中国5个群体D20S85基因座的遗传多态性

目的 了解中国5个群体D20S85基因座的群体遗传学数据,比较它们之间的遗传学差异,探讨其在法医学应用中的意义。方法 分别收集5个群体622名无关个体的血样,Chelex-100快速抽提法或饱和酚/氯仿法抽提DNA;扩增后经PAGE垂直板电泳、银染,进行D20S85基因座分型。结果 在5个群体622名无关个体中,共检出9个等位基因,并首次在广东汉族和广西壮族群体中检出等位基因14;每个群体基因频率大于0.05的均为6个,D20S85*6为最常见等位基因。5个群体共观察到35种基因型,群体内基因型频率分布均符合Hardy-Weinberg氏平衡,各群体间基因型构成比无显著性差异。观察140次减数分裂未发现突变。各群体的期望杂合度为0.7720～0.7912;非父排除率,在三联体为0.7538～0.7594,二联体为0.3988～0.4297;个人识别率为0.9175～0,9272;多态信息含量为0.7442～0.7656。应用于亲子鉴定和个人识别案例,效果满意。结论 D20S85基因座是法医学应用价值较高的遗传标记系统。     

浙江宣城地区汉族人群18个STR基因座遗传多态性

目的 调查浙江宣城地区汉族人群5000例无关个体18个STR基因座多态性分布.方法 应用AmpFlSTR Identifiler荧光标记复合扩增系统检测,统计计算群体遗传学参数.结果 18个STR基因座的基因型分布均符合Hardy-Weinberg平衡（P＞0.05）,共检出270个等位基因,频率在0.0001～0.5260之间,共有1289种基因型,在13个基因座上检出共44个微变异等位基因.18个基因座的杂合度观察值（Ho）在0.6238～0.9120之间,杂合度理论值（He）在0.6961～0.9601之间,多态信息含量（PIC）在0.5578～0.9126之间,累计个人识别率（TDP）为0.999 999 999 999 999 999 999 953,三联体累计非父排除概率（CPE）为0.999 999 993487 306,二联体累计非父排除率（CPE＊）为0.985819169.结论 本文调查结果与以往文献报道的不同地区民族的人群等位基因频率资料有一定程度的差异性.上述18个STR基因座适用于宣城地区汉族群体各类案件的法医学个体识别和亲权鉴定.     

Comparisons between Japanese and Han Chinese populations for 261 autosomal STR loci

In this study, Japanese and Han Chinese individuals (n = 32, each) were genotyped for 261 autosomal STRs, and allele frequencies were calculated for each locus in each population. The average number of alleles for all loci in Japanese and Han Chinese populations was 6.65 and 6.56, respectively. The tests for deviations from HWE performed using an exact test showed that the number of STRs (P > 0.05) in Japanese and Han Chinese populations was 236 and 241, respectively. Calculation of forensic parameters showed heterozygosity, and the exclusion means in the Japanese population were 0.7185 and 4813 and those in the Han Chinese population were 0.7308 and 0.5008. In addition, population genetic analyses, such as principal component analysis and factorial correspondence analysis, were performed and a differential formula with likelihood ratios was applied for various number of STR loci based on the effectiveness of differentiation between the two populations. Accordingly, this study suggests that statistical differentiation between genetically close populations, such as the Japanese and Han Chinese populations, is possible if approximately 40–50 effective STR loci are analyzed.     

D3S1754、D18S535基因座在中国北方汉族的多态性分析

目的 了解D3S1754、D18S535基因座多态性在中国北方人群中的分布特点及其应用价值。方法 使用PCR、聚丙烯酰胺垂直板电泳及银染的方法。结果D3S1754基因座检出9个等位基因（n=184）,D185535基因座检出8个等位基因（n=201）,两个位点的等位基因频率在群体中的分布符合Hardy-Weinberg平衡（P>0.05）,它们的杂合率（He）分别为0.706和0.807,个人识别机率（DP）分别是0.859和0.934,非父排除率（EPP）分别为0.464和0.629。结论 D3S1754、D18S535两个遗传标记的个人识别率高、非父排除能力较强且能稳定遗传,具有较高的应用价值。     

Y-chromosomal STR haplotypes in Pakistani populations

16 Y-specific STR loci have been analysed in 711 males from 12 populations in Pakistan. Individual loci showed between 4 and 10 alleles, and diversities ranged from 0.07 to 0.77. A total of 527 different haplotypes were found and the haplotype diversity ranged from 0.92 to 0.99 for the different populations. 446 haplotypes occurred in single individuals, and only 19 haplotypes were present in more than three males, but two striking examples of haplotype sharing were found, one involving 13 individuals, and the other 17. The 13 individuals were all Parsis, and 16 of the 17 were Brahuis, providing evidence for population substructuring.     

Genetic polymorphism revealed by 13 tetrameric and 2 pentameric STR loci in four Mongoloid tribal population

The short tandem repeat allelic profiles at to 15 autosomal polymorphic loci were analyzed in four tribal populations of Mizoram (India). The analysis was performed on 354 unrelated healthy individuals belonging to Mongoloid races. All the samples were subjected to sex test (Amelogenin marker) besides the STR typing and in all instances; it has shown no deviation from expectation. The allele frequencies for all the analyzed loci in the studied populations are within expected range in comparison to the populations from same racial background. No significant deviation from the Hardy-Weinberg Equilibrium was observed for all the populations. In no cases the observed heterozygosity is less than that of expected values and it varied from 0.978 (Penta E) to as low as 0.425 (THO1). The discriminatory power and exclusion probability values for all the analyzed markers are significantly high and thus reveal high forensic significance. There is no evidence for association of alleles among the 15 studied loci. This allele frequency data will be useful for human identity testing in Mizo population.     

The analysis of three short tandem repeat (STR) loci in the Slovene population by multiplex PCR

Allele frequencies for three tetrameric short tandem repeat (STR) loci D3S1358, HUMVWA, and HUMFGA were determined in a Slovene Caucasian population sample. DNA samples from a total of 221 Slovenes were amplified by multiplex PCR using the commercial kit AmpFISTR Blue (Perkin-Elmer). Separation and detection of the amplified STR fragments were carried out using a 377 automated genetic analyzer (Applied Biosystem Division/Perkin Elmer). Seven alleles at the D3S1358 locus, 8 alleles at the HUMVWA31A locus, and 13 alleles at the HUMFGA locus were observed. A deviation from Hardy-Weinberg equilibrium was observed, only at the HUMVWA31A locus (p = 0.045, exact test). The departure at this locus was not significant after Bonferroni correction. There were no detectable departures between pairwise comparisons of the loci. The combined power of discrimination for all three loci is 0.9998, and the power of exclusion is 0.9526. The observed allele frequencies for the loci D3S1358, HUMVWA31A, and HUMFGA are similar to those in European and U.S. Caucasian populations.     

Introducing eNoC – A simple,excel-based tool for improved assignment of the number of contributors (NoC) to a mixture

Assigning NoC in a mixed STR profile is an important preliminary step in computing a likelihood ratio (LR). A common metric is maximum allele count (MAC) whereby the locus exhibiting the largest number of alleles is used to set the NOC. This metric can be supplemented by considering total allele count (TAC) and locus allele count (LAC). TAC is the total number of alleles across all loci and is compared with probability distributions generated in silico. LAC works similarly, save that the probability distributions are generated at the locus level. Herein, we present a comparative analysis of these three metrics using a dataset of 10,000 of each of 2–7 person simulated ground truth mixtures. These datasets were used to generate parameter distributions for each NoC. This analysis showed LAC to be the most accurate single metric in all circumstances tested. We have developmentally validated an excel-based tool to automate calculations for use by operational caseworkers.     

Analysis of eight STR loci in two Hungarian populations

A collection of eight STR loci (D3S1358, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) was used to generate allele frequency databases for two Hungarian population samples, Caucasians from the Budapest area and Romanies from Baranya county. During the analysis two intermediate sized alleles and a sequence variant allele were observed at the D7S820 locus. All three types of allelic variants were found to have modification (deletion, insertion, transversion) in the same block of a (T)(9) stretch located within the 3' flanking region of each allele, which may indicate a possible higher mutation rate of this (T)(9) block. For the loci D3S1358 and D7S820 the Romany population database showed departures from Hardy-Weinberg equilibrium. The forensic efficiency values for the Romany population were slightly different from those found in the Hungarian Caucasian population. Comparing the allele frequency values by G-statistic, calculating the F(st) indices and with the pairwise comparisons of inter-population variance, the two Hungarian populations could be distinguished using data of the eight STR loci.     

A novel fluorescent quadruplex STR typing system and the allele frequency distributions in a Thai population

We have previously reported a new triplex amplification and typing system by silver staining for three short tandem repeat (STR) loci, 9q2h2 (D2S3020), D15S233, and D14S299 without "microvariant" alleles such as .1, .2, and, .3 alleles in the Japanese population. In the present study, we established a new quadruplex system with an additional locus D7S809 using primer sets labeled with fluorescent multi-color dyes. Using this system, we genotyped 183 Thai people, found only one "microvariant" allele (allele 20.2) at D7S809, and calculated allele frequencies and some statistical properties at these four STR loci. From these allele frequencies at four STR loci, we performed three statistical analyses including a homozygosity test, a likelihood ratio test, and an exact test for Hardy-Weinberg equilibrium (HWE). Deviations from HWE (p < 0.05) were observed only in the two tests at the locus D7S809. In the present study, we compared the allele frequencies at these four loci in the Thai population to those in the Japanese population described previously. Consequently, all observed heterozygosities and power of discrimination (PD) at those loci in the Thai population were higher than 0.8 and 0.9, respectively, and all statistical values for discriminating power in the Thai population were slightly higher than those in the Japanese population. The combined paternity exclusion rate (combined PE) in the Thai population (0.978) was almost the same as that in the Japanese population (0.971). Therefore, this novel PCR amplification and typing system for four STR loci would be a convenient and informative DNA profiling system in the forensic field.     

Haplotype frequencies and population data of nine Y-chromosomal STR polymorphisms in a German and a Chinese population

Y-chromosomal STR loci are of increasing interest in paternity testing, forensic casework, anthropological and evolutionary studies. We participate in a cooperation to establish an international reference database of at least nine Y-chromosomal STR loci to be used for biostatistic calculations. We present frequency distributions of nine Y-chromosome specific STR polymorphisms and frequencies of compound haplotypes in two populations. We chose the loci DYS393, DYS19, DYS392, DYS385I, DYS385II, DYS390, DYS391 and DYS389I and II. Blood samples were taken from 136 unrelated male individuals from Cologne (Germany) and of 63 unrelated males from Chengdu (Sichuan Province, PR China). DNA was extracted by a salting out procedure or chelex extraction. PCR was carried out in two multiplex reactions. Fragment analysis was conducted on an ALF- or ALF-express sequencer. Frequency profiles of the German men showed no significant differences compared to most European populations. Mean exclusion chances were between 0.44 for DYS393 and 0.94 for DYS385. Haplotype diversity for the complete haplotype was 86.66% in Germans and 98% in Chinese. The Chinese men showed for all analysed loci except for DYS389I and DYS390 remarkably different allele distributions.     

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.     

Allele frequencies of six miniSTR loci of three ethnic populations in Singapore

MiniSTR loci has demonstrated to be an effective approach to recover genetic information from degraded sample, due to the improved PCR efficiency of their reduced PCR product sizes. This study investigated the allele frequency of six miniSTR loci, D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045, in three Singapore populations. All loci showed a moderate degree of polymorphism with observed heterozygosity >0.6 for all three populations. The allele frequencies, forensic parameters and heterozygosity comparison with other CODIS STR in similar populations are presented.     

中国北方汉族与维吾尔族群体8个STR位点的遗传多态性

目的调查中国北方汉族与维吾尔族群体8个STR位点的遗传多态性。方法应用荧光标记引物试剂盒及基因扫描技术检测vWA、TH01、TPOX、CSF1PO、D5S818、D13S317、D7S820、D16S539位点等位基因。结果100例汉族群体共检出62个等位基因,累计非父排除率为0.9975;50例维吾尔族群体共检出52个等位基因,累计非父排除率为0.9973。2群体总个人识别机率均超过0.9999。基因频率分布2群体间存在显著性差异。结论8个STR位点在汉族与维吾尔族群体中具有较高的遗传多态性,频率分布有民族差别。     

成都汉族、甘肃东乡族群体D10S1432和D10S1213 位点的遗传多态性分析

目的本研究的目的是了解人类基因组中D10S1432及D10S1213两个STR位点在成都汉族和甘肃东乡族群体中的遗传多态性分布及两个群体之间的关系。方法采用PCR、聚丙烯酰胺凝胶电泳及银染技术,共调查了209例样本。结果在D10S1432位点上观察到5个等位基因,15种基因型。在D10S1213位点上观察到9个等位基因,31种基因型。两位点的基因型频率在调查的两个群体中的分布符合Hardy-Weinberg平衡定律（P>0.05）。经统计,D10S1432在这两个群体中的杂合度为0.664和0.737,个人识别几率为0.827和0.820。D10S1213的杂合度为0.664和0.657,个人识别几率为0.836和0.882。结论结果表明,D10S1432和D10S1213两个位点在法医学个人识别和亲子鉴定中有较高应用价值。     

Practical applications of genotypic surveys for forensic STR testing

Legitimate genotype frequency estimation for multiallelic loci relies on component allele frequencies, as population surveys represent only a fraction of possible DNA profiles. Multilocus genotypes from two ethnic human populations, African American (n=195) and U.S. Caucasian (n=200), were compiled at 13 STR loci that are used worldwide in forensic investigation (D3S1358, vWA, FGA, D16S539, TH01, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820). Sex-specific AmpFlSTR multiplexes provided stringent PCR-based STR typing specifically optimized for multicolor fluorescence detection. Heterozygosity at each STR locus ranged from 0.57 to 0.89 and encompassed from seven (TH01) to twenty-one (D21S11) alleles. Homozygosity tests, tests based on the distinct numbers of observed homozygous and heterozygous classes, log likelihood ratio tests, and exact tests assessed that the degree of divergence from theoretical Hardy-Weinberg proportions for all 13 STRs does not have practical consequence in genotype frequency estimation. Departures from linkage equilibrium, between loci, that imposed significance to forensic calculations were not indicated by observed variance of the number of heterozygous loci or Karlin interclass correlation tests. For forensic casework, reliable multilocus profile estimates may be obtained from the product of component genotype frequencies, each calculated through application of the Hardy-Weinberg equation to population database allele frequency estimates reported here. The average probability that two randomly selected, unrelated individuals possess an identical thirteen-locus DNA profile was one in 1.8x10(15) African Americans and one in 3.8x10(14) U.S. Caucasians.     

海南汉族人群19个STR基因座遗传多态性及其应用

目的建立海南地区汉族人群19个常染色体STR基因座的遗传多态性数据资料,并探讨此19-STR基因座系统在亲子鉴定中的应用。方法对海南汉族462例无血缘关系个体,采用Goldeneye~(TM) 20A系统复合扩增并检测,得到19个STR基因座的遗传数据信息;在283例亲子鉴定案例中,评价19-STR基因座系统的应用。结果 19个STR基因座的基因频率分布均符合Hardy-Weinberg平衡(P0.05),杂合度在0.603~0.914之间,累积个体识别率大于0.999 999 999 999 999,累积三联体非父排除率为0.999 999 994。283例亲子鉴定中,三联体170例,二联体113例;认定案例247例(87.3%),排除案例36例(12.7%);发生等位基因突变案例14例(4.9%),均为一步突变。结论 19个STR基因座中的14个基因座具有高度遗传多态性,19-STR基因座复合扩增分型系统具有较高的非父排除效能,可满足海南地区亲子鉴定的需要,同时应注意亲子鉴定中的基因突变现象。     

广西地区3个群体15个STR基因座频率多态性

目的调查广西地区仡佬族、仫佬族、瑶族无关个体的15个STR基因座(D8S1179、1321S11、D7S820、CSF1PO、D3S1358、TH01、D13S317、D16S539、D2S1338、D19S433、vWA、TPOX、D18S51、D5S818、FGA)多态性,研究其在法医学检验中的应用价值。方法 应用AmpFISTR IdentifilerTM荧光标记复合扩增系统,对314例仡佬族、332例仫佬族、238例瑶族无关个体血样DNA进行15个STR基因座的复合扩增,用ABI 3100遗传分析仪对扩增产物进行检测,GeneScan、GenoTyper软件进行基因分型,统计计算15个STR基因座的群体遗传学参数。结果IdertifilerTM系统的15个STR基因座在仡佬、仫佬、瑶族的累积偶合率为1.839×10-16~5.073×10-17,累积非父排除率为0.9999983~0.9999991。结论该15个STR基因座足可满足仡佬族、仫佬族、瑶族法医学的个体识别及亲权鉴定的需要。     

广西地区壮族人群17个STR基因座遗传多态性研究

目的调查广西地区壮族人群17个STR基因座遗传多态性,为法医物证鉴定和群体遗传研究提供基础数据。方法收集2624份广西地区壮族人群无关个体样本采用Chelex-100提取样本DNA,用PowerPlex■18D System试剂盒进行PCR扩增及检测,计算群体遗传学参数。结果17个常染色体STR基因型分布均符合Hardy-Weinberg平衡定律(P>0.05),共检测出235个等位基因,971种基因型,累积个体识别率(TDP)为0.999999999999999,累积非父排除率(CPE)为0.999999772。结论17个STR基因座在广西地区壮族人群中具有较好的遗传多态性,可以用于法医学中个体识别和亲权鉴定,也可用于群体遗传学及法医学研究。     

Genetic diversity at two pentanucleotide STR and thirteen tetranucleotide STR loci by multiplex PCR in four predominant population groups of central India

Genetic diversity study at STR loci in 208 individuals belonging to two backward groups, one caste and one tribal community of Central India called "Chhattisgarh" has been carried out to evaluate significance of Powerplex System loci in human identification and population diversity. Populations are Agharia (72), Satmani (50), Dheria Gond (36) and Teli (50). Fifteen loci (Powerplex 16 Kit) studied are Penta E, D18S51, D21S11, THO1, D3S1358, FGA, TPOX, D8S1179, vWA, Amelogenin, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818. The studied penta nucleotide STR (two) and 13 tetranucleotide (CODIS ) STR are found to be highly polymorphic genetic markers in all studied populations. Most common allele for the four studied population has been found to be same at THO1 (allele 9), D8S1179 (allele 14), CSF1PO (allele 12), Penta E (allele 11) and D16S539 (allele 11). Penta E is found to be most polymorphic (PD=0.89373) among studied 15 STR loci in four populations of Central India.