Showing papers in "Forensic Science International-genetics in 2008"
TL;DR: SNPs in large multiplexes are found to be much more informative for both low initial probabilities or ambiguous exclusions and at the same time provide a more reliable genotyping approach for the highly degraded DNA encountered in many identification cases.
Abstract: When using a standard battery of STRs for relationship testing a small proportion of analyses can give ambiguous results - where the claimed relationship cannot be confirmed by a high enough paternity index or excluded with fully incompatible genotypes. The majority of such cases arise from unknowingly testing a brother of the true father and observing only a small number of exclusions that can each be interpreted as one- or two-step mutations. Although adding extra STRs might resolve a proportion of cases, there are few properly validated extra STRs available, while the commonly added hypervariable SE33 locus is four times more mutable than average, increasing the risk of ambiguous results. We have found SNPs in large multiplexes are much more informative for both low initial probabilities or ambiguous exclusions and at the same time provide a more reliable genotyping approach for the highly degraded DNA encountered in many identification cases. Eight relationship cases are outlined where the addition of SNP data resolved analyses that had remained ambiguous even with extended STR typing. In addition we have made simulations to ascertain the frequency of failing to obtain exclusions or conclusive probabilities of paternity with different marker sets when a brother of the true father is tested. Results indicate that SNPs are statistically more efficient than STRs in resolving cases that distinguish first-degree relatives in deficient pedigrees.
129 citations
TL;DR: The results showed that the 52 SNP-plex assay is a very useful alternative to currently used methods in relationship testing and the usefulness of SNP markers with low mutation rates in paternity and immigration casework is discussed.
Abstract: The performance of a multiplex assay with 52 autosomal single nucleotide polymorphisms (SNPs) developed for human identification was tested on 124 mother–child–father trios. The typical paternity indices (PIs) were 10 5 –10 6 for the trios and 10 3 –10 4 for the child–father duos. Using the SNP profiles from the randomly selected trios and 700 previously typed individuals, a total of 83,096 comparisons between mother, child and an unrelated man were performed. On average, 9–10 mismatches per comparison were detected. Four mismatches were genetic inconsistencies and 5–6 mismatches were opposite homozygosities. In only two of the 83,096 comparisons did an unrelated man match perfectly to a mother–child duo, and in both cases the PI of the true father was much higher than the PI of the unrelated man. The trios were also typed for 15 short tandem repeats (STRs) and seven variable number of tandem repeats (VNTRs). The typical PIs based on 15 STRs or seven VNTRs were 5–50 times higher than the typical PIs based on 52 SNPs. Six mutations in tandem repeats were detected among the randomly selected trios. In contrast, there was not found any mutations in the SNP loci. The results showed that the 52 SNP-plex assay is a very useful alternative to currently used methods in relationship testing. The usefulness of SNP markers with low mutation rates in paternity and immigration casework is discussed.
95 citations
TL;DR: This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real- time human identification.
Abstract: An integrated lab-on-a-chip system has been developed and successfully utilized for real-time forensic short tandem repeat (STR) analysis. The microdevice comprises a 160-nL polymerase chain reaction reactor with an on-chip heater and a temperature sensor for thermal cycling, microvalves for fluidic manipulation, a co-injector for sizing standard injection, and a 7-cm-long separation channel for capillary electrophoretic analysis. A 9-plex autosomal STR typing system consisting of amelogenin and eight combined DNA index system (CODIS) core STR loci has been constructed and optimized for this real-time human identification study. Reproducible STR profiles of control DNA samples are obtained in 2 h and 30 min with ≤0.8 bp allele typing accuracy. The minimal amount of DNA required for a complete DNA profile is 100 copies. To critically evaluate the capabilities of our portable microsystem as well as its compatibility with crime scene investigation processes, real-time STR analyses were carried out at a mock crime scene prepared by the Palm Beach County Sheriff's Office (PBSO). Blood stain sample collection, DNA extraction, and STR analyses on the portable microsystem were conducted in the field, and a successful “mock” CODIS hit was generated on the suspect's sample within 6 h. This demonstration of on-site STR analysis establishes the feasibility of real-time DNA typing to identify the contributor of probative biological evidence at a crime scene and for real-time human identification.
93 citations
TL;DR: This paper optimised post-PCR purification techniques applied after only 28 cycles of PCR, as well as using modified capillary electrophoresis injection conditions and investigated the progressive application of these enhanced approaches, finding comparable sensitivity to 34-cycle PCR.
Abstract: The investigation of samples with low amounts of template DNA remains at the forefront of forensic DNA research and technology as it becomes increasingly important to gain DNA profile information from exceedingly trace levels of DNA. Previous studies have demonstrated that it is possible to obtain short tandem repeat (STR) profiles from <100pg of template DNA by increasing the number of amplification cycles from 28 to 34, a modification often referred to as "low copy number" or LCN analysis. In this study, we have optimised post-PCR purification techniques applied after only 28 cycles of PCR, as well as using modified capillary electrophoresis injection conditions and have investigated the progressive application of these enhanced approaches. This paper reviews the characteristics of the profiles obtained by these methods compared with those obtained on the same samples after 34-cycle PCR. We observed comparable sensitivity to 34-cycle PCR in terms of the number of profiles with evidence of DNA and the number of allelic peaks per profile and we noted improved peak height and area magnitude with some sample types. Certain parameters reported to be adversely affected in 34-cycle LCN investigations, such as non-donor allele peaks and increased stutter peak ratio, were reduced by this approach. There are a number of advantages for trace samples in progressing from the standard 28-cycle process to the post-PCR processing method as compared to 34-cycle PCR method, including reduced sample consumption, reduced number of PCR amplifications required, and a staged approach to sample processing and profile interpretation.
92 citations
TL;DR: Evaluated samples include species specificity, sensitivity, precision, reproducibility, male-female mixtures, population samples and applications to various casework-type samples as indicated by the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines.
Abstract: A quadruplex real-time qPCR assay was developed to simultaneously assess total human DNA, human male DNA, DNA degradation and PCR inhibitors in forensic samples. Specifically, the assay utilizes a approximately 170-190bp target sequence that spans the TH01 STR locus to quantify total human DNA (nuTH01), a 137 bp target sequence directly adjacent to the SRY gene to quantify human male DNA (nuSRY), a 67 bp target sequence flanking the CSF1PO STR locus (nuCSF) to assess degradation (nuCSF:nuTH01 ratio) and a 77 bp synthetic DNA template used as an internal PCR control target sequence (IPC) for the assessment of PCR inhibition. Validation studies, performed on an ABI 7500 SDS instrument using TaqMan and TaqManMGB detection, indicate each of the targets in the quadruplex assay performs effectively and is informative even when challenged with DNase-degraded and hematin-inhibited samples. The nuTH01-nuSRY-nuCSF-IPC quadruplex qPCR assay is envisioned to assist in the choice of the most informative DNA typing system available, which may include standard autosomal STR typing when the results indicate the presence of non-degraded, single gender DNA or non-degraded, male:female mixtures at ratios expected to yield probative alleles; Y STR typing in samples containing a male component that is overwhelmed by the presence of an excess of female DNA; reduced amplicon size STR typing ("MiniSTRs") where the nuCSF:nuTH01 ratio indicates the sample is highly degraded; enhanced STR amplification with additional AmpliTaq Gold/BSA and/or sample clean-up when the presence of PCR inhibitors is suggested by a delayed IPC C(T) value or mitochondrial DNA typing in samples where little to no nuclear DNA is detected. The present study includes evaluations of species specificity, sensitivity, precision, reproducibility, male-female mixtures, population samples and applications to various casework-type samples as indicated by the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines.
89 citations
TL;DR: It is proposed that the likelihood ratio is qualified with additional robustness parameters to indicate the probability of misleading evidence in favour of the prosecution, under the assumption that a random man was a contributor instead of the suspect.
Abstract: A new methodology is presented in order to report complex DNA profiles. We have brought together a number of different theories in order to devise a new protocol to interpret complex cases using likelihood ratios. The calculations are designed to be highly conservative and are widely applicable. We apply a low copy number (LCN) interpretation framework, which includes the probabilities of dropout and contamination, to 'conventional' DNA cases. In conventional casework, stutters often compromise calculations when they are observed with the same height as a minor contributor to a mixture. Stutters cannot be distinguished from minor alleles. We compensate by treating them as real alleles and including them in the calculation. By increasing the number of potential contributors to the DNA profile, we can account for the extra alleles that result. We propose that the likelihood ratio is qualified with additional robustness parameters to indicate the probability of misleading evidence in favour of the prosecution, under the assumption that a random man was a contributor instead of the suspect. To do this we apply a new kind of case-specific 'Tippett' test. Although the method is complex, we suggest a 'user-friendly' way to explain the results to a court. The method is easily extended to carry out ranked likelihood ratio (LR) searches for suspects in national DNA databases.
86 citations
TL;DR: The STR panel presented here provides a powerful tool for solving complex kinship in the case that X-chromosomal lineages can be taken under investigation by presenting single STR allele frequencies, haplotype frequencies of the respective STR pairs and further population genetic parameters of forensic interest.
Abstract: The evaluation of four pairs of X-chromosomal short tandem repeats (STRs), i.e. DXS10135-DXS8378, DXS7132-DXS10074, HPRTB-DXS10101 and DXS7423-DXS10134 was carried out using the Argus X-8 Multiplex amplification kit. These eight STRs are distributed as four closely linked pairs over the entire X-chromosome (ChrX), and for practical reasons they are assigned to four linkage groups 1-4. The genetic distance within the STR pairs is assumed to be <1cM, whereas the pair to pair space is about 50 cM or more. Here, we present single STR allele frequencies, haplotype frequencies of the respective STR pairs and further population genetic parameters of forensic interest. Most data refer to a German population, however small samples from Ghana and Japan were also investigated. Furthermore, sequencing of all STR loci displayed the presence of microvariant alleles and variations in the repeat flanking region. A total of 350 meioses investigated here revealed only one sperm DXS7132 mutation. For analysis of linkages within the STR pairs a study involving 104 female meiosis with respect to recombination events was performed. The STR panel presented here provides a powerful tool for solving complex kinship in the case that X-chromosomal lineages can be taken under investigation.
82 citations
TL;DR: A range of established and recently developed forensic marker sets that included mini-STRs and SNPs were used to type the sample and confirm identity by comparison to a claimed daughter of the deceased, suggesting a modified ancient DNA extraction procedure offers improved typing success from degraded skeletal material.
Abstract: Applying two extraction protocols to isolate DNA from a charred femur recovered after a major forest fire, a range of established and recently developed forensic marker sets that included mini-STRs and SNPs were used to type the sample and confirm identity by comparison to a claimed daughter of the deceased. Identification of the remains suggested that the individual had been dead for 10 years and the DNA was therefore likely to be severely degraded from the combined effects of decomposition and exposure to very high temperatures. We used new marker sets specifically developed to analyze degraded DNA comprising both reduced-length amplicon STR sets and autosomal SNP multiplexes, giving an opportunity to assess the ability of each approach to successfully type highly degraded material from a challenging case. The results also suggest a modified ancient DNA extraction procedure offers improved typing success from degraded skeletal material.
80 citations
TL;DR: In this article, the authors demonstrate a rapid cycling protocol that amplifies 15 short tandem repeat (STR) loci and the sex-typing marker amelogenin from the Identifiler STR typing kit in less than 36 min.
Abstract: Current forensic DNA typing is conducted in approximately 8–10 h. Steps include DNA extraction, quantification, polymerase chain reaction (PCR) amplification of multiple short tandem repeat (STR) loci, capillary electrophoresis separation with fluorescence detection, data analysis and DNA profile interpretation. The PCR amplification portion of the workflow typically takes approximately 3 h with standard thermal cycling protocols. Here we demonstrate a rapid cycling protocol that amplifies 15 STR loci and the sex-typing marker amelogenin from the Identifiler STR typing kit in less than 36 min. This rapid protocol employs commercially available polymerases and the widely used GeneAmp 9700 thermal cycler. Complete concordance of STR allele calls (for 60 samples) between the rapid and standard thermal cycling protocols were observed although there was incomplete adenylation at several of the loci examined and some PCR artifacts were detected. Using less than 750 pg of template DNA and 28 cycles, STR peaks for all loci were above a 150 relative fluorescent unit (RFU) detection threshold with fully adequate inter-locus balance and heterozygote peak height ratios of greater than 0.84.
76 citations
TL;DR: The 15 AmpFlSTR Identifiler loci were analyzed in a sample of 378 unrelated individuals from Mexico City, Mexico and revealed significant deviations from HW equilibrium in 14/15 STR loci alleles were not detected.
Abstract: The 15 AmpFlSTR Identifiler loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were analyzed in a sample of 378 unrelated individuals from Mexico City, Mexico. Significant deviations from HW equilibrium in 14/15 STR loci alleles were not detected. The D18S51 locus had the highest power of discrimination (0.970). Genetic admixture estimations revealed a 69% of Amerindian, 26% of European and 5% of African contribution. Comparative analyses between Mexicans and other neighboring populations reveal significant differences in genetic diversity. Our results are important for future comparative genetic studies in different Latin American ethnic groups, particularly Mexican Mestizos and Amerindians. They should also be helpful in genetics, population evolution, forensic and paternity testing.
75 citations
TL;DR: A morphological and immunohistochemical investigation of nuclear DNA in differentiating keratinocytes in the skin and also a genetic analysis of DNA on swabs of human skin showed that single-stranded DNA was found both in the cornified layer of theskin and in swabs.
Abstract: In recent years, forensic scientists showed that an individual’s genetic profile can be retrieved from touched objects. Degraded DNA is believed to originate from epidermal cells and to be responsible for this phenomenon, yet the mechanism has not been confirmed. In the present study, we carried out a morphological and immunohistochemical investigation of nuclear DNA in differentiating keratinocytes in the skin and also a genetic analysis of DNA on swabs of human skin. Immunoelectron microscope analysis showed that single-stranded DNA was found both in the cornified layer of the skin and in swabs. Real-time-PCR assay proved that the DNA in the swabs was derived from the human DNA. Electron microscopic analysis of shadow-cast showed the presence of small DNA fragments in the swabs. It is conceivable that these DNA fragments on touched objects may originate from the epidermal cells of the cornified layer that are constantly sloughed off and leave for skin surface with sweat.
TL;DR: It was found that whilst certain paper types, such as newspaper, magazine and filter paper allowed for the good recovery of DNA, common office paper and white card, strongly interfered with the recovery ofDNA resulting in poor quality profiles.
Abstract: This study investigated the various factors affecting DNA profiling from DNA recovered from fingerprints deposited on paper before and after fingerprint enhancement treatments. The DNeasy plant mini kit (QIAGEN) was found to improve DNA recovery from paper by over 150% compared with the QIAamp mini kit. A significant decrease in the amount of DNA recovered was observed following treatment with DFO and/or Ninhydrin. This decrease in yield did not have a comparably significant effect on the quality of the SGM Plus profiles. Furthermore, this study found that whilst certain paper types, such as newspaper, magazine and filter paper allowed for the good recovery of DNA, common office paper and white card, strongly interfered with the recovery of DNA resulting in poor quality profiles.
TL;DR: The Plexor HY System as discussed by the authors is a multiplex quantitative PCR assay to quantify total human and male DNA for forensic applications, which can be used to quantify human specificity, sensitivity, quantification of degraded DNA, impact of inhibitors, male/female mixture and Yassay male specificity.
Abstract: Multiplex human short tandem repeat analysis demands reliable DNA quantification to consistently produce interpretable genotypes. The Plexor HY System is a multiplex quantitative PCR assay to quantify total human and male DNA. We performed developmental validation of the Plexor HY System to demonstrate the performance capabilities and limitations of the assay for forensic applications. Validation studies examined: (a) human specificity, (b) sensitivity, (c) quantification of degraded DNA, (d) impact of inhibitors, (e) male/female mixture and Y-assay male specificity, (f) reproducibility and concordance and (g) population studies.
TL;DR: Six commercial preparations of human genomic DNA were quantified using five quantification methods: UV spectrometry, SYBR-Green dye staining, slot blot hybridization with the probe D17Z1, Quantifiler Human DNA Quantification kit and RB1 rt-PCR.
Abstract: Six commercial preparations of human genomic DNA were quantified using five quantification methods: UV spectrometry, SYBR-Green dye staining, slot blot hybridization with the probe D17Z1, Quantifiler Human DNA Quantification kit and RB1 rt-PCR. All methods measured higher DNA concentrations than expected based on the information by the manufacturers. UV spectrometry, SYBR-Green dye staining, slot blot and RB1 rt-PCR gave 39, 27, 11 and 12%, respectively, higher concentrations than expected based on the manufacturers' information. The DNA preparations were quantified using the Quantifiler Human DNA Quantification kit in two experiments. The measured DNA concentrations with Quantifiler were 125 and 160% higher than expected based on the manufacturers' information. When the Quantifiler human DNA standard (Raji cell line) was replaced by the commercial human DNA preparation G147A (Promega) to generate the DNA standard curve in the Quantifiler Human DNA Quantification kit, the DNA quantification results of the human DNA preparations were 31% higher than expected based on the manufacturers' information. The results indicate a calibration problem with the Quantifiler human DNA standard for its use with the Quantifiler Human DNA Quantification kit. The possible reasons for the problem are discussed and a solution is suggested. The results emphasise the need for standard reference DNA material and standard methods for DNA quantification.
TL;DR: It is concluded that the two matters that appear to have real force are: (1) LRs are more difficult to present in court and (2) the RMNE statistic wastes information that should be utilised.
Abstract: DNA mixture interpretation is undertaken either by calculating a LR or an exclusion probability (RMNE or its complement CPI). Debate exists as to which has the greater claim. The merits and drawbacks of the two approaches are discussed. We conclude that the two matters that appear to have real force are: (1) LRs are more difficult to present in court and (2) the RMNE statistic wastes information that should be utilised.
University of Copenhagen1, University of Mainz2, Innsbruck Medical University3, National Institute of Standards and Technology4, University of Santiago de Compostela5, Queen Mary University of London6, Forensic Science Service7, International Commission on Missing Persons8, German Criminal Police Office9, University of Cologne10
TL;DR: The results of the collaborative exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases demonstrate that SNP typing with SBE, capillary electrophoresis and multicolour detection methods can be developed for forensic genetics.
Abstract: We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised the exercise. A total of 11 European and one US forensic genetic laboratories tested a subset of a 52 SNP-multiplex PCR kit developed by the SNPforID consortium. The 52 SNP-multiplex kit amplifies 52 DNA fragments with 52 autosomal SNP loci in one multiplex PCR. The 52 SNPs are detected in two separate single base extension (SBE) multiplex reactions with 29 and 23 SNPs, respectively, using SNaPshot kit, capillary electrophoresis and multicolour fluorescence detection. For practical reasons, only the 29 SBE multiplex reaction was carried out by the participating laboratories. A total of 11 bloodstains on FTA cards including a sample of poor quality and a negative control were sent to the laboratories together with the essential reagents for the initial multiplex PCR and the multiplex SBE reaction. The total SNP locus dropout rate was 2.8% and more than 50% of the dropouts were observed with the poor quality sample. The overall rate of discrepant SNP allele assignments was 2.0%. Two laboratories reported 60% of all the discrepancies. Two laboratories reported all 29 SNP alleles in all 10 positive samples correctly. The results of the collaborative exercise were surprisingly good and demonstrate that SNP typing with SBE, capillary electrophoresis and multicolour detection methods can be developed for forensic genetics.
TL;DR: This case study presents a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles, and can act as a framework for others attempting to develop wildlife forensic profiling systems.
Abstract: Developing short tandem repeat (STR) profiling systems for forensic identification is complicated in animal species. Obtaining a representative number of individuals from populations, limited access to family groups and a lack of developed STR markers can make adhering to human forensic guidelines difficult. Furthermore, a lack of animal specific guidelines may explain why many wildlife forensic STR profiling systems developed to date have not appropriately addressed areas such as marker validation or the publication and analysis of population data necessary for the application of these tools to forensic science. Here we present a methodology used to develop an STR profiling system for a legally protected wildlife species, the Eurasian badger Meles meles. Ten previously isolated STR loci were selected based on their level of polymorphism, adherence to Hardy-Weinberg expectations and their fragment size. Each locus was individually validated with respect to its reproducibility, inheritance, species specificity, DNA template concentration and thermocycling parameters. The effects of chemical, substrate and environmental exposure were also investigated. All ten STR loci provided reliable and reproducible results, and optimal amplification conditions were defined. Allele frequencies from 20 representative populations in England and Wales are presented and used to calculate the level of population substructure (theta) and inbreeding (f). Accounting for these estimates, the average probability of identity (PI(ave)) was 2.18 x 10(-7). This case study can act as a framework for others attempting to develop wildlife forensic profiling systems.
TL;DR: This study showed that the tested markers all have highly informative forensic values and that there is a significant degree of linkage disequilibrium between the STR markers within the four linkage groups, and demonstrated that two of the linkage groups are partially linked.
Abstract: X-chromosomal short tandem repeats (X-STR) have proven to be informative and useful in complex relationship testing. The main feature of X-STR markers, compared to autosomal forensic markers, is that all loci are located on the same chromosome. Thus, linkage and linkage disequilibrium may occur. The aim of this work was to study population genetic parameters of eight X-STR markers, located in four linkage groups. We present haplotype frequencies, based on 718 Swedish males, for the four linkage groups included in the Argus X-8 kit. Forensic efficiency parameters have been calculated as well as the allelic association between the tested markers for detection of linkage disequilibrium. To study the occurrences of recombination between the loci, both Swedish and Somali families were typed. A mathematical model for the estimation of recombination frequencies is presented and applied on the family samples. Our study showed that the tested markers all have highly informative forensic values and that there is a significant degree of linkage disequilibrium between the STR markers within the four linkage groups. Furthermore, based on the tested families, we also demonstrated that two of the linkage groups are partially linked. A consequence of these findings is that both linkage and linkage disequilibrium should be accounted for when producing likelihood ratios in relationship testing with X-STR markers.
TL;DR: Three polymorphic X-chromosomal STR markers within a 79 kb region at Xq28 were studied and registered in the GDB as DXS10146, DXS 10134 andDXS10147, and these markers were molecular characterised and evaluated for their forensic usage.
Abstract: Three polymorphic X-chromosomal STR markers within a 79 kb region at Xq28 were studied and registered in the GDB as DXS10146, DXS10134 and DXS10147. These markers were molecular characterised and evaluated for their forensic usage. As a result DXS10134 was recently integrated in the commercial available test kit Mentype Argus X-8. At locus DXS10146 we found 23 alleles with PIC and HET values of 0.878 and 0.887. Locus DXS10134 showed 17 alleles with PIC and HET values of 0.844 and 0.858. At locus DXS10147 only 5 alleles with some lower PIC and HET values of 0.636 and 0.692 were found. Additionally, the already known and closely linked STR DXS7423 was included into the haplotyping and recombination studies. Testing this cluster a German population of 404 males revealed the presence of 311 haplotypes. Recombination analysis was performed in 109 father-daughter-grandson trios in which two crossing over events were observed located in the 65.8 kb region between DXS10146 and DXS10134. By using this STR complex for haplotyping in kinship testing further genetic analyses are required to establish an exact recombination rate.
TL;DR: It is suggested that RSID--Blood is effective and useful for the detection of human blood on forensic exhibits, and offers improved blood detection when compared to other currently used methods.
Abstract: Human blood is the body fluid most commonly encountered at crime scenes, and blood detection may aid investigators in reconstructing what occurred during a crime. In addition, blood detection can help determine which items of evidence should be processed for DNA-STR testing. Unfortunately, many common substances can cause red-brown stains that resemble blood. Furthermore, many current human blood detection methods are presumptive and prone to false positive results. Here, the developmental validation of a new blood identification test, Rapid Stain Identification--Blood (RSID--Blood), is described. RSID--Blood utilizes two anti-glycophorin A (red blood cell membrane specific protein) monoclonal antibodies in a lateral flow strip test format to detect human blood. We present evidence demonstrating that this test is accurate, reproducible, easy to use, and highly specific for human blood. Importantly, RSID--Blood does not cross-react with ferret, skunk, or primate blood and exhibits no high-dose hook effect. Also, we describe studies on the sensitivity, body fluid specificity, and species specificity of RSID--Blood. In addition, we show that the test can detect blood from a variety of forensic exhibits prior to processing for DNA-STR analysis. In conclusion, we suggest that RSID--Blood is effective and useful for the detection of human blood on forensic exhibits, and offers improved blood detection when compared to other currently used methods.
TL;DR: The Technical UK DNA working group comprises representatives from all of the major suppliers of the UK and Ireland who contribute to the UK national DNA database and has the following terms of reference: to act as a peer review body.
Abstract: The Technical UK DNA working group comprises representatives from all of the major suppliers of the UK and Ireland who contribute to the UK national DNA database. The group has the following terms of reference:To act as a peer review body.To agree experimental designs, to provide advice to the custodian to facilitate the development of the NDNAD.To support the CJS by the development of a coordinated UK strategy.To be inclusive, rather than exclusive, with regard to the introduction and use of methods.To define best scientific practice.To define guidelines for analysis and interpretation of evidence.To produce guidance that can be used by the UK Accreditation Services (UKAS).The group falls under the European Network of Forensic Science Institutes (ENFSI) umbrella. We will feed back recommendations to the ENFSI group for further discussion in order to facilitate European Policy. The group recently met in order to consider in detail the ISFG DNA Commission recommendations on the interpretation of mixtures, to place them in the context of the UK jurisdictions.
TL;DR: A method to accurately quantify, sensitive to 100 copies (1.7fg), mtDNA from human and non-human sources when present as a mixture when presentAs a mixture is reported on.
Abstract: The number of mitochondria per cell varies by cell type and the number of mitochondrial DNA (mtDNA) genomes varies per mitochondrion. Biological samples from unknown species are encountered frequently in forensic science investigations and are often contaminated with human mtDNA making analysis difficult. Currently, no techniques to quantify non-human mtDNA are available. We report on a method to accurately quantify, sensitive to 100 copies (1.7 fg), mtDNA from human and non-human sources when present as a mixture. The test developed uses the cytochrome b (cytb) and the ribosomal 12S genes on the mitochondrial genome. Universal and human specific fragments of similar size are amplified and quantified using SYBR Green. We validate the test with 24 human samples and 27 non-human mammalian samples. The human fraction of a sample can then be subtracted from the universal fraction for an accurate estimation of non-human mtDNA copy number.
TL;DR: Entire mitochondrial genome (mtGenome) sequences of 265 unrelated African American and U.S. "Hispanic" individuals were generated and it was found that mitochondrial DNA in these individuals is similar to that in other races.
Abstract: Entire mitochondrial genome (mtGenome) sequences of 265 unrelated African American and U.S. "Hispanic" individuals were generated.
TL;DR: Examination of father/son sample pairs from U.S. Caucasians, African Americans, Hispanics and Asians using the 17 Y-STR loci in the Yfilertrade mark kit observed a total of 24 differences between father and son.
Abstract: We have examined 389 father/son sample pairs from U.S. Caucasians, African Americans, Hispanics and Asians using the 17 Y-STR loci in the Yfiler™ kit and observed a total of 24 differences between father and son. Thirteen mutations resulted in the gain of a repeat in the son and 11 resulted in a loss of a repeat. All samples resulted in single repeat mutations except one sample which contained a two repeat loss at Y-GATA-H4. Furthermore, two different sample pairs were found to have two mutations. An African American sample pair had a mutation at DYS458 and a second at DYS635 and an Asian sample pair had mutations at DYS439 and Y-GATA-H4.
TL;DR: This work investigates the efficiency of two extraction methods for DNA in ancient tissue based on magnetic separation of the targeted molecules, and one based on silica binding, both of which seem to be identical.
Abstract: The major problems concerning ancient DNA studies are related to the amount of extractable DNA and the precautions needed to avoid contamination. From the very first step of the analyses, the DNA extraction, these problems must be confronted. There are several extraction methods available for DNA in ancient tissue; several of them are complicated and time consuming, and none of the methods have reached an acceptance level such that they are routinely used on a widespread basis. Here we investigate the efficiency of two methods, one based on magnetic separation of the targeted molecules, and one based on silica binding. The efficiency rate of these two on the material studied seems to be identical. The silica binding method has the benefit of relative simplicity, but the magnetic separation technique also has advantages. For example, it is possible to reuse the extract several times for different loci, and it is possible to concentrate all extracted DNA from one locus into one PCR.
TL;DR: Here, allele frequencies regarding the markers in the Identifiler-kit are described and three sets of population samples; Swedish, European and non-European to investigate how these three groups ofpopulation samples differ.
Abstract: 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.
TL;DR: The studied population data were compared with the previously published population data of other ethnics or areas and significant differences were found between Chinese Han population in Xi'an and Korean, Tibetan, Uigur, ChineseHan population in Guangdong Province, Hui population, Chinese Salar, Dongxiang and Tu ethnic minority living in Qinghai Province of China.
Abstract: Fifteen autosomal STRs loci were analyzed from a population sample of 446 unrelated healthy individuals of Chinese Han population residing in Xi'an city of Shaanxi Province using a multiplex PCR system. We report allele frequencies distribution and statistical parameters for all STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA. The observed genotype frequencies and expected of genotype frequencies were evaluated by chi(2)-test and the Fisher exact tests. Chi-Square test showed all STR loci were in Hardy-Weinberg equilibrium (p<0.05). Our studied population data were compared with the previously published population data of other ethnics or areas. After comparing, significant differences were found between Chinese Han population in Xi'an and Korean, Tibetan, Uigur, Chinese Han population in Guangdong Province, Hui population, Chinese Salar, Dongxiang and Tu ethnic minority living in Qinghai Province of China at some loci. The forensic parameters from the data showed high values. The data in the present study can be used greatly for routine forensic application in the region of Xi'an city.
TL;DR: Nails are very easy to collect and contain large amounts of good quality DNA that can be extracted within a few hours, and may represent an attractive DNA source not only for routine, but also for urgent genetic identification of decomposed cadavers.
Abstract: Blood or muscle can be used as a DNA source for the genetic identification of recently deceased persons. If the post mortem interval increases, bones and teeth are used. In this case, collection and DNA isolation will be more difficult and time consuming. The aim of this study was to evaluate the use of nails as an alternative DNA source for the genetic identification of decomposed cadavers. DNA extraction from 5 mg of fingernails from 7 volunteers using 1 h cell lysis in a standard buffer and a DNA purification on QIAamp DNA mini kit columns allowed to acquire a mean quantity of 100 ng DNA/mg nail. This was unexpected, as blood and muscle contain comparable amounts of DNA. Our protocol allowed to obtain full PowerPlex 16 DNA profiles from 10 cadavers characterized by post mortem intervals ranging from 5 days to more than 6 months. The good quality of these profiles indicated that DNA from nail is well preserved. In conclusion, nails are very easy to collect and contain large amounts of good quality DNA that can be extracted within a few hours. They may therefore represent an attractive DNA source not only for routine, but also for urgent genetic identification of decomposed cadavers.
TL;DR: The data presented can be used to enhance the accuracy of the data collection process through an improved sample collection form, streamlining the DNA kinship identification process and decreasing the burden on valuable resources.
Abstract: A mass fatality DNA identification effort is a complex process in which direct matching and kinship analysis is used for identifying human remains. Kinship DNA identification is an important tool in the identification process in which victim's DNA profiles are compared to the profiles of "known" biologically related reference samples. Experience from the 9/11 World Trade Center DNA identification efforts showed that forms used to record biological relationships are important and that inaccurately documented information may hamper the kinship analysis and DNA identification process. In the identification efforts following Hurricane Katrina, a Family and/or Donor Reference Collection (FDRC) form was used as a means to document the reported relationship between the reference DNA donor and the purported missing individual. This FDRC form was developed based upon lessons learned from 9/11 and the Tsunami identification efforts. This paper analyses the effectiveness of the FDRC form used in the Hurricane Katrina kinship DNA identification efforts and proposes an improved sample collection form for kinship and other donor reference samples. The data presented can be used to enhance the accuracy of the data collection process through an improved sample collection form, streamlining the DNA kinship identification process and decreasing the burden on valuable resources.
TL;DR: The main message of this paper is that linked autosomal markers deserve greater attention in forensic genetics and that the required laboratory and statistical analyses can be performed based on existing technology and freeware.
Abstract: This paper considers identification problems based on DNA marker data. The topics we discuss are general, but we will exemplify them in a simple context. There is DNA available from two persons. There is uncertainty about the relationship between the two individuals and a number of hypotheses describing the possible relationship is available. The task is to determine the most likely pedigree. This problem is fairly standard. However, there are some problems that cannot be solved using DNA from independently segregating loci. For example, the likelihoods for (i) grandparent–grandchild, (ii) uncle–niece and (iii) half-sibs coincide for such DNA data and so these relations cannot be distinguished on the basis of markers normally used for forensic identification problems: the likelihood ratio comparing any pair of hypotheses will be unity. Sometimes, but not in the examples we consider, other sources of DNA like mtDNA or sex chromosomes can help to distinguish between such equally likely possibilities. Prior information can likewise be of use. For instance, age information can exclude alternative (i) above and also indicate that alternative (iii) is apriori more likely than alternative (ii). More generally, the above problems can be solved using linked autosomal markers. To study the problem in detail and understand how linkage works in this regard, we derive an explicit formula for a pair of linked markers. The formula extends to independent pairs of linked markers. While this approach adds to the understanding of the problem, more markers are required to obtain satisfactory results and then the Lander–Green algorithm is needed. Simulation experiments are presented based on a range of scenarios and we conclude that useful results can be obtained using available freeware (MERLIN and R). The main message of this paper is that linked autosomal markers deserve greater attention in forensic genetics and that the required laboratory and statistical analyses can be performed based on existing technology and freeware.