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.     

Forensic databases,a perspective from the penitentiary centers of Spain

Scientific and technological progress in the field of forensic genetics is very useful in the resolution of criminal cases, but it entails the need for a deep ethical reflection, as the individual Fundamental Rights may be violated.This project aims to collect and compare the opinion of prisoners and prison officials on what characteristics the country's forensic database should have. In this context, 210 subjects were surveyed, 101 of them prisoners and the rest prison officials, from three different Spanish penitentiary centers.Among the results obtained, most prisoners and officials consider the national DNA database to be useful, and additionally, a 40% of the participants would support the integration of the profiles of the entire population. 64% considered it ethical to use the DNA profiles of the database as a tool for familial searching. Despite this, half of the respondents are concerned about the future uses of the DNA database.Integrating the opinion of these analyzed groups with other relevant judicial, scientific and ethical convictions, ensures the regulation between security and individual’s Human Rights.     

Distribution of Y chromosomal STRs loci in Mayan and Mestizo populations from Guatemala

In this study, a sample of 225 Guatemalan males, comprising 115 Mestizo-Guatemalan and 110 Mayan-Guatemalan, was typed for 17 Y-short tandem repeats (STRs) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATA_H4.1 and DYS385a/b). The haplotype diversity (H = 1) and discrimination capacity (96.86%) were calculated. Analysis of molecular variance (AMOVA) demonstrated a low but significant interpopulation differentiation when compared with the results obtained when we confront the Mestizo and Mayan populations with the European populations.Furthermore, the genetic variability and differences among the American, African, Asian, and European populations were analyzed with the software Statistica 9.1. In addition, the genetic distances were also calculated using other published data. Reynolds and Slatkińs genetic distance was visualized using the multidimensional scaling (MDS) analysis. All the analysis performed locates the Mayan population next to the Native American population, while Guatemalan-Mestizo population was found to be between these populations and the European population, similar to other Mestizo one.The implementation of the estimation of individual ancestry proportions of the whole population sample showed the presence of two well-differentiated population groups.     

The calculation of DNA match probabilities in mixed race populations

A coherent method is offered to estimate likelihood ratios for DNA match probabilities from mixed racial populations that avoids the approach of reporting separate estimates for each race. The method is demonstrated for some cases involving profiles derived from several individuals and incorporates a correction for 'subpopulation' effects.     

重庆地区汉族群体Amelogenin及9个STR基因座的群体遗传学调查

对重庆地区汉族群体200例无关个体进行Amelogenin及9个STR基因座群体遗传学调查,并对人血液（痕）、精斑、组织、染色的细胞涂片、毛发、牙齿及骨骼组织进行基因型测定,并用于法科学检查。采用Chelex或酚-氯仿提取DNA荧光标记复合扩增法对Amelogenin及9个STR基因座,即D3S1358、VWA、FGA、TH01．TPOX、CSF1PO、DSS818、D135317、D75820进行复合扩增,扩增产物由毛细管电泳进行分离和荧光检测。9个STR基因座分别发现6、7、17、7、5、8、7、7、7个等位基因,其最高的基因频率分别是0．3900、0．2480、0．1650、0．5380、0．5280、0．4500、0．3140、0．3150、0．4000。发现的基因型数分别是16、25、71、20、12、22、26、22、26个。基因型频率均符合Hardy－Weinberg平衡,未发现基因连锁。9个STR基因座的DP值分别是0．8610、0．9220、0．9750、0．8020、0．7730、0．8780、0．9210、0．9140、0．8990,累计DP值是0．9999;非父排除率分别是0．5990、0．5450、0．7650、0．2950、0．3620、0．4520、0．6840、0．6660、0．5180,累积非父排除率是0．9995;杂合度分别是0．8000、0．7700、0．8850、0．6030、0．6550、0．7150、0．8440、0．8350、0．7550,累积杂合度是0．9999。证明这些基因座均适用于重庆     

Genetic analysis of 15 STR loci in the population of Zhejiang Province (Southeast China)

Fifteen autosomal STR loci were analyzed from a population sample of 598 unrelated individuals residing in Zhejiang Province. We report allele frequencies distribution and statistical parameters for all 15 STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA. Allele frequencies, the observed heterozygosity (Ho), the polymorphic information content (PIC), and the probability of paternity exclusion (PE) were calculated. All loci were in accordance with Hardy–Weinberg equilibrium (P > 0.05). Our studied population data were compared with the previously published population data of other ethnic groups or areas in China. Our results of present study were valuable for human identification and paternity tests in Zhejiang Province.     

Investigation into the usefulness of DNA profiling of earprints

DNA profiling of biological trace evidence has been used for many years. The application of this technique specifically to the DNA profiling of earprints has not to date been thoroughly investigated. This report presents the results of 60 earprints collected from three healthy adult volunteers under controlled laboratory conditions. DNA profile analysis revealed that high levels of non-donor alleles are observed when earprints are collected for DNA profiling. The source of these non-donor alleles is investigated and the impact that their presence within the profile may have on the use of this technique is discussed.     

Paternity probability when a relative of the father is an alleged father

When scientists use DNA evidence in court, coancestry effects such as population structure and relatedness are usually ignored. In paternity cases, only if a particular man has the child's paternal allele at a certain locus, can he not be excluded in the paternity dispute. However, it is certainly true that close relatives will be far more likely to have the child's paternal allele than will random members of the reference population. In particular, the probability that the true father's brother has the paternal allele is very much greater than that for any other relationship. In this paper, the authors describe a method for inference in a case where the true father may be a relative of the alleged father. This paper also reports that most current methods overstate the probability that the alleged father is the father.     

Genetic STRs variation in a large population from Tuscany (Italy)

Allele frequencies for 17 STRs, together with some parameters of forensic interest, were estimated in a sample of 835 unrelated individuals born in Tuscany, an Italian region. These data were compared with Italian, Chinese, Kosovo Albanian, Romanian and Tunisian populations, strongly represented in this area. No significant differences in single loci were detected, except for Chinese in comparison with all the other populations.     

Assessment of STR Typing Success Rate in Soft Tissues from Putrefied Bodies Based on a Quantitative Grading System for Putrefaction

To date, there is no systematic investigation of the association of short tandem repeat (STR) typing success rate in soft tissues with different signs of putrefaction. Herein, putrefaction was rated using a newly developed 19‐parameter system in soft tissues from a collective of 68 decaying bodies, and DNA yield was determined in 408 samples. DNA integrity was rated using a self‐devised pentaplex PCR generating an “integrity score” (S_i). STR typing success rate was then assessed for selected cases. DNA yield and S_i differed significantly between tissues with kidney on average exhibiting the highest S_i values. Statistical analysis revealed that nine parameters were significantly and positively correlated with S_i. The observed values for each of these nine parameters were summed up to generate a putrefaction score (S_p) for each sample. Our results show that STR typing success rate can be predicted based on S_p before expensive multiplex STR profiling is performed.     

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.     

Tri-allelic SNP markers enable analysis of mixed and degraded DNA samples

For the analysis of degraded DNA in disaster victim identification (DVI) and criminal investigations, single nucleotide polymorphisms (SNPs) have been recognized as promising markers mainly because they can be analyzed in short sized amplicons. Most SNPs are bi-allelic and are thereby ineffective to detect mixtures, which may lead to incorrect genotyping. We developed an algorithm to find non-binary (i.e. tri-allelic or tetra-allelic) SNPs in the NCBI dbSNP database. We selected 31 potential tri-allelic SNPs with a minor allele frequency of at least 10%. The tri-allelic nature was confirmed for 15 SNPs residing on 14 different chromosomes. Multiplex SNaPshot™ assays were developed, and the allele frequencies of 16 SNPs were determined among 153 Dutch and 111 Netherlands Antilles reference samples. Using these multiplex SNP assays, the presence of a mixture of two DNA samples in a ratio up to 1:8 could be recognized reliably. Furthermore, we compared the genotyping efficiency of the tri-allelic SNP markers and short tandem repeat (STR) markers by analyzing artificially degraded DNA and DNA from 30 approximately 500-year-old bone and molar samples. In both types of degraded DNA samples, the larger sized STR amplicons failed to amplify whereas the tri-allelic SNP markers still provided valuable information. In conclusion, tri-allelic SNP markers are suited for the analysis of degraded DNA and enable the detection of a second DNA source in a sample.     

Genetic peopling of Pakistan: Influence of consanguinity on population structure and forensic evaluation of traces

Pakistan is one of the most consanguineous country in the world [1] where the cousin marriages account for more than half of the total unions. To investigate the genetic evidence of consanguinity in Pakistani populations, 1020 samples were collected from the volunteers belonging to four different populations. The magnitude of the effect of population structure and consanguinity on the calculation of likelihood ratios were also explored.     

Influence of the luminol chemiluminescence reaction on the confirmatory tests for the detection and characterization of bloodstains in forensic analysis

Preliminary tests for the detection of stains at crime scenes aim to focus the police work making them more efficient in the combat of criminality. The application of the luminol chemiluminescence reaction (3-aminoftalhidrazida) in presumptive tests for the detection of bloodstains is known for more than 40 years in forensic science. This reaction is based on the emission of light through the chemical reaction of luminol mixed with hydrogen peroxide and a hydroxide in the presence of a catalytic molecule (iron from the hemoglobin) (Laux [1]).This work evaluates the luminol interference and its effect on subsequent serological and DNA testing. Samples prepared with blood and different concentrations of luminol solution containing luminol, peroxide of hydrogen and sodium carbonate, were analyzed. Additionally, samples of serial dilutions of standard DNA mixed with luminol solution were also analyzed. Although presumptive tests with luminol do not establish the characterization and identification of stains at crime scenes, preliminary results indicated that it is suitable for the detection of invisible bloodstains for forensic analysis, with few detrimental effects on the serological tests and subsequent DNA recovery and typing.     

A database of mitochondrial DNA hypervariable regions I and II sequences of individuals from Slovakia

In order to identify polymorphic positions and to determine their frequencies and the frequency of haplotypes in the human mitochondrial control region, two hypervariable regions (HV1 and HV2) of the mitochondrial DNA (mtDNA) of 374 unrelated individuals from Slovakia were amplified and sequenced. Sequence comparison led to the identification of 284 mitochondrial lineages as defined by 163 variable sites. Genetic diversity (GD) was estimated at 0.997 and the probability of two randomly selected individuals from population having identical mtDNA types (random match probability, RMP) for the both regions is 0.60%.     

An interpretation of the genetic polymorphism and population genetic background of Ankang Han population via a novel InDel panel

In this research, genotyping data of 43 InDel loci in 311 Han individuals in Ankang City, Shaanxi Province, China were detected using a self-developed five-dye multiplex amplification panel. The allelic frequencies and forensic parameters of all InDel loci were calculated. The combined power of discrimination and probability of exclusion values were 0.999 999 999 999 999 998 827 39 and 0.999 887 424, respectively, which demonstrated that this 43-InDel panel was powerful for individual identifications in Ankang Han population. Moreover, genetic distances, pairwise F_ST values, principal component analyses, phylogenetic trees and STRUCTURE analyses were performed to investigate the genetic affinities between Ankang Han and reference groups. Population genetic investigations indicated that Ankang Han population had a close genetic relationship with Southern Han population compared with other reference groups.     

Calculating likelihood ratios for a mixed DNA profile when a contribution from a genetic relative of a suspect is proposed

This technical note describes a practical method for evaluating evidence in the case of a two person conditioned DNA mixture where the defence proposition is that the unknown contributor is genetically related to the suspect. A conditioned mixture is one where the presence of DNA from one of two individuals is accepted by both prosecution and defence. A typical example would be a vaginal swab in an alleged rape case, where the presence of the complainant's DNA would be expected and samples have been taken from the complainant and a suspect. Much has been written about the interpretation of such mixtures and the calculation of the conditional genotype probabilities that must be carried out. In general, such treatments assume that the unknown contributor, under the defence proposition, is unrelated to the known individuals. In this paper, we consider the case where the defence proposition is that the unknown contributor is genetically related to the suspect. We describe a method, incorporating a flow chart and reference tables that facilitate manual calculations of the likelihood ratio for several postulated genetic relationships.     

RNA/DNA co-analysis from blood stains—Results of a second collaborative EDNAP exercise

A second collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling was organized by the European DNA Profiling Group (EDNAP). Six human blood stains, two blood dilution series (5-0.001 μl blood) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by the participating laboratories using a RNA/DNA co-extraction or solely RNA extraction method. Two novel mRNA multiplexes were used for the identification of blood: a highly sensitive duplex (HBA, HBB) and a moderately sensitive pentaplex (ALAS2, CD3G, ANK1, SPTB and PBGD). The laboratories used different chemistries and instrumentation. All of the 18 participating laboratories were able to successfully isolate and detect mRNA in dried blood stains. Thirteen laboratories simultaneously extracted RNA and DNA from individual stains and were able to utilize mRNA profiling to confirm the presence of blood and to obtain autosomal STR profiles from the blood stain donors. The positive identification of blood and good quality DNA profiles were also obtained from old and compromised casework samples. The method proved to be reproducible and sensitive using different analysis strategies. The results of this collaborative exercise involving a RNA/DNA co-extraction strategy support the potential use of an mRNA based system for the identification of blood in forensic casework that is compatible with current DNA analysis methodology.