Deduction of paternity index from DNA mixture

Determination of individual genotypes in DNA mixture remains a challenge in forensic science. Using an approach of mixture of distributions, this article provides formula for calculation of paternity index (PI) in cases where only tissue mixture of the mother and alleged father, the genotypes of the mother and child, but not that of the alleged father are available. The formula has been used to solve a real case using mother's vaginal tissue contaminated with semen from alleged father.     

What is she doing here? Klinefelter syndrome in forensic casework

In this case report, we describe a sexual assault incident in which the male victim’s seminal fluid contained no sperm cells, as indicated by sperm cell staining and microscopic screening, and DNA profiling results from the non-sperm cell fraction showed a major/minor DNA mixture that could be interpreted as female and male. DNA profiling of a sample from a disposable drinking cup used by the victim at the crime scene provided a single source profile, and showed a 2:1 imbalance between the heights of the X and Y chromosomes, respectively. The victim’s DNA reference sample showed a similar imbalance of the X and Y chromosomes. These observations suggested that the victim might suffer from Klinefelter syndrome, a genetic disorder related to the sex chromosomes.Here, we describe the first reported use of the QIAGEN Investigator® Argus X-12 kit for characterization of X-chromosomal STR loci to potentially identify a case of Klinefelter syndrome. This commercially available kit is primarily used in forensic laboratories to investigate kinship relations and for paternity testing in alleged father/daughter cases. Results of the X chromosome DNA profiling from the victim’s disposable drinking cup and reference samples revealed two alleles at various X-chromosomal STR loci. Moreover, this kit can also amplify a Y chromosome specific sequence (AMEL-Y), and the results indicated that this sample actually originated from a male. Evidence of two X chromosomes in the victim's DNA suggested that he was likely to have Klinefelter syndrome. In this case report, we propose the use of the QIAGEN Investigator® Argus X-12 kit as a practical forensic tool for the detection of potential genetic syndromes related to the sex chromosomes, which can affect test results and, at times, make them difficult to interpret. We also aim to increase awareness within the forensic science community regarding the existence of genetic anomalies, which should be considered when analyzing DNA profiles.     

Paternal half-sisters or unrelated – How can the X-chromosomal evidence be quantified when one female presents trisomy X?

The X chromosome has unique features, such as haplodiploid mode of genetic transmission, which can be crucial to complement autosomal profiling or to disentangle complex kinship problems. Indeed, for some cases (e.g. full- or paternal half-sisters, or paternal grandmother-granddaughter hypotheses), X-markers are expected to provide a similar or a higher power to the one obtained with autosomes in paternity/maternity investigations. Both theoretical and informatics frameworks for pairwise X-linked kinship analyses are well established for individuals with a regular number of chromosomes, but these are still lacking for individuals exhibiting an X chromosome aneuploidy, such as females with Triple X (47, XXX) syndrome. Indeed, this work was motivated by a real forensic case involving the evaluation with X-chromosomal markers of the hypotheses that two women were related either as paternal half-sisters or as unrelated, one of them showing a trisomy X. In this case, the analysis of X-chromosomal markers would yield stronger results than autosomes, as females had to share at least one identical allele in each analyzed X chromosome marker under the paternal half-sibling hypothesis, unless a mutation occurs. To fulfill this gap, we present in this work algebraic formulae for some genotypic configurations, which will allow quantification of the evidence on the referred cases. A general approach, comprising other X chromosome aneuploidies, kinship hypotheses, and genotypic configurations, is currently being developed by us. This work is the starting point to analyze X-chromosomal data under the scope of kinship problems, involving individuals with aneuploidies. This will improve the quantification of DNA evidence not only in forensic casework, but also in the field of medical genetics, whenever individuals with X-chromosomal aneuploidies are involved.     

Y-SNP-genotyping - a new approach in forensic analysis

Y-chromosomal DNA polymorphisms, especially Y-STRs are well established in forensic routine case work. The STRs are used for identification in paternity deficiency cases and stain analysis with complicate mixtures of male and female DNA. In contrast, Y-chromosomal SNPs are a new tool in forensic investigations. At present, Y-SNPs are mainly used in molecular anthropology for evolutionary studies. Nevertheless, these markers could also provide very useful information for the analysis of forensic cases. The aim of the presented study was to test Y-SNP-typing for stain analyses using different methods-SNaPshot and MALDI-TOF MS. Both methods are based on the principle of minisequencing. The selected Y-SNP markers are suited to define the most important European haplogroups.     

A case of tri-allelic pattern at locus D3S1358 on chromosome 3p21 inherited from paternal grandmother

We are reporting a case of tri-allelic inheritance at locus D3S1358 commonly used for genetic identification in forensic DNA testing. This case was encountered during routine paternity testing using commercial DNA profiling kits. The tri-allelic inheritance identified was probably a result of duplication at this locus, supported by the equal peak intensities and inheritance pattern from grandparent to child.     

遗传标记微单倍型在法医学中的研究进展

微单倍型作为一种新型的法医学遗传标记,在国际法医学界已经引起了越来越多的关注。微单倍型是在较短片段内(例如200bp),包含2个或以上个SNP,具有单倍型多态性的序列。相较于STR,微单倍型突变率低,在混合斑鉴定中具有一定优势;与SNP相比较,微单倍型的多态性更高。选择含有祖先信息特征的微单倍型,在种群分析鉴定中具有应用价值。本文就微单倍型的演变,分型方法,命名及群体特征等方面作一综述。     

The 1998-1999 collaborative exercises and proficiency testing program on DNA typing of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG)

A total of 28 laboratories (labs) submitted results for the 1998 collaborative exercise and the proficiency testing program of the Spanish and Portuguese Working Group of the International Society for Forensic Genetics (GEP-ISFG) group. This number increased to 46 labs in 1999. Six bloodstains were submitted, each one with 200 microl soaked in cotton except the sample no. 6 submitted for DNA quantification which had 2 microl. One of the samples was a mixed stain. A paternity testing case and a criminal case in the 1998 trial (GEP'98) and two paternity testing cases in 1999 (GEP'99) were included and the statistical evaluation of the evidence was requested in both cases. In the GEP'99 trial, a theoretical paternity testing case was included. A total of 52 DNA genetic markers were used by the participants in the GEP'98 trial, which increased to 101 in GEP'99. Despite this increasing number of participating labs, results remained quite satisfactory. All the labs used PCR-based DNA polymorphisms with an increasing number of markers, obtaining good results. SLPs were used by a decreasing number of labs but the results indicated a good level of expertise despite the different protocols used.Good results were also obtained for mtDNA despite the difficulties presented by the samples due to the presence of length heteroplasmy in some samples in both trials. The detection of heteroplasmy should, however, be improved.Similar conclusions were reached for both, the paternity and the criminal case by all the labs. Common methodologies for the statistical evaluation of the paternity case were used and the paternity index and the probability of paternity (with an a priori value of 0.5) reported by most of the labs. Also, a great uniformity was found in the evaluation of the criminal case despite the lack of a specific hypothesis in the design of the exercise. Some errors in statistical programs or in calculations were detected in a theoretical paternity case included in the GEP'99 trial for statistical analysis.     

Possible difficulties in molecular-genetic expertise in cases with insufficiently high individual significance of the results (as exemplified by a complex case with disputable maternity)

Molecular genetic technologies used in forensic medical expert evaluations help quantitatively evaluate the significance of coincidence or non-coincidence of signs in personality identification and in expert evaluation of kinship identification (disputable paternity or maternity). The level of validity of evidences, which can be considered necessary and sufficient, is the principal problem in such cases. Analyzing a complex case with disputable maternity, the authors discuss problems illustrating the necessity of attaining a high level of validity of the results for drawing a justified expert conclusion. Only high validity standard can rule out errors in interpretation of the results, otherwise the significance of the detected complex of signs can be insufficient for an unambiguous solution of an expert task.     

DNAc: A clustering method for identifying kinship relations between DNA profiles using a novel similarity measure

After decades of refinement, DNA testing methods have become essential tools in forensic sciences. They are essentially based on likelihood ratio test principle, which is utilized specifically, by using as prior knowledge the allele frequencies in the population, to confirm or refute a given kinship hypothesis made on two genotypes. This makes these methods ill suited when allele frequencies or kinship hypotheses are unavailable. In this paper, we introduce DNAc, a new clustering methodology for DNA testing based on a new similarity measure that allows an accurate retrieval of the degree of relatedness among two or more genotypes, without relying on kinship hypotheses or allele frequencies in the population. We used DNAc in analyzing microsatellite DNA sequences distributed among 12 genotypes from normal individuals from two distinct families. The results show that DNAc accurately determines kinship among genotypes and further gathers them in the appropriate kinship groups.     

表观遗传学在法医学应用探讨

表观遗传学指没有DNA序列变化的、可遗传的基因表达改变。主要包括DNA甲基化、X染色体剂量补偿、组蛋白修饰、基因组印记、表观基因组学和人类表观基因组计划等方面的内容。在法医实际检案中常遇到一些特殊问题,如妊娠期胎儿父权的认定,单亲鉴定中亲代必需等位基因的确定,同卵双生子的区分,微量组织来源的鉴定等。本文对表观遗传学的基本内容和在法医学中的应用进行综述,以期为相关研究及实践提供参考。     

Population genetic data of 38 autosomal InDels in San Basilio de Palenque,the first free town in America

In order to increase the information about Indels, we report allele frequencies and statistical parameters of forensic efficiency obtained typing a sample of 114 unrelated healthy individuals living in San Basilio de Palenque – Colombia using a panel of 38 autosomal InDels. No significant deviations from Hardy–Weinberg expectations were found except in the marker rs10629077 (p = 0.0002). The present database will be useful for forensic and paternity purposes for the region studied. Moreover, these additional markers can help forensic laboratories to solve parentage testing as well as to improve the analysis of degraded DNA samples.     

Object-oriented Bayesian networks for paternity cases with allelic dependencies

This study extends the current use of Bayesian networks by incorporating the effects of allelic dependencies in paternity calculations. The use of object-oriented networks greatly simplify the process of building and interpreting forensic identification models, allowing researchers to solve new, more complex problems. We explore two paternity examples: the most common scenario where DNA evidence is available from the alleged father, the mother and the child; a more complex case where DNA is not available from the alleged father, but is available from the alleged father’s brother. Object-oriented networks are built, using HUGIN, for each example which incorporate the effects of allelic dependence caused by evolutionary relatedness.     

Mutations at 17 STR loci in Chinese population

Knowledge about mutation rates and the mutational process of short-tandem-repeat (STR) or microsatellite loci used in forensic analysis is crucial for the correct interpretation of resulting genetic profiles. We analysed a total of 19,754 samples from 6532 paternity testing cases at 17 STR loci which are commonly applied to forensics. The parenthood in each of these cases was highly validated (probability>99.99%). We identified 178 mutations. Locus-specific mutation rate estimates varied between 7.0 x 10(-5) and 2.2 x 10(-3), and the overall average mutation rate estimate was 8.4 x 10(-4). The observed mutational features for STRs have important consequences for forensic application such as the definition of criterions for exclusion in paternity testing and the interpretation of DNA profiles in identification analysis. In order to enrich the reference data of STRs mutations which are valuable for forensic application, we suggest the establishment of such database and ask the whole forensic community for data contribution including China.     

Beyond traditional paternity and identification cases. Selecting the most probable pedigree

The paper extends on the traditional methodology used to quantify DNA evidence in paternity or identification cases. By extending we imply that there are more than two alternatives to choose between. In a standard paternity case the two competing explanations H(1): "John Doe is the father of the child and H(2): "A random man is the father of the child, are typically considered. A paternity index of 100000 implies that the data is 100000 more likely assuming hypothesis H(1) rather than H(2). If H(2) is replaced by "A brother of John Doe is the father", the LR may change dramatically. The main topic of this paper is to determine the most probable pedigree given a certain set of data including DNA profiles. In the previous example this corresponds to determining the most likely relation between John Doe and the child. Based on DNA obtained from victims of a fire, bodies found in an ancient grave or from individuals seeking to confirm their anticipated family relations, we would like to determine the most probable pedigree. The approach we present provides the possibility to combine non-DNA evidence, say age of individuals, and DNA profiles. The program familias, obtainable as shareware from http://www.nr.no/familias, delivers the probabilities for the various family constellations. More precisely, the information (if any) prior to DNA is combined with the DNA-profiles in a Bayesian manner to deliver the posterior probabilities. We exemplify using the well published Romanov data where the accepted solution emerges among 4536 possibilities considered. Various other applications based on forensic case work are discussed. In addition we have simulated data to resemble an incest case. Since the true family relation is known in this case, we may evaluate the method.     

二代测序技术在法医遗传学中的应用研究进展(2011～2016)

对生物检材进行DNA分型是解决法医遗传学实践中个体识别和亲权鉴定问题的重要步骤,法医学实践中复杂生物检材和复杂亲缘关系鉴定等一直是现有的检测分析技术的难点和挑战。随着DNA技术的发展,新的检测分析技术不断引入到法医遗传学领域,以期提高检测效能。二代测序技术具有测序通量高、成本低等特点,能够获得样本DNA详细序列和相对含量等信息,有助于生物检材的检测和案件的分析。二代测序技术在法医遗传学领域的应用受到广泛关注,相关的应用研究逐渐增多。本文就目前法医遗传学领域借助二代测序技术对遗传标记分析的研究进展进行总结,希望能为相关研究和应用提供参考。     

Bayesian networks for DNA-based kinship analysis: Functionality and validation of the GENis missing person identification module

GENis is a recently published open-source multi-tier information system developed to run forensic DNA databases. It relies on a Bayesian Networks framework and it is particularly well suited to efficiently perform large-size queries against databases of missing individuals. In this contribution we present a validation of the missing person identification capabilities of GENis. To that end we introduce fbnet, a free-software package written in the R statistical language that implements the complete GENis functionality to perform kinship analysis based on DNA profiles. With the aid of fbnet, we could validate likelihood ratios against estimations draw with Familias and forrel (two well-recognized R packages for kinship quantification) for complex pedigrees provided by the Argentinian reference databank (Banco Nacional de Datos Geneticos, BNDG). We found that our methodological approach presented an excellent performance in terms of accuracy and computation times.     

SNPs and MALDI-TOF MS: tools for DNA typing in forensic paternity testing and anthropology

DNA markers used for individual identification in forensic sciences are based on repeat sequences in nuclear DNA and the mitochondrial DNA hypervariable regions 1 and 2. An alternative to these markers is the use of single nucleotide polymorphisms (SNPs). These have a particular advantage in the analysis of degraded or poor samples, which are often all that is available in forensics or anthropology. In order to study the potential of SNP analysis in these fields, 41 SNPs were selected on the basis of following criteria: conservation, lack of phenotypic expression, and frequency of occurrence in populations. Thirty-six autosomal SNPs were used for genotyping 21 inclusionary and 3 exclusionary paternity cases. The behavior of 5 X-chromosome SNPs was analyzed in a French representative population. Our approach to SNP typing is a multiplex PCR based amplification followed by simultaneous detection by primer extension (PEX) analyzed by Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). The selected autosomal SNPs showed independent inheritance and gave clear results in paternity investigation. All X-SNPs were useful as both paternity and identification markers. PEX and MALDI-TOF MS, with their high sensitivity, precision and speed, gave a powerful method for forensic and anthropological exploitation of biallelic markers.     

法医DNA分析的其他应用

综述了法医DNA的多种用途,如人死后根据体内DNA变化情况推断死后时间间隔,利用线粒体DNA4977bp的缺失以及端粒的长度推断年龄;利用昆虫mtDNA的细胞色素氧化酶亚基I进行昆虫种属鉴定,以帮助确定人的腐尸死亡时间;利用一些食血昆虫体内的人DNA帮助了解与案件的关系;利用DNA标记进行动物如犬、牛、马及猪等个体识别与亲子鉴定,解决因动物引起的纠纷,或者利用DNA分析嫌疑人周围的动物毛发、植物及土壤微生物等,确定嫌疑人与案件的关系。     

Y-STR基因座应用于刑事案件的独特作用

目的探讨Y-STR基因座在刑事案件中的应用价值。方法采用Y-STR荧光标记复合扩增技术,结合案例应用。结果Y-STR基因座对于涉及男女混合、多名男性混合样本、性别鉴定、父权鉴定等案例中具有特有应用价值。结论Y-STR基因座可应用于法庭科学中的个体识别与同一认定,但在应用中要注意各种特例的发生。