Population data from the New South Wales Aboriginal Australian sub-population for the profiler plus autosomal short tandem repeat (STR) loci

It is a requirement that forensic DNA profiling evidence be accompanied by an estimation of its weight, in order that the court can assign an appropriate probative value to it during legal proceedings. There are various models by which this estimation can be made, but each relies on approximations of the allele frequencies in the relevant population. This report provides the results of population genetic analyses at nine autosomal short tandem repeat (STR) loci for the Aboriginal Australian sub-population of New South Wales, Australia.     

Autosomal microsatellite allele frequencies for 15 regionally defined Aboriginal Australian population datasets

DNA profiling results presented in court must be accompanied by a statistical estimate of its evidential weight. In calculating such statistics, allele frequencies from the tested loci are required. These allele frequencies should be collected at a level that appropriately represents the genetic diversity that exists in the population. This paper reports allele frequencies and the results of population genetic testing of autosomal microsatellite profiles from indigenous Australian donors. In contrast to previous practice these data have been collated according to traditional regional boundaries rather than recently imposed State and Territory borders.     

Use of subpopulation data in Australian forensic DNA casework

DNA profiling evidence presented in court should be accompanied by a reliable estimate of its evidential weight. In calculating such statistics, allele frequencies from commonly employed autosomal microsatellite loci are required. These allele frequencies should be collected at a level that appropriately represents the genetic diversity that exists in the population. Typically this occurs at broadly defined bio-geographic categories, such as Caucasian or Asian. Datasets are commonly administered at the jurisdictional level. This paper focuses on Australian jurisdictions and assesses whether this current practice is appropriate for Aboriginal Australian and Caucasian populations alike. In keeping with other studies we observe negligible differences between Caucasian populations within Australia when segregated geographically. However segregation of Aboriginal Australian population data along contemporary State and Territory lines appears to mask the diversity that exists within this subpopulation. For this reason datasets collated along more traditional lines may be more appropriate, particularly to distinguish the most genetically differentiated populations residing in the north of the continent.     

Reporting of highly individual genetic typing results: a practical approach.

This paper considers the interpretation of serological typing data as a problem in forensic science, as opposed to a problem in population genetics or statistics. Controversies arising in this area are partly due to an overly narrow perspective that ignores basic forensic science principles. After an initial discussion of the special problem that deoxyribonucleic acid (DNA) blood typing poses to forensic science, the three difficulties common to all the proposed interpretive methods are discussed. These are: predicting genotype incidence from allele frequencies, predicting frequencies for the joint occurrence of genotypes in a number of different genetic marker systems, and determining the appropriate population to use to measure the frequencies. The inability to test assumptions that are inherent in our routine methods is noted. This is a procedural weakness that unnecessarily limits the admissibility of DNA typing evidence in court. A practical solution to this problem is offered that begins with minimal assumptions. Initially a statement is made based on (1) how many reference samples the laboratory has typed and (2) how many of these samples show genotypes corresponding to the case samples. The second stage of the presentation begins with a statement that additional assumptions are necessary to fully interpret the evidence and that although these assumptions are scientifically very reasonable, they cannot be absolutely proven. The presentation can then proceed, if desired, to consideration of the specific assumptions and frequency estimates of any of the methods that have been proposed to date. To follow this approach population data must be kept in a form that allows the simple first-stage statement to be made. This means that each individual's record would include typing results in each genetic marker system. Although this method of data storage differs from that used in most forensic science laboratories, it is exceptionally versatile, and allows great flexibility in data analysis.     

云南怒族X染色体5个STR基因座遗传多态性

目的以云南怒族无关个体为研究对象,调查怒族群体DXS6804、DXS6799、DXS8378、DXS7130、DXS7132基因座的基因频率及基因型频率分布,建立群体遗传数据库。方法用聚合酶链反应(PCR)、变性聚丙烯酰胺凝胶电泳结合银染的方法,检测100名云南怒族个体X染色体上5个STR基因座的重复序列长度变化。结果云南怒族群体5个STR基因座具有遗传多态性,χ2检验表明多态性分布符合Hardy-Weinberg平衡定律。结论云南怒族群体DXS6804、DXS6799、DXS8378、DXS7130和DXS7132基因座,可用于法医学个体识别、亲子鉴定等研究。     

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.     

Genetic variation of 13 STR loci in the four endogamous tribal populations of Eastern India

We have analysed 13 autosomal STR loci in four endogamous tribal populations from two eastern states (Orissa and Nagaland) of India. The Gadaba, Kuvi Khond and Lotha Naga populations have not been analysed for microsatellite genetic variation previously. The allele frequencies for all loci are within the range observed in the geographical region and racial background, though some alleles showed greater variation. Departures from the Hardy-Weinberg equilibrium were tested by three methods and two loci (THO1 and TPOX) showed significant departures for all measures in Gadaba and Lotha Naga populations. The exclusion probability and discrimination probability were high for all analysed loci in all populations. There is no evidence for association of alleles among the STR loci studied. This allele frequency information will be useful for forensic, paternity and population genetic studies.     

Thousands of years of Malay and Chinese population history in Indonesia and its implication on Paternity Index in DNA paternity testing

The existence of the Chinese population in the predominantly Malay population in Indonesia can be traced back thousands of years, and it has been suspected that it played an essential role in the history of the Malay population origin in Maritime South East Asia. With the fact that the Malay-Indonesian population is currently predominant compared to the Chinese population in Indonesia (Chinese-Indonesian), the selection of the origin of the STRs allele frequency panel population becomes an issue in DNA profiling, including in paternity testing. This study analyses the genetic relationship between the Chinese-Indonesian and Malay-Indonesian populations and how this affects the Paternity Index (PI) ??calculation in paternity test cases. The study of the relationship between populations was carried out using neighbour-joining (NJ) tree analysis and multidimensional scaling (MDS) on the allele frequency panel of 19 autosomal STRs loci of Malay-Indonesian (n = 210) and Chinese-Indonesian (n = 78) populations. Four population groups were used as references: Malay-Malaysian, Filipino, Chinese, and Caucasian. An MDS analysis was also performed based on the pairwise F_ST calculation. The combined Paternity Index (CPI) calculation was carried out on 132 paternity cases from the Malay-Indonesian population with inclusive results using a panel of allele frequencies from the six populations. The pairwise F_ST MDS indicates a closer relationship between the Chinese-Indonesian and Malay-Indonesian compared to the Chinese population, which is in line with the CPIs comparison test. The outcome suggests that the alternative use of allele frequency database between Malay-Indonesian and Chinese-Indonesian for CPI calculations is not very influential. These results can also be considered in studying the extent of genetic assimilation between the two populations. In addition, these results support the robustness claim of multivariate analysis to represent phenomena that phylogenetic analyses may not be able to demonstrate, especially for massive panel data.     

A new method for the evaluation of matches in non-recombining genomes: application to Y-chromosomal short tandem repeat (STR) haplotypes in European males

A 9-locus microsatellite framework (minimal haplotype), previously developed for forensic purposes so as to facilitate stain analysis, personal identification and kinship testing, has been adopted for the establishment of a large reference database of male European Y-chromosomal haplotypes. The extent of population stratification pertaining to this database, an issue crucial for its practical forensic application, was assessed through analysis of molecular variance (AMOVA) of the 20 regional samples included. Despite the notion of some significant haplotype frequency differences, which were found to correlate with known demographic and historic features of Europeans, AMOVA generally revealed a high level of genetic homogeneity among the populations analyzed. Owing to their high diversity, however, accurate frequency estimation is difficult for Y-STR haplotypes when realistic (i.e. moderately sized) datasets are being used. As expected, strong pair-wise and higher order allelic associations were found to exist between all markers studied, implying that haplotype frequencies cannot be estimated as products of allele frequencies. A new extrapolation method was therefore developed which treats haplotype frequencies as random variables and generates estimates of the underlying distribution functions on the basis of closely related haplotypes. This approach, termed frequency 'surveying', is based upon standard population genetics theory and can in principle be applied to any combination of markers located on the Y-chromosome or in the mitochondrial genome. Application of the method to the quality assured reference Y-STR haplotype database described herein will prove very useful for the evaluation of positive trace-donor matches in forensic casework.     

Extraction of the relevant population from a forensic database

Evaluation of forensic evidence using Bayesian statistics requires the formulation of hypotheses. Many hypotheses, especially those presenting the defence viewpoint imply that traces can be attributed to an arbitrary member of a relevant population. The exact items or persons that comprise the relevant population may vary from case to case. Therefore, the statistical evaluation of evidential value based on databases cannot make use of a fixed set of items or persons. In the current paper, methodology is presented to filter the contents of a database such that only items that are considered relevant are selected. Six scenarios, including those related to fibre, textile, and glass evidence are described, together with the hypotheses and relevant populations that may be evaluated by an expert. In addition, we show how items representing the defined relevant population can be extracted from a database using SQL code. Images of the items in the (filtered) relevant population provide an overview of the selected items and hence direct feedback to the examiner. In this way, erroneous codes or unwanted side effects can be identified and corrected. It is concluded that the filtering procedure is effective in cases where the relevant population is demarcated accurately.     

西安汉族HLA-Cw基因座遗传多态性研究

目的研究西安汉族HLA-Cw基因座遗传多态性,建立西安汉族HLA-Cw基因座基因频率数据库。方法采用序列特异性寡核苷酸探针杂交技术(PCR-SSOP)对130位西安汉族无关个体HLA-Cw基因座进行基因分型。结果共检出16种等位基因,基因频率分布在0.0077～0.1588,其中HLA-Cw*01、03、07基因频率较高,PCR-SSOP分型技术使西安汉族HLA-Cw空白频率降至0.0182。结论西安汉族HLA-Cw基因座基因型分布符合Handy-Weinberg平衡定律,所得到的基因频率数据可为临床器官移植配型、人类学、法医学提供重要的群体遗传学资料。     

Developing STR databases on structured populations: The native South Siberian population versus the Russian population

Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of θ-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus и AmpFlSTR Profiler Plus. The groups differentiate from each other with average θ-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on θ-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on θ-values.     

Autosomal microsatellite allele frequencies for a nationwide dataset from the Australian Caucasian sub-population

DNA profiling results presented in court must be accompanied by a statistical estimate of its evidential weight. In calculating such statistics, allele frequencies from the tested loci are required. This paper reports allele frequencies and the results of population genetic testing of datasets of autosomal microsatellite profiles from Australian Caucasian donors. In contrast to previous practice in Australia these data have been collated at the national level rather than at the State and Territory level. We consider that this national dataset could be used in forensic DNA casework throughout Australia as previously recommended by Ayres et al. [K.L. Ayres, J. Chaseling, D.J. Balding, Implications for DNA identification arising from an analysis of Australian forensic databases, Forensic Sci. Int. 129 (2002) 90-98].     

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。     

Allele distribution of three X-chromosome STR loci in an antioquian population sample

The X-linked short tandem repeats (STR) markers have proven to be very useful tools for paternity testing when the disputed child is female. The aim of this study was to describe the polymorphism of three X-chromosomal STR loci (DXS6797, DXS6800 and HPRTB) in an Antioquian (Colombian) population sample. PCR products were separated in 4% acrylamide-bis-acrylamide denaturing gels followed by silver staining. Allele size determination and genotyping were performed according to recommendations of the DNA Commission of the International Society of Forensic Genetic using the allelic ladder manufactured at home and based on DNA controls including K562 and 9947A (Promega). Gene frequencies were calculated using ARLEQUIN version 3.11. Population genetic data were obtained by analyzing 127-400 unrelated males and 135 unrelated females from Antioquian (Colombian) population. Distribution of the allele frequencies of these systems for Antioquia population is similar to the European populations.     

Jordanian population data on the PCR-based loci: LDLR, GYPA, HBGG, D7S8 and GC.

Genotype and allele frequency distributions for PM polymerase chain reaction (PCR)-based genetic markers were determined in a Jordanian sample population. Results were obtained using the AmpliType PM PCR Amplification and typing kit. All loci were in agreement with the Hardy-Weinberg equilibrium expectations. The predominant alleles for LDLR, GYPA, HBGG, D7S8 and GC loci were B, A, B, A and C respectively. No statistically significant variation was detected in allele frequencies of these loci in Jordanians compared to that in Israeli Arab, U.S Caucasian and Japanese populations. Data presented here can be used to estimate the frequency of a specific DNA profile in the Jordanian population for forensic analyses and paternity testing.     

Blood group frequencies of the population of Trinidad and Tobago, West Indies.

The results of grouping tests performed on blood samples collected over a five-year period at the Trinidad and Tobago Forensic Science Centre are presented. The samples were tested using the ABO, PGM, EAP and GLO blood group systems. Phenotypic frequencies and allele frequencies for each system were calculated for the two major ethnic groups of the population, the African and East Indian. Matching probabilities, which can be used in the interpretation of physical evidence in forensic cases, were also calculated.     

A study on polymerase chain reaction-based HLA DQ alpha locus in Elaziğ, Turkey

The polymerase chain reaction (PCR) was used for genetic characterization of 45 samples taken from the city of Elazi? in Turkey. The polymorphism at the human leukocyte antigen DQalpha locus was detected. Allele and genotype frequencies were determined for unrelated individuals at this locus. Laboratory analyses were done by PCR amplification of DNA. Hybridization to allele specific oligonucleotide probes was performed using a reversed dot-blot typing method. The collected genotype and allele frequencies have been tested, and a comparison was made with other population surveys of this locus. Allele frequencies ranged from 3.3% (allele 1.3) to 36.7% (allele 4), with a discrimination power of 0.92. No deviation was seen from Hardy-Weinberg equilibrium in the findings.     

STR data for the AmpFℓSTR Identifiler loci from Swedish population in comparison to European, as well as with non-European population

The modern Swedish population is a mixture of people that originate from different parts of the world. This is also the truth for the clients participating in the paternity cases investigated at the department. Calculations based on a Swedish frequency database only, could give us overestimated figures of probability and power of exclusion in cases including clients with a genetic background other than Swedish. Here, we describe allele frequencies regarding the markers in the Identifiler-kit. We have compared three sets of population samples; Swedish, European and non-European to investigate how these three groups of population samples differ. Also, all three population sets were compared to data reported from other European and non-European populations.Swedish allele frequencies for the 15 autosomal STRs included in the Identifiler kit were obtained from unrelated blood donors with Swedish names. The European and non-European frequencies were based on DNA-profiles of alleged fathers from our paternity cases in 2005 and 2006.     

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...