999 in males for these 6 populations and the CDP value in females was all reached 0.999999999. The combined mean exclusion chance (CMEC) was ranged from 0.999998336 to 0.999999926 in duo paternity cases and 0.999999987 to 0.999999999 in trio paternity cases in 6 populations. All of the 12 loci were in accordance with Hardy–Weinberg equilibrium after Bonferroni's correction. Linkage disequilibrium was observed for DXS10103–DXS10101 pair in 6 populations. Significant differences between all pairs of populations were observed at 2–11 loci respectively. The phylogenetic tree consisted of two main branches for these 6 populations, which was consistent with the geographic and historic distributions.     

Study of the Cytochrome b Gene Sequence in Populations of Taiwan

Abstract:  The cytochrome b gene (MTCYB) has been widely used in taxonomic research. In this study, the sequence polymorphism of the MTCYB gene was determined in 417 subjects of eight populations living in Taiwan (Taiwanese Han, indigenous Taiwanese, Tao, mainland Chinese, Filipino, Thai, Vietnamese, and Caucasian). Sequence variation from the revised Cambridge Reference Sequence and genetic distance between these populations were analyzed. There were 108 variable positions with a total of 99 haplotypes. Population-specific positions of MTCYB gene were noted in Tao and Caucasian populations. There were statistically significant differences of genetic distance between Taiwanese Han and Caucasian, between Taiwanese Han and Tao, and between Taiwanese Han and Filipino. A phylogenetic tree presents the genetic distances between these populations. In conclusion, there are sufficient sequence polymorphisms of the MTCYB gene in individuals of different populations, which may be used in the analyses of human ethnic groups in forensic casework.     

Development of 30 InDel markers typing system and genetic analysis in five different Chinese populations

Allele frequencies of 30 InDel markers previously selected and validated for forensic purpose were assessed in 419 unrelated individuals originating from five different populations of Chinese Han, Chinese Hui, Uighur, Mongolian and Tibetan in P.R. China. Hardy–Weinberg equilibrium tests and linkage disequilibrium analysis were performed and the results showed that allele frequency distributions of the 30 InDel markers had meet the genetic equilibrium in all of the five populations and the InDel markers on same chromosome did not generate any linkage block. Analysis of molecular variance (AMOVA) indicated that genetic variation among the 5 studied populations represent only 4.00% of the total genetic diversity. We observed the cumulative power of discrimination (CPD) for each studied population was 0.99999999999841 in Chinese Han population, 0.99999999999690 in Chinese Hui population, 0.99999999999709 in Uighur population, 0.99999999999772 in Mongolian population and 0.99999999999854 in Tibetan population.     

Characterization of human control region sequences of the African American SWGDAM forensic mtDNA data set

The scientific working group on DNA analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of control region mtDNA profiles obtained from evidence samples and of profiles used for identification of missing persons. In this study, the African American haplogroup patterns in the SWGDAM data were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Africans observed in these data sets. Over 200 SNPs (n=217) were observed in the African American data set (n=1148). These SNPs ranged from having 1-39 changes in the phylogenetic tree, with sites 152 and 16519 being the most variable. On average there were 5.8 changes for a character on the tree. The most variable sites (with 19 or more changes each) observed included 16093, 16129, 16189, 16311, 16362, 16519, 146, 150, 152, 189, and 195. These rapidly changing sites are consistent with other published analyses. Only 34 SNPs are needed to identify all clusters containing 10 or more individuals in the African American data set. The results show that the African American SWGDAM mtDNA data set contains variation consistent with that described in continental African populations. Thirteen of the 18 haplogroups previously observed in African populations were observed and include: L1a, L1b, L1c, L2a, L2b, L2c, L3b, L3d, L3e1, L3e2, L3e3, L3e4 and L3f. Haplogroup L2a is the most commonly observed cluster (18.8%) in the African American data set. The next most common haplogroups in the African American data set include the clusters L1c (11.0%), L1b (9.1%), L3e2 (9.0%) and L3b (8.1%). Approximately 8% of the haplogroups observed within African Americans were common in European Caucasians or East Asians; these were H (n=32), J (n=4), K (n=5), T (n=2), U5 (n=6), U6 (n=9 also known from North Africa), A (n=12), B (n=7), C (n=4), and M (n=16), respectively. The European Caucasian and East Asian haplogroups are expected due to admixture between individuals with recent ancestry in Western Eurasia and sub-Saharan Africa. The genetic characterization of these relevant data sets is fully consistent with other published mtDNA genetic variation. The sequence diversity observed in this data set makes it a valuable tool for forensic applications.