Discrimination of half-siblings when maternal genotypes are known

Given the DNA profiles of two individuals and one parent (say the mother) of each, we present likelihood ratios (LRs) comparing the hypothesis that they have the same father with the hypothesis of unrelated fathers. If the individuals have the same mother, the problem is to distinguish full- from half-siblings, otherwise we are comparing a half-sibling relationship with unrelated. We simulate STR profiles at up to 60 loci, based on allele proportions observed at 15 loci in three populations, and use them to approximate misclassification rates both for binary classification (e.g. "half-sib" versus "unrelated"), and when a third "cannot say" category is included. We find that reliable inferences in the absence of the mothers' profiles require many more STR loci than the 10-25 loci that are currently routinely available. However, profiling the two mothers conveys more discriminatory power than profiling the same number of additional loci in the individuals themselves. Our likelihood ratio formulas include a theta (or Fst) adjustment to allow for the individuals concerned to have recent shared ancestry (coancestry), relative to the population from which the allele frequency database is drawn. We illustrate that using an appropriate value of theta can reduce the average misclassification rate.     

Application of subpopulation theory to evaluation of DNA evidence

The strength of any evidence can be assessed using a likelihood ratio (from Bayes' point of view). This is the ratio of the probabilities that the evidence would have been obtained given that the suspect is guilty and innocent, respectively. This, in turn, depends upon the probability that a match will be produced if the suspect is innocent. An essential population genetics parameter is the 'coancestry coefficient', or θ, or F(ST), which is the correlation between two genes sampled from distinct individuals within a subpopulation. In this paper, θ coefficients for the southern Polish population were calculated for three loci of forensic interest: TH01, TPOX and CSF1PO. Three small southern Polish subpopulations of different ethnic origin were analysed. The results suggest that values of θ appropriate to forensic applications are quite small in the southern Polish population (they vary in the range of 0.002 to 0.013), and the value of θ=0.03 suggested by the National Research Council is too conservative for the defendant.     

常染色体STR遗传标记在同胞鉴定中的应用

目的 探讨常染色体STR遗传标记用于鉴定两个体同胞关系的可行性。方法 用Power Plex~(TM)16体系15个STR基因座检测150对同胞个体和150对无关个体,ITO法计算同胞关系指数(PI_(FS))与同胞关系概率(W_(FS)),并比较两组W_(FS)值及两个体间等位基因匹配情况的差异,对前者进行组间差异的x~2检验。结果 100对(66.67％)同胞个体的W_(FS)大于0.9995;无关个体W_(FS)均小于0.8,其中100对(66.67％)W_(FS)小于0.27。同胞个体两个体间等位基因全相同的基因座个数为1～10个不等,平均5.49个,无关个体0～5个不等,平均1.33个;等位基因全不同的基因座个数,同胞个体0～6个不等,平均1.66个,无关个体2～11个不等,平均6.57个;等位基因半相同的基因座个数,同胞个体3～13个不等,平均7.85个,而无关个体1～13个不等,平均7.11个。经x~2检验,同胞个体和无关个体间全相同和全不同的基因座数差异均有极显著意义(P<0.001),半相同的基因座数差异无显著意义(P>0.05)。结论 PowerPlex~(TM)16体系可用于鉴定同胞关系。当两个体全不同基因座个数大于或等于6个,或全相同基因座数为0时,提示为无关个体;当两个体全不同基因座个数小于或等于1个,或全相同基因座数大于或等于6个时,提示为同胞。     

广东广西地区5个群体9个STR基因座的频率调查

目的 调查广东汉族、广西汉族、广西侗族、广西壮族、广西苗族5个群体9个STR基因座多态性,探讨其在法医学检验中的应用价值。方法 应用AmpFISTR Profiler PlusTM荧光标记复合扩增系统,对广东广西5个群体4个民族的1191个无关个体的血样DNA进行9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分型,统计9个STR基因座的群体遗传学参数。结果 9个STR基因座在广东广西地区5个群体中的累积偶合率为1.51×10-11～8.08×10-11,累积非父排除率为0.99981—0.99990。,结论 该9个STR基因座可满足汉族、壮族、侗族、苗族群体法医学的个体识别及亲权鉴定的需要。     

PCR-based DNA analysis of vWA31A,TH01, F13A01, FESFPS,TPOX and CSF1PO

The allele and genotype frequencies of 6 tetranucleotide STR loci were investigated in a sample of 132 unrelated individuals from Chinese Han population. The PCR products were analyzed on 6% denaturing PAGE and detected using fluorescently labeled primers in an automated 377 sequencer(PE). All loci meet Hardy-Weinberg equilibrium. There was no random association of alleles among the 6 loci. The allele frequencies were compared with other population databases. Except locus vWA31A, the observed heterozygosity at other 5 loci was significantly lower than that reported in Caucasian and Black population studies. The calculated DP = 0.99999, PE = 0.9708, pM = 1.059 x 10(-5). The allelic frequency data can be used in forensic identification and paternity testing.     

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。     

Investigation of 74 microhaplotypes for kinship testing in US populations

Microhaplotypes are markers that consist of haplotype blocks of SNPs, which can be analyzed by massively parallel sequencing technologies. These allow determining the haplotype phase at every locus by clonal sequencing each DNA strand. MHs are polymorphic loci with same size alleles, no stutter, and lower mutation rate than STRs. They can provide the same power of discrimination of STR-kits, thus useful for mixture deconvolution, but more accurate ancestry prediction than STRs. In this study we investigated the potential of a recently developed 74plex-MH panel for kinship testing using the Familias software.Samples from families of four major US population groups were collected and genotyped using the 74plex-MH panel. MH allele frequency data from 347 individuals were imported into Familias software along with STR allele frequency data of 29 loci (NIST dataset) from 1036 individuals. Different family scenarios were tested and these included unrelated vs parent-child, unrelated vs full siblings, unrelated vs half siblings, unrelated vs cousin pairs. The prediction of the kinship relation for the four populations of interest was reported as Log10 of the likelihood ratio (LR).Overall, the panel of 74MHs and 29STRs showed similar performance in predicting the correct kinship scenarios tested. Correct prediction was reported for parent-child, full siblings, and half sibling scenarios, but not for the cousin pairs scenario. The panel of 74 MHs showed larger Log10LR values than the 29 STR-assay, thus demonstrating the effectiveness of this biomarker as a tool for kinship testing in addition to mixture deconvolution and ancestry prediction.     

Allele sharing in first-degree and unrelated pairs of individuals in the Ge F I AmpFlSTR Profiler Plus database

Eleven Italian forensic laboratories participated in a population study based on the AB Profiler Plus loci with proficiency testing. The validated database, including 1340 individuals, is available on-line. Tests for Hardy-Weinberg equilibrium, gametic unbalance, and heterogeneity of gene frequency were generally not significant. Gene frequencies at each locus were consistent with those of two previously published Italian studies, but different from a third. Individuals of each subsample were paired, and the total number of alleles shared across the nine loci was determined in each pair. The analysis was replicated over the total sample. In addition, two samples of mother-child pairs (N=315) and full-sib pairs (N=91) were subjected to allele sharing analysis. The resulting distributions were sufficiently distinct from the sample of unrelated pairs as to be of practical usefulness.     

Allele frequencies of 15 STR loci of Luoba ethnic group in Tibet (Southwestern China)

Allele frequency data for 15 short tandem repeat (STR) loci included in the AmpFlSTR Identifiler kit were obtained from a sample of 93 healthy unrelated individuals of Luoba population born in Tibet Autonomy Region of China (Southwestern China). In these samples, 141 alleles and 365 genotypes were observed for 15 STR loci. The distribution of these observed genotypes were not significantly different from the expected distribution according to Hardy-Weinberg equilibrium.     

Analysis of genotype frequencies and interlocus association for the PM, DQA1, and D1S80 loci in four populations

Allele frequencies of the LDLR, HBGG, GYPA, D7S8, GC, DQA1, and D1S80 loci are presented and genotypes are analyzed for each of four ethnic groups: African Americans (n = 200), US Caucasians (n = 200), US Hispanics (n = 200), and Japanese (n = 89). Hardy-Weinberg genotypic proportions were observed in all but two of the 28 population-locus tests undertaken. Those two instances are attributable to type I statistical error. Gametic equilibrium among loci is an assumption invoked for application of the product rule to utilize the discriminatory power from two or more loci simultaneously. Two statistical methods, a genotype matching statistic and log-linear modeling, were used to evaluate gametic disequilibrium. The match statistic, comparing observed to expected likelihood of genotypic identity for seven loci among pairs of individuals within the database, revealed only one statistically significant deviation among 20 tests. As expected, the probability of match was generally lowest in the test on all ethnic groups combined, indicating that allele frequencies differ among ethnic groups for some of the loci. This was confirmed with the statistic theta to measure ethnic stratification, in which about 0.10 of the genetic variation is apportioned among the four ethnic groups for four of the structural loci (LDLR, HBGG, GC, and DQA1), while for GYPA, D7S8, and D1S80, variation is more uniformly distributed among ethnic groups. Log-linear modeling was also applied to the five PM loci. The most parsimonious log-linear model included only three higher order terms: the two-way interactions of three of the PM loci with ethnic group. These three instances (LDLR, HBGG, and GC) indicated differences in allele frequencies between ethnic groups. No two or higher way interaction (disequilibrium) was observed among loci. In summary, the assumptions of Hardy-Weinberg and gametic equilibrium that facilitate the use of the five PM loci, DQA1 and D1S80 in forensic applications are consistent with the allele and genotype frequencies observed in these populations.     

IBD法在堂表亲缘关系鉴定中的应用

目的使用血缘一致性(identity by descent,IBD)法计算堂表亲缘关系的堂表关系指数(first cousin index,FCI)和累积堂表关系指数(combined first cousin index,CFCI),为IBD法鉴定两个个体是否具有堂表亲缘关系提供科学手段。方法取124对堂表兄弟姐妹和186对无亲缘关系个体的口腔拭子,检验每人18个常染色体STR基因座的等位基因,用IBD法计算堂表对和无关个体对的FCI和CFCI,并用判别分析的方法对两组样本的FCI和CFCI计算结果进行分析。结果 CFCI在堂表对和无关个体对中的频率分布呈偏正态分布,前者的平均值和标准差为11.864和21.678,后者为0.605和0.988,两者具有显著差异。以CFCI/(CFCI+1)≥0.6为标准,堂表对和无关个体对判别准确率为88.387%;依据各常STR基因座的FCI计算结果建立判别方程,多元判别方程和多元逐步判别方程的判别准确率分别为92.258%和91.935%。结论用IBD法和依据IBD建立的判别分析法可以用于堂表亲缘关系的筛选。     

中国汉族人群15个STR基因座的等位基因频率调查

目的 调查10071名中国汉族无关个体15个STR基因座的等位基因的类型及其频率，并与以往相关文献报道的汉族群体资料进行统计比较。方法 应用PowerPlex~(TM)16荧光标记复合扩增系统，对10071份中国汉族无关个体的血样DNA进行15个STR基因座的复合扩增；用ABI 377或3100遗传分析仪对扩增产物进行分型，统计15个STR基因座的基因频率。结果 15个STR基因座共发现226个等位基因，频率在0.0001～0.5512；除D8S1179基因座外，其它基因座均发现稀有等位基因，数目1～7个不等，共34个。在中国汉族人群，稀有D21S11基因座的等位基因32.1和36.2，D18S51基因座的等位基因15.2和17.2，Penta E基因座的等位基因15.2、17.4、18.4、19.4、26和27，D7S820基因座的等位基因9.2、10.1、11.1和15，Penta D基因座的等位基因18、19和20，TPOX基因座的等位基因14，FGA基因座的等位基因13，以及较常见但欧洲稀有的D21S11基因座的等位基因30.3和D7S820基因座的等位基因9.1和9.2等均为首次报道。结论 大样本基因频率调查有利于观察STR基因座的稀有等位基因；本研究结果与以往相关文献报道的结果有不同程度的差异。     

67个X-SNP位点的分型检测和连锁不平衡检验

目的 筛选一组在中国汉族人群中具有法医学应用前景的X-SNP位点.方法 根据dbSNP和HapMap两个数据库提供的位点信息和频率数据从X染色体上筛选出67个候选X-SNP位点,采用多重PCR联合基质辅助激光解析电离飞行时间质谱技术检测中国汉族人群428名无关个体,获得67个候选X-SNP位点在中国汉族人群中的频率数据...     

24个Y-STR基因座等位基因频率的群体差异分析

目的调查华东地区汉族无关个体24个Y-STR基因座的群体遗传学多态性,比较华东汉族和广东汉族人群间的群体差异性。方法应用GFS 24Y STR荧光检测试剂盒,对华东地区268名汉族无关个体24个Y-STR基因座进行群体遗传学分析。比较华东汉族和广东汉族人群的等位基因频率,进行群体差异分析。结果华东地区268名汉族无关个体24个Y-STR基因座共检出235个等位基因,267种单倍型,GD值范围为0.564 9~0.966 8。华东汉族和广东汉族人群在DYS622、DYS552、DYS443等12个基因座的等位基因间的差异有统计学意义。结论 GFS 24Y STR荧光检测试剂盒中的Y-STR基因座具有良好的遗传多态性,可应用于父系亲缘关系鉴定。     

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。     

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.     

两种计数法预测叔侄关系的对比研究

目的对比等位基因全不同基因座及共有等位基因计数法预测叔侄关系的差异性、相似性及其效能,为侦破案件提供参考。方法以已知叔侄关系的204对作为实验组,无关个体的204对作为对照组,采用PowerPlex 21系统检测20个常染色体STR基因座,然后进行统计分析。结果设定等位基因全不同基因座数预测界值≤6个,发现叔侄关系的灵敏度为83.82%,特异性为74.02%,漏判率为8.82%,误判率为11.76%,系统效能为78.92%。共有等位基因数预测界值≥17个,发现叔侄关系的灵敏度为75.98%,特异性为77.45%,漏判率与误判率均为7.84%,系统效能为76.72%。结论等位基因全不同基因座计数法与共有等位基因数计数法有互补优势,联合应用能提高预测叔侄血亲关系的能力,对侦查具有良好的指导意义。     

A PCR multiplex and database for forensic DNA identification of dogs

Animal-derived trace evidence is a common finding at crime scenes and may provide an important link between victim(s) and suspect(s). A database of 558 dogs of pure and mixed breeds is described and analyzed with two PCR multiplexes of 17 microsatellites. Summary statistics (number of alleles, expected and observed heterozygosity and power of exclusion) are compared between breeds. Marked population substructure in dog breeds indicates significant inbreeding, and the use of a conservative theta value is recommended in likelihood calculations for determining the significance of a DNA match. Evidence is presented that the informativeness of the canine microsatellites, despite inbreeding, is comparable to the human CODIS loci. Two cases utilizing canine DNA typing, State of Washington v. Kenneth Leuluaialii and George Tuilefano and Crown v. Daniel McGowan, illustrate the potential of canine microsatellite markers for forensic investigations.     

Empirical analysis of the STR profiles resulting from conceptual mixtures

Samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors can be challenging and associated uncertainties can have dramatic effects on the interpretation of testing results. Using an FBI genotypes dataset, containing complete genotype information from the 13 Combined DNA Index System (CODIS) loci for 959 individuals, all possible mixtures of three individuals were exhaustively and empirically computed. Allele sharing between pairs of individuals in the original dataset, a randomized dataset and datasets of generated cousins and siblings was evaluated as were the number of loci that were necessary to reliably deduce the number of contributors present in simulated mixtures of four or less contributors. The relatively small number of alleles detectable at most CODIS loci and the fact that some alleles are likely to be shared between individuals within a population can make the maximum number of different alleles observed at any tested loci an unreliable indicator of the maximum number of contributors to a mixed DNA sample. This analysis does not use other data available from the electropherograms (such as peak height or peak area) to estimate the number of contributors to each mixture. As a result, the study represents a worst case analysis of mixture characterization. Within this dataset, approximately 3% of three-person mixtures would be mischaracterized as two-person mixtures and more than 70% of four-person mixtures would be mischaracterized as two- or three-person mixtures using only the maximum number of alleles observed at any tested locus.     

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.