The frequencies of mutated alleles of CYP2D6 gene in a Turkish population

Allele and genotype frequency distribution of CYP2D6*3, *4, *5, *6 and *10 variants were analyzed in blood samples of 100 unrelated healthy individuals by Real-Time PCR. The allele frequencies of CYP2D6*3(A2549del), *4(G1846A), *6(T1707del) and *10(C100T) were 1%, 10%, 2.5% and 14.5% respectively, while allele frequency of CYP2D6*5 was 3% of the subjects tested. Extensive, poor and intermediate metabolizer (EM, PM, IM) genotype frequencies were 63%, 4% and 12%, respectively. CYP2D6 gene duplication was 4%. Our results show that the frequencies of the mutated alleles of CYP2D6 in Turkish populations are similar to some European populations. 4% of Turkish people who have two nonfunctional defective allele are a high risk group and 12.5% of Turkish people who have two decreased functional defective allele or one normal and one non functional defective allele were also in the risk group. Findings of this study demonstrate the importance of genetic variation in drug intoxicants.     

Autosomal STR data on the enigmatic Andaman Islanders

We have analyzed nine autosomal STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820) in 97 samples of enigmatic Andaman islanders including: 15 Great Andamanese, 46 Onge and 36 Nicobarese. Data was compared with the available data on Indian and South East Asian populations. Heterozygosity (H), power of discrimination (PD), probability exclusion (PE), typical paternity index (TPI), polymorphism information content (PIC), AMOVA and Arlequin analysis were carried out. Average heterozygosity observed was high and almost equal in all the populations. Similarly, PD, PE, TPI and PIC have been almost equal in all the populations.     

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.     

Genetic profile of nine STR loci among Goud and Padmashali populations of Andhra Pradesh, India

We have analysed nine autosomal STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) in Goud and Padmashali populations belonging to Chittoor and Cuddapah districts of Andhra Pradesh, India, respectively. This data was compared with the available data on Indian populations. Heterozygosity (H), power of discrimination (PD), probability exclusion (PE), typical paternity index (TPI), polymorphism information content (PIC), exact test with Bonferroni corrections and Arlequin analysis were carried out. Average heterozygosity observed in Goud and Padmashali populations were 0.82 and 0.81, respectively. Similarly, PD, PE, TPI and PIC have been found to be almost same between these two populations. Overall data analysis suggests the existence of sub-structuring in Indian populations.     

云南玉溪汉族15个STR基因座多态性及遗传关系分析

目的调查玉溪汉族人群15个STR基因座的遗传多态性,并分析与国内部分地区汉族群体的遗传关系。方法采用AmpFLSTR Identifiler试剂盒,复合扩增15个STR基因座,计算基因频率及法医学参数;收集国内其他10个群体的遗传学资料进行遗传距离和聚类分析。结果玉溪汉族群体15个STR基因座等位基因及基因型分布符合Hardy-Weinberg平衡定律,PD值在0.790 6～0.968 1之间,PE值在0.315 9～0.733 5之间,PIC值在0.554 6～0.856 4之间,15个基因座累积个体识别力为0.999 999 999 999 999 99,累积非父排除率为0.999 998。不同地区汉族群体间遗传距离分析提示,玉溪汉族与成都汉族遗传距离最近(0.004 0),其次是河南(0.004 5)和潮汕(0.004 7);内蒙古最远(0.036 1)。结论云南玉溪汉族15个STR基因座具有较高的遗传多态性,适于该群体的法医学应用,遗传关系分析结果可为该群体的起源、迁徙及与其他群体的遗传关系分析提供参考。     

Jewish population genetic data in 20 polymorphic loci

Frequency data of 20 polymorphisms (13 autosomal and 6 Y-chromosome STRs and the Alu-insertion YAP) were determined in a sample of 124 unrelated Jewish individuals from Ashkenazi, Sephardic, North African and Oriental origin. The a priori statistical power of the set of studied loci was highly discriminating (PD=1 in 2.393 E+15 individuals for autosomal STRs, and a probability of finding two unrelated males with the same haplotype of less than 0.01). Some significant population differences were registered between Jews and other Circummediterranean populations in Y-chromosome loci frequencies.     

Population genetics data of 23 autosomal STR loci for three Populations in United Arab Emirates

In the present study, forensic parameters were estimated for three populations residing in the United Arab Emirates (UAE) including UAE Arabs, Pakistanis and Indians based on the population data of 23 autosomal short tandem repeats (STRs). The UAE Arabs is a vital population to study due to high rates of consanguineous marriages. Therefore, it is essential to estimate the allele distribution and frequencies within this population. In addition, it is crucial to study the largest communities living in the UAE such as Indians and Pakistanis. A total of 1272 blood samples were collected on FTA® cards, comprising of 571 UAE Arabs, 352 Indians and 349 Pakistanis. All of these samples were amplified directly using Verifiler® Express PCR Amplification Kit that focuses on 23 autosomal STR loci, namely D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D10S1248, D1S1656, D12S391, D2S1338, D6S1043, Penta D and Penta E loci. The PCR products were electrophoresed on ABI 3500 Genetic Analyzer and analyzed using GeneMapper ID-X v1.4 software. Arlequin v3.5 and PowerStats software were utilized to determine the forensic parameters and population structure using AMOVA. Gene diversity, ranged from 0.67406 (TPOX) to 0.9226 (Penta E) in the UAE Arabs, 0.69955 (TPOX) to 0.9214 (Penta E) in Indian and 0.69853 (TPOX) to 0.921 (Penta E) in Pakistani population. The most discriminating autosomal STR loci observed was Penta E (PD = 0.985), (PD = 0.986), (PD = 0.986) in the UAE Arabs, Indian and Pakistani population, respectively. The obtained results showed the 23 STR loci had a relatively high genetic variation, confirming the suitability for forensic identification and kinship analysis, in the relevant populations. The significance of this study is to build an allelic frequency database for one of the most powerful commercially available STR amplification kits by using the current forensic workflow.     

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。     

A multivariate statistical approach to for the evaluation of the biogeographical ancestry information from traditional STRs

The capability to achieve biogeographic ancestry (BGA) information from DNA profiles have been largely explored in forensic genetics because of its potential usefulness in providing investigative clues. For law enforcement and security purposes, when genetic data have been obtained from unknown evidence, but no reference samples are available and no hints come out from DNA databases, it would be extremely useful at least to infer the ethno-geographic origin of the stain donor by just examining traditional STRs DNA profiles.Current protocols for ethnic origin estimation using STRs profiles are usually based on Principal Component Analysis approaches and Bayesian methods. The present study provides an alternative approach that involves the use of target multivariate data analysis strategies for estimation of the BGA information from unknown biological traces. A powerful multivariate technique such as Partial Least Squares-Discriminant Analysis (PLS-DA) has been applied on NIST U.S. population datasets containing, for instance, the allele frequencies of African-American, Asian, Caucasian and Hispanic individuals. PLS-DA approach provided robust classifications, yielding high sensitivity and specificity models capable of discriminating the populations on ethnic basis. Finally, a real casework has been examined by extending the developed model to smaller and more geographically-restricted populations involving, for instance, Albanian, Italian and Montenegrian individuals.     

Combined phenotyping of glucose 6-phosphate dehydrogenase (G6PD; EC 1.1.1.49) and 6-phosphogluconate dehydrogenase (PDG; EC 1.1.1.44)

The addition of negroid phenotypes to the already heterogeneous population of Israel caused us to reuse the enzymes G6PD and PGD which are known to have a better discrimination power in a negroid population than in caucasians. We have developed a system for combined phenotyping of G6PD and PGD. This system answers the requirements of the above enzymes and results in a negroid population than in caucasians. We have developed a system for combined phenotype-amount of sample and reagents needed and time spent.     

A method for subtyping group-specific component in bloodstains

A method is described for subtyping group-specific component (Gc) derived from human bloodstains. Bloodstained cuttings were extracted in 6 M urea. The extracts were subjected to ultrathin-layer polyacrylamide gel isoelectric focusing in the pH 4.5-5.4 range. After isoelectric focusing, Gc was detected by immunofixation in cellulose acetate membranes. This method permitted the successful typing of Gc in at least four-month-old bloodstains maintained at room temperature. Bloodstains from 266 liquid blood samples of known origin were subjected to both this method and immunofixation conventional agarose gel electrophoresis with no phenotypic discrepancies observed. The Gc population data for Whites from Baltimore, Maryland, were homogeneous with white sample populations from other geographical locations within the U.S.A.; while Gc data from northern U.S.A. black sample populations appeared to be heterogeneous compared with a southern United States black sample population.     

Application of HLA-DRB1 genotyping by oligonucleotide micro-array technology in forensic medicine

The human leukocyte antigen (HLA) system is known to be the most complex polymorphic system in the human genome. Among all of the HLA loci, HLA-DRB1 has the second largest number of alleles. The purpose of this study is to develop an oligonucleotide micro-array based HLA-DRB1 typing system for use in forensic identification, anthropology, tissue transplantation, and other genetic research fields. The system was developed by analyzing the HLA-DRB1 (DRB1) genotypes in 1198 unrelated healthy Chinese Han individuals originating from various parts of China and residing in Shanghai, China. METHOD: Polymerase chain reaction (PCR) coupled with the oligonucleotide micro-array technology was used to detect and type HLA-DRB1 alleles of the sample individuals. The reliability, sensitivity, consistency and specificity were evaluated for use in forensic identification. Furthermore, a meta-analysis was carried out by comparing the allele frequencies of the HLA-DRB1 locus with those of other Chinese Han groups, Chinese minorities and other ethnic populations. RESULTS: All the DNA samples yielded a 273 bp amplification product, with no other amplification products in this length range. The minimum quantity of DNA detected by this method is 15 ng in a PCR reaction system of 25 microl. The population studied appeared to be not in Hardy-Weinberg equilibrium. Observed heterozygosity (Ho), expected heterozygosity (He), expected probability of exclusion (PE), polymorphic information content (PIC), and discrimination power (DP) of the HLA-DRB1 locus from the Shanghai Han ethnic group were evaluated to be 0.8022, 0.8870, 0.7741, 0.8771, 0.9750, respectively. A total of 25 HLA-DRB1 alleles were identified. HLA-DRB1*09XX, *04XX, *12XX and *15XX were the most frequent DRB1 alleles, which were observed in 58.76% of the sample. One hundred and sixteen genotypes were found. The five most frequent genotypes were: *04XX/*04XX (0.0626), *09XX/*09XX (0.0593), *04XX/*09XX (0.0551), *09XX/*15XX (0.0384) and *08XX/*12XX (0.0351). The meta-analysis showed that there were uniquely distributed features of DRB1 alleles among various ethnic populations and among the studied population groups from various regions with the same ethnic origin. CONCLUSIONS: An HLA-DRB1 genotyping system has been developed and established based on the oligonucleotide micro-array technology. The HLA-DRB1 typing of the Han population in Shanghai has revealed a relatively high heterogeneity. Information obtained in this study will be useful for medical and forensic applications as well as in anthropology research. Large-scale micro-array detection is highly accurate and reliable for DNA-based HLA-DRB1 genotyping. These results suggest that HLA-DRB1 DNA polymorphisms and the database of the Shanghai Han group have useful applications in processing forensic casework (as personal identification, paternity test), tracing population migration and genetic diagnosis.     

人类D19S40基因座在不同人种中的遗传多态性研究

采用ＰＣＲ技术分析中国汉族、德国人、斯洛伐克人和美国黑人群体Ｄ１９Ｓ４００基因座的遗传多态性及世界三大人种之间的差异。四个群体共调查了６２０人,发现了１１个等位基因,观察到４７种基因型。各群体观察杂合度为：０．７８～０．８８,个人识别机率为：０．９３８５０～０．９６６４。四个群体基因型频率分布符合Ｈａｒｄｙ－Ｗｅｉｎｂｅｒｇ平衡（Ｐ＞０．０５）,三大人种（蒙古人种、高加索人种、美国黑人）之间Ｄ１９Ｓ４００基因座等位基因频率分布存在极显著差异（Ｐ＜０．０１）。结果显示Ｄ１９Ｓ４００基因座在群体遗传学研究和法医学个人识别中有较高应用价值     

Properdin factor B(Bf) polymorphism in the population of Veneto, Italy

The distribution of Bf phenotypes in the population of Veneto was investigated by agarose gel electrophoresis and immunofixation. In our sample (n = 592), the seven common phenotypes F, S, F-S, S-S0.7, S-F1, F-S0.7, F-F1 were observed and the following gene frequencies calculated: Bf*S = 0.7399; Bf*F = 0.2280; Bf*F1 = 0.0177; Bf*S0.7 = 0.0144. These gene frequencies are compared to those found in other populations. Analysis of 21 mother-child pairs was in agreement with an autosomal codominant inheritance.     

16 STR data of a Greek population

Allele frequencies for 16 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, and SE33) were calculated for a sample of 300 unrelated individuals from Greece. No deviations from Hardy–Weinberg equilibrium were observed for all loci. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 16 tested STR loci were 0.999999999 and 0.999999816, respectively. Population comparisons were carried out and low genetic distances were found between our data and those previously published for other neighbouring European populations.     

Allele frequencies for 15 autosomal STR loci and admixture estimates in Puerto Rican Americans

Allelic frequencies of 15 short tandem repeats (STR) markers (CSF1PO, FGA, THO1, TPOX, VWA, D3S11358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D19S433 and D2S1338) were determined using the AmpFl STR Identifiler PCR Amplification Kit in Puerto Rican American individuals (N=205) from Massachusetts. The FGA, D18S51 and D2S1338 loci had a high power of discrimination (PD) with values of 0.967, 0.965 and 0.961, respectively. Significant deviations from the Hardy-Weinberg (HW) equilibrium were not detected. An important genetic contribution of Caucasian European (76.4%) was detected in Puerto Rican Americans. However, comparative analysis between Puerto Rican American and other neighboring populations from United States mainly with African and Caucasian Americans, revealed significant differences in the distribution of STR markers. Our results are important for future comparative genetic studies of different American ethnic groups, in particular a cultural group called Hispanic-Americans and should be helpful for forensic and paternity testing.     

Comparison of drug abuse in different military populations

Quantitative analytical data, generated at the Navy Drug Screening Laboratory, Great Lakes, Illinois, expressed as percent confirmed positives for four drugs of abuse (marijuana metabolite, cocaine metabolite, amphetamines, and opiates) are summarized and compared according to their population of origin. The four populations of interest included U.S. Navy and Marine Corps recruits and service school members. Conformed positive urines for marijuana showed a small but significant decline (p less than 0.001) from about 1.2% confirmed positive among U.S. Navy recruits entering service school commands in 1984 to 0.9% among Navy service school members in 1988 and from 2.0% among U.S. Marine Corps recruits entering service schools in 1984 to 0.8% among Marine Corps service school members in 1988. Navy and Marine Corps recruits showed a significantly higher (p less than 0.001) confirmed positive use rate (6.1 and 3.3%, respectively) compared to service school members, perhaps reflecting their recent civilian use pattern. The relatively high confirmed positive cocaine rate among all groups may have reflected an increasing trend in all populations, confirming a similar trend in high school and other civilian populations. Generally, the frequency of confirmed positive urines with amphetamines and opiates, based upon the findings at the Navy Drug Screening Laboratory at Great Lakes, has been static except for an apparent recent increase in amphetamine use in 1988. The decline in confirmed positive drug urinalyses among service school members from both the Navy and Marine Corps indicated that perhaps education and maturity had a positive effect upon their behavior.     

A study on ten short tandem repeat systems: African immigrant and Spanish population data

This work presents the results obtained from a genetic–population study for the D1S1656 system in the population of Southwest Spain (Huelva, Cádiz and Sevilla), Spaniards of Caucasian origin from North Africa (Ceuta), as well as in the black Central West African and Moroccan immigrant populations in Spain. The results of a study of the autochtonous population of the Canary Islands (n=138), and immigrant Central West African populations in Spain (n=132), obtained for nine short tandem repeat (STR) loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820), as well as the amelogenin locus, all contained in Profiler Plus™ (Perkin-Elmer) PCR amplification kits, are also presented. Except for the FGA and VWA data on immigrant Central West African populations in Spain, no deviations from the Hardy–Weinberg equilibrium were detected.     

The Upper Silesia (Poland) population and forensic usefulness of 15 autosomal STR loci

Allele frequencies, forensic parameters for the 15 STR loci in the AmpFlSTR^® Identifiler Kit (Applied Biosystems), D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D19S433, VWA, TPOX, D18S51, D5S818 and FGA were determined in a sample of 150 unrelated dead and alive adults from the Upper Silesia region (Poland). The values of heterozygosity (Ht), polymorphic information content (PIC), power of discrimination (PD), matching probability (PM), mean exclusion chance (MEC) and mean exclusion probability (MEP) were calculated. Possible divergence from HWE was determined. Comparison of allele frequencies for examined STR loci between the Upper Silesia population and other Polish populations was carried out.     

SNaPshot技术检测Y-SNP位点O3-M122单倍群的应用

目的采用SNaPshot技术检测案例检材O3-M122位点6个亚群的分型,并调查其在云南3个民族无关男性人群中的频率分布。方法建立5-plex Y-SNPs复合扩增体系,采用SNaPshot Multiplex试剂盒,检测案例检材O3-M122单倍群下O3*-M122、O3a*-M324、O3a3*-P201、O3a3b*-M7、O3a3c*-M134、O3a3c1*-M117共6个Y-SNPs分型,并对上述6个Y-SNPs在云南佤族、白族、傣族共174名无关男性个体中的分布进行调查。结果 17份案例检材均得到良好的分型结果。上述3个民族分别在3个、5个、5个位点上发现多态性,其中佤族O3a3*-P201分布频率最高(0.430 0);白族O3a*-M324频率最高(0.212 3);傣族O3a3c1*-M117频率最高(0.158 2)。结论多重PCR反应及SNaPshot技术的联合应用适用于法医案件检材DNA检测,3个民族多态性数据可为相关应用所参考。