Forensic Science International: Genetics RSS feed: Current Issue. Forensic Science International: Genetics is specifically devoted to Forensic Genetics. This branch of Forensic Science can be defined as the application of genetics to human and non-human material (in the sense of a science with the purpose of studying inherited characteristics for the analysis of inter- and intra-specific variations in populations) for the resolution of legal conflicts. The scope of the journal includes: Forensic applications of human polymorphism. Testing of paternity and other family relationships, immigration cases, typing of biological stains and tissues from criminal casework, identification of human remains by DNA testing methodologies. Description of human polymorphisms of forensic interest, with special interest in DNA polymorphisms. Autosomal DNA polymorphisms, mini- and microsatellites (or short tandem repeats, STRs), single nucleotide polymorphisms (SNPs), X and Y chromosome polymorphisms, mtDNA polymorphisms, and any other type of DNA variation with potential forensic applications. Non-human DNA polymorphisms for crime scene investigation. Population genetics of human polymorphisms of forensic interest. Population data, especially from DNA polymorphisms of interest for the solution of forensic problems. DNA typing methodologies and strategies. Biostatistical methods in forensic genetics. Evaluation of DNA evidence in forensic problems (such as paternity or immigration cases, criminal casework, identification), classical and new statistical approaches. Standards in forensic genetics. Recommendations of regulatory bodies concerning methods, markers, interpretation or strategies or proposals for procedural or technical standards. Quality control. Quality control and quality assurance strategies, proficiency testing for DNA typing methodologies. Criminal DNA databases. Technical, legal and statistical issues. General ethical and legal issues related to forensic genetics http://www.fsigenetics.com/?rss=yesElsevier Inc.en © 2012 Published by Elsevier Inc. All rights reserved. Forensic Science International: Genetics1872-497363May 2012 © 2012 Published by Elsevier Inc. All rights reserved. healthpermissions@elsevier.comhttp://www.fsigenetics.com/article/PIIS1872497312000555/abstract?rss=yesEditorial Board10.1016/S1872-4973(12)00055-5Forensic Science International: Genetics 6, 3 (2012)2012-05-01Forensic Science International: Genetics2012-05-0163S1872-4973(12)X0003-6CO2CO2http://www.fsigenetics.com/article/PIIS1872497311001797/abstract?rss=yesAbstract: Polymerase chain reaction (PCR) is currently the method of choice for the identification of human remains in forensic coursework. DNA samples from crime scenes often contain co-purified impurities which inhibit PCR. PCR inhibition is the most common cause of PCR failure when adequate copies of DNA are present. Inhibitors have been routinely reported in forensic investigations of DNA extracted from a variety of templates. Humic compounds, a series of substances produced during decay process have been considered as the materials contaminating DNA in soil, natural waters and recent sediments. Those compounds have been frequently assigned as PCR inhibitors. The current report reviews the characteristics of PCR inhibition, including the proposed mechanisms of inhibition, detection methods and the available technologies to remove or overcome the inhibitory activities.Forensic implications of PCR inhibition—A reviewReza Alaeddini10.1016/j.fsigen.2011.08.006Forensic Science International: Genetics 6, 3 (2012)2011-09-14Forensic Science International: Genetics2011-09-1463S1872-4973(12)X0003-6Review Article297305http://www.fsigenetics.com/article/PIIS1872497311001335/abstract?rss=yesAbstract: DNA methylation is an important event in epigenetic changes in cells, and a fundamental regulator of gene transcription. Bisulfite genomic sequencing is a powerful technique used in studies of DNA methylation. However, the established procedures often require relatively large amounts of DNA. In everyday practice, samples submitted for analysis might contain very small amounts of poor quality material, as is often the case with forensic stain samples. In this study, we assess a modified, more efficient method of bisulfite genomic sequencing. Genomic DNA extracted from 3-mm dried blood spots using QIAamp micro kit was treated with sodium bisulfite (using EpiTect kit). Subsequent methylation-specific PCR (MSP) followed by DNA sequencing displayed the differentially methylated region of imprinted gene SNRPN. Our results show that this new combination of efficient DNA extraction and bisulfite treatment provides high quality conversion of unmethylated cytosine to uracil for bisulfite genomic sequencing analysis. This reliable method substantially improves the DNA methylation analysis of forensic stain samples.Bisulfite genomic sequencing of DNA from dried blood spot microvolume samplesHongmei Xu, Yun Zhao, Zhiping Liu, Wei Zhu, Yueqin Zhou, Ziqin Zhao10.1016/j.fsigen.2011.06.007Forensic Science International: Genetics 6, 3 (2012)2011-07-07Forensic Science International: Genetics2011-07-0763S1872-4973(12)X0003-6Research Articles306309http://www.fsigenetics.com/article/PIIS1872497311001347/abstract?rss=yesAbstract: SE33 is one of the most informative markers in forensic use due to its high power of discrimination. During the course of developing the AmpFℓSTR® NGM SElect™ PCR Amplification Kit several SE33 primer designs were screened with one primer pair yielding a high frequency of discordant alleles when compared to the AmpFℓSTR® SEfiler Plus™ PCR Amplification Kit. This discordance was mostly specific to samples of African descent with an estimated frequency of 5.1% and was a result of a mobility shift of approximately +0.84nt. The sequence analysis of the affected alleles revealed that the only difference from the wild type sequence was a single nucleotide polymorphism (SNP) outside of the SE33 repeat but within the amplicon of this particular set of experimental primers. In total, we identified three different SNPs all within 9nt of each other, each of which could cause the mobility shift individually. Further characterization of this region via site directed mutagenesis and thermostability measurements strongly suggests that this polymorphic region contains a secondary structure that, when disrupted due to the presence of a variant SNP, results in a mobility shift relative to the wild type sequence. To overcome this problem, the SE33 primers used in the final configuration of the NGM SElect™ Kit avoided the amplification of this polymorphic region yielding in turn results highly concordant with the SEfiler Plus™ Kit.Identification and secondary structure analysis of a region affecting electrophoretic mobility of the STR locus SE33Dennis Y. Wang, Robert L. Green, Robert E. Lagacé, Nicola J. Oldroyd, Lori K. Hennessy, Julio J. Mulero10.1016/j.fsigen.2011.06.008Forensic Science International: Genetics 6, 3 (2012)2011-07-15Forensic Science International: Genetics2011-07-1563S1872-4973(12)X0003-6Research Articles310316http://www.fsigenetics.com/article/PIIS1872497311001360/abstract?rss=yesAbstract: Composite profiles are created by combining DNA profiling information from replicate profiles derived from the same DNA extract. In this paper we have shown that, provided the probability of drop-in is low or nil, the creation of composite profiles is an acceptable approximation to a Bayesian approach, as long as simple samples are analysed.Composite profiles in DNA analysisJo-Anne Bright, Peter Gill, John Buckleton10.1016/j.fsigen.2011.07.001Forensic Science International: Genetics 6, 3 (2012)2011-08-16Forensic Science International: Genetics2011-08-1663S1872-4973(12)X0003-6Research Articles317321http://www.fsigenetics.com/article/PIIS1872497311001426/abstract?rss=yesAbstract: In the past decades, microarray technology has definitely put an edge to the field of genetic research. Our aim was to determine whether single nucleotide polymorphism (SNP) microarrays could be used as a tool in establishing genetic relationships where current molecular genetic methods are not sufficient. We used the Genechip, Affymetrix GenomeWide SNP Array 6.0, which detects more than 900,000 SNP markers dispersed throughout the human genome. The intention was to find a good selection of SNP markers that could be used for statistical evaluation of relatedness in a forensic setting. We conducted pairwise comparisons in the R-package FEST as well as pedigree comparisons in Merlin. Our methods were applied on two separate families, where relationships as distant as 3rd cousins were known. In addition, a question about a possible common ancestry between the two families was tested. Relationships as distant as 2nd cousins could be readily distinguished both from unrelated and other, genetically, closer relationships. This was achieved with a selection of 5774 markers, where each pair of markers was separated by a genetic distance of at least 0.5cM (centiMorgan). When considering 3rd cousins, and more distant relationships, the number of markers needs to be extended, consequently decreasing the genetic distance between the markers. However, inclusion of a too large number of markers presents new challenges and our results imply that the use of too dense sets of markers always yields the highest probability for the genetically closest relationship hypothesis. Simulations confirm that this is most probably caused by the fact that the computational model assumes linkage equilibrium between markers, a problem that will be further evaluated. Our results do however suggest that SNP-data derived from microarrays are well suited for kinship determination provided linkage disequilibrium is properly accounted for.DNA microarray as a tool in establishing genetic relatedness—Current status and future prospectsDaniel Kling, Jenny Welander, Andreas Tillmar, Øivind Skare, Thore Egeland, Gunilla Holmlund10.1016/j.fsigen.2011.07.007Forensic Science International: Genetics 6, 3 (2012)2011-08-03Forensic Science International: Genetics2011-08-0363S1872-4973(12)X0003-6Research Articles322329http://www.fsigenetics.com/article/PIIS187249731100144X/abstract?rss=yesAbstract: The ability to predict Externally Visible Characteristics (EVCs) from DNA, also referred to as Forensic DNA Phenotyping (FDP), is an exciting new chapter in forensic genetics holding great promise for tracing unknown individuals who are unidentifiable via standard forensic short tandem repeat (STR) profiling. For the purpose of DNA-based eye colour prediction, we previously developed the IrisPlex system consisting of a multiplex genotyping assay and a prediction model based on genotype and phenotype data from 3804 Dutch Europeans. Recently, we performed a forensic developmental validation study of the highly sensitive IrisPlex assay, which currently represents the only validated tool available for DNA-based prediction of eye colour in forensic applications. In the present study, we validate the IrisPlex prediction model by extending our initially described model towards genotype and phenotype data from multiple European populations. We performed IrisPlex analysis on 3840 individuals from seven sites across Europe as part of the European Eye (EUREYE) study for which DNA and high-resolution eye images were available. The accuracy rate of correctly predicting an individual's eye colour as being blue or brown, above the empirically established probability threshold of 0.7, was on average 94% across all seven European populations, ranging from 91% to 98%, despite the large variation in eye colour frequencies between the populations. The overall prediction accuracies expressed by the area under the receiver characteristic operating curves (AUC) were 0.96 for blue and 0.96 for brown eyes, which is considerably higher than those established before. The IrisPlex prediction model parameters generated from this multi-population European dataset, and thus its prediction capabilities, were highly comparable to those previously established. Therefore, the increased information regarding eye colour phenotype and genotype distributions across Europe, and the system's ability to provide eye colour predictions across Europe accurately, both highlight additional evidence for the utility of the IrisPlex system in forensic casework.DNA-based eye colour prediction across Europe with the IrisPlex systemSusan Walsh, Andreas Wollstein, Fan Liu, Usha Chakravarthy, Mati Rahu, Johan H. Seland, Gisele Soubrane, Laura Tomazzoli, Fotis Topouzis, Johannes R. Vingerling, Jesus Vioque, Astrid E. Fletcher, Kaye N. Ballantyne, Manfred Kayser10.1016/j.fsigen.2011.07.009Forensic Science International: Genetics 6, 3 (2012)2011-08-03Forensic Science International: Genetics2011-08-0363S1872-4973(12)X0003-6Research Articles330340http://www.fsigenetics.com/article/PIIS1872497311001451/abstract?rss=yesAbstract: There is growing evidence that the histone–DNA complexes found in nucleosomes offer protection from DNA degradation processes, including apoptotic events in addition to bacterial and environmental degradation. We sought to locate human nucleosome regions and build a catalogue of SNPs sited near the middle of these genomic segments that could be combined into a single PCR multiplex specifically for use with extremely degraded human genomic DNA samples. Using recently optimized bio-informatics tools for the reliable identification of nucleosome sites based on sequence motifs and their positions relative to known promoters, 1395 candidate loci were collected to construct an 18-plex single base extension assay. Genotyping performance of the nucleosome SNPs was tested using artificially degraded DNA and 24 casework samples where the likely state of degradation of DNA was established by comparison to profile completeness in four other forensic assays: a standard 15-plex STR identification test, a miniaturized STR multiplex and two autosomal SNP multiplexes. The nucleosome SNP assay gave genotyping success rates 6% higher than the best existing forensic SNP assay: the SNPforID Auto-2 29-plex and significantly higher than the mini-STR assay. The nucleosome SNPs we located and combined therefore provide a new type of marker set that can be used to supplement existing approaches when the analysed DNA is likely to be extremely degraded and may fail to give sufficient STR genotypes for a reliable identification.A new SNP assay for identification of highly degraded human DNAA. Freire-Aradas, M. Fondevila, A.-K. Kriegel, C. Phillips, P. Gill, L. Prieto, P.M. Schneider, Á. Carracedo, M.V. Lareu10.1016/j.fsigen.2011.07.010Forensic Science International: Genetics 6, 3 (2012)2011-09-12Forensic Science International: Genetics2011-09-1263S1872-4973(12)X0003-6Research Articles341349http://www.fsigenetics.com/article/PIIS1872497311001463/abstract?rss=yesAbstract: DNA markers are routinely used to reveal both simple and complex family relationships. Likelihood based approaches have been traditionally used to estimate relationships using relatively few unlinked markers. However it is widely recognized that when using such limited numbers of loci distant relationships between two individuals cannot be distinguished from the average level of allele sharing found in random pairwise comparisons in the same population. As a real example, we demonstrate the usefulness of genome-wide SNP genotyping to analyze a claimed second cousin relationship that could not be resolved using standard forensic markers, confirming theoretical expectations for very distant relationships. Genome profiles derived from Affymetrix 6.0 SNP arrays obtained from the claimed second cousins were compared to profiles obtained from unrelated individuals and simulated data. Significance of the high estimated probabilities in favor of the second cousin relationship hypothesis was proved from the results obtained with both real and simulated unrelated pairs. As a final cautionary note, it is important to consider that successful identification of the claimed distant relationship reported here is largely due to a well-founded hypothesis being compared to the alternative hypothesis of the claimants being unrelated, but where there are several possible alternative hypotheses, the approach we outline here can yield false indications of unfounded alternative relationships.Analysis of a claimed distant relationship in a deficient pedigree using high density SNP dataM.V. Lareu, M. García-Magariños, C. Phillips, I. Quintela, Á. Carracedo, A. Salas10.1016/j.fsigen.2011.07.011Forensic Science International: Genetics 6, 3 (2012)2011-08-25Forensic Science International: Genetics2011-08-2563S1872-4973(12)X0003-6Research Articles350353http://www.fsigenetics.com/article/PIIS1872497311001475/abstract?rss=yesAbstract: Family studies can be used to measure the genetic distance between same-chromosome (syntenic) STRs in order to detect physical linkage or linkage disequilibrium. However, family studies are expensive and time consuming, in many cases uninformative, and lack a reliable means to infer the phase of the diplotypes obtained. HapMap provides a more comprehensive and fine-scale estimation of recombination rates using high density multi-point SNP data (average inter-SNP distance: 900 nucleotides). Data at this fine scale detects sub-kilobase genetic distances across the whole recombining human genome. We have used the most recent HapMap SNP data release 22 to measure and compare genetic distances, and by inference fine-scale recombination rates, between 29 syntenic STR pairs identified from 39 validated STRs currently available for forensic use. The 39 STRs comprise 23 core loci: SE33, Penta D & E, 13 CODIS and 7 non-CODIS European Standard Set STRs, plus supplementary STRs in the recently released Promega CS-7™ and Qiagen Investigator HDplex™ kits. Also included were D9S1120, a marker we developed for forensic use unique to chromosome 9, and the novel D6S1043 component STR of SinoFiler™ (Applied Biosystems). The data collated provides reliable estimates of recombination rates between each STR pair, that can then be placed into haplotype frequency calculators for short pedigrees with multiple meiotic inputs and which just requires the addition of allele frequencies. This allows all current STR sets or their combinations to be used in supplemented paternity analyses without the need for further adjustment for physical linkage. The detailed analysis of recombination rates made for autosomal forensic STRs was extended to the more than 50 X chromosome STRs established or in development for complex kinship analyses.The recombination landscape around forensic STRs: Accurate measurement of genetic distances between syntenic STR pairs using HapMap high density SNP dataC. Phillips, D. Ballard, P. Gill, D. Syndercombe Court, Á. Carracedo, M.V. Lareu10.1016/j.fsigen.2011.07.012Forensic Science International: Genetics 6, 3 (2012)2011-08-29Forensic Science International: Genetics2011-08-2963S1872-4973(12)X0003-6Research Articles354365http://www.fsigenetics.com/article/PIIS1872497311001487/abstract?rss=yesAbstract: The possibilities and strategies for using DNA characteristics to link a botanical sample to a specific source plant or location vary with its breeding system. For inbreeding species, which often form small patches of identical genotypes, knotgrass (Polygonum aviculare L.) is a suitable model species because of its (1) occurrence in a wide range of natural environments, (2) abundant presence in pieces of evidence, and (3) ease in molecular processing. The value of knotgrass for forensic casework was demonstrated using data from a homicide case. Using the DNA fingerprinting technique AFLP® we were able to identify the knotgrass population at the crime site as the most likely origin of the botanical evidence. We expect that the development of tailored marker systems for knotgrass and other frequently occurring (model) species will considerably accelerate the use of botanical DNA evidence in criminal cases.Botanical DNA evidence in criminal cases: Knotgrass (Polygonum aviculare L.) as a model speciesWim J.M. Koopman, Irene Kuiper, Dick J.A. Klein-Geltink, Gerda J.H. Sabatino, Marinus J.M. Smulders10.1016/j.fsigen.2011.07.013Forensic Science International: Genetics 6, 3 (2012)2011-08-31Forensic Science International: Genetics2011-08-3163S1872-4973(12)X0003-6Research Articles366374http://www.fsigenetics.com/article/PIIS1872497311001499/abstract?rss=yesAbstract: Deoxyribonucleic acid (DNA) extracted from skeletal tissue can be invaluable in genetic profiling applications, as it is often the only source available. Like all forensic samples, skeletal tissue may have been exposed to a variety of environmental insults, including heat. This study has focussed upon characterising changes in the material properties of bone that has been compromised by controlled heat treatments. These changes were then examined in relation to the subsequent success or failure of nuclear DNA (nDNA) amplification, using a range of differently sized amplicons, relevant to alternate profiling strategies. The results presented demonstrate that the ability to amplify nDNA correlates well with particular changes in mineral and organic content of bone. As such, we propose the application of a ‘diagnostic triage tool’ that can be performed quickly and at low cost on individual bone samples, in order to determine whether nDNA analysis is likely to be a viable option.FTIR spectroscopy: A new diagnostic tool to aid DNA analysis from heated boneJamie Daniel Fredericks, Phil Bennett, Anna Williams, Keith Derek Rogers10.1016/j.fsigen.2011.07.014Forensic Science International: Genetics 6, 3 (2012)2011-10-03Forensic Science International: Genetics2011-10-0363S1872-4973(12)X0003-6Research Articles375380http://www.fsigenetics.com/article/PIIS1872497311001505/abstract?rss=yesAbstract: Well defined estimates of mutation rates are a prerequisite for the use of short tandem repeat (STR-) loci in relationship testing. We investigated 65 isolated genetic inconsistencies, which were observed within 50,796 allelic transfers at 23 STR-loci (ACTBP2 (SE33), CD4, CSF1PO, F13A1, F13B, FES, FGA, vWA, TH01, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1132, D8S1179, D12S391, D13S317, D16S539, D17S976, D18S51, D19S433, D21S11) in Caucasoid families residing in Austria and Switzerland. Sequencing data of repeat and flanking regions and the median of all theoretically possible mutational steps showed valuable information to characterise the mutational events with regard to parental origin, change of repeat number (mutational step size) and direction of mutation (losses and gains of repeats). Apart from predominant single-step mutations including one case with a double genetic inconsistency, two double-step and two apparent four-step mutations could be identified. More losses than gains of repeats and more mutations originating from the paternal than the maternal lineage were observed (31 losses, 22 gains, 12 losses or gains and 47 paternal, 11 maternal mutations and 7 unclear of parental origin). The mutation in the paternal germline was 3.3 times higher than in the maternal germline. The results of our study show, that apart from the vast majority of single-step mutations rare multi-step mutations can be observed. Therefore, the interpretation of mutational events should not rigidly be restricted to the shortest possible mutational step, because rare but true multi-step mutations can easily be overlooked, if haplotype analysis is not possible.Germline mutations of STR-alleles include multi-step mutations as defined by sequencing of repeat and flanking regionsEva-Maria Dauber, Adelgunde Kratzer, Franz Neuhuber, Walther Parson, Michael Klintschar, Walter Bär, Wolfgang R. Mayr10.1016/j.fsigen.2011.07.015Forensic Science International: Genetics 6, 3 (2012)2011-08-29Forensic Science International: Genetics2011-08-2963S1872-4973(12)X0003-6Research Articles381386http://www.fsigenetics.com/article/PIIS1872497311001517/abstract?rss=yesAbstract: Over the recent years, the national databases of STR profiles have grown in size due to the success of forensic DNA analysis in solving crimes. The accumulation of DNA profiles implies that the probability of a random match or near match of two randomly selected DNA profiles in the database increases.We analysed 53,295 STR profiles from individuals investigated in relation to crime case investigations at the Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Denmark. Incomplete STR profiles (437 circa 0.8% of the total), 48 redundant STR profiles from monozygotic twins (0.09%), 6 redundant STR profiles of unknown cause and 1283 STR profiles from repeated testing of individuals were removed leaving 51,517 complete 10 locus STR profiles for analysis. The number corresponds to approximately 1% of the Danish population. We compared all STR profiles to each other, i.e. 1.3×109 comparisons.With these large number of comparisons, it is likely to observe DNA profiles that coincide on many loci, which has concerned some commentators and raised questions about “overstating” the power of DNA evidence. We used the method of Weir and Curran et al. to compare the observed and expected number of matches and near matches in the data set. We extended the methods by computing the covariance matrix of the summary statistic and used it for the estimation of the identical-by-descent parameter, θ. The analysis demonstrated a number of close relatives in the Danish data set and substructure. The main contribution to the substructure comes from close relatives. An overall θ-value of 1% compensated for the observed substructure, when close familial relationships were accounted for.Analysis of matches and partial-matches in a Danish STR data setTorben Tvedebrink, Poul Svante Eriksen, James Michael Curran, Helle Smidt Mogensen, Niels Morling10.1016/j.fsigen.2011.08.001Forensic Science International: Genetics 6, 3 (2012)2011-09-07Forensic Science International: Genetics2011-09-0763S1872-4973(12)X0003-6Research Articles387392http://www.fsigenetics.com/article/PIIS1872497311001529/abstract?rss=yesAbstract: The interpretation of lineage markers is usually carried out as a count in a database. The count is a factual statement and does not take into account subpopulation effects that may be acting on the data. Subpopulation effects are usually taken into consideration for autosomal DNA genotype interpretation by the incorporation of a correction, θ. The question has arisen as to whether lineage markers should also have such a correction. This paper discusses if and how subpopulation effects could be considered.Interpreting lineage markers in view of subpopulation effectsSarah Cockerton, Kurt McManus, John Buckleton10.1016/j.fsigen.2011.04.020Forensic Science International: Genetics 6, 3 (2012)2011-09-05Forensic Science International: Genetics2011-09-0563S1872-4973(12)X0003-6Research Articles393397http://www.fsigenetics.com/article/PIIS1872497311001554/abstract?rss=yesAbstract: During the 7 year period from 2002 to 2009 a high volume, silica-binding DNA extraction protocol for bone, based on modified QIAGEN's Blood Maxi Kit protocol was highly successful permitting the DNA matching of >14,500 missing persons from former Yugoslavia. This method, however, requires large amount of bone material and large volumes of reagents. The logical evolution was to develop a more efficient extraction protocol for bone samples that uses significantly less starting material while increasing the success in obtaining DNA results from smaller, more challenging samples. In this study we compared the performance of ICMP's original protocol against an automatable full demineralization approach. In order to provide reliable results and to simulate a wide variety of cases, we analyzed 40 bone samples in a comparative study based on DNA concentrations and quality of resulting STR profiles. The new protocol results in the dissolution of the entire bone powder sample, thus eliminating the possibility that DNA is left behind, locked in remaining solid bone matrix. For the majority of samples tested, the DNA concentrations obtained from half a gram of fully digested bone material were equivalent to or greater than the ones obtained from 2g of partially demineralized bone powder. Furthermore, the full demineralization process significantly increases the proportion of full profiles reflecting the correlation with better DNA quality. This method has been adapted for the QIAcube robotic platform. The performance of this automated full demineralization protocol is similar to the manual version and increases overall lab throughput. It also simplifies the process by eliminating quality control procedures that are advisable in manual procedures, and overall reduces the chance of human error. Finally we described a simple and efficient post-extraction clean-up method that can be applied to DNA extracts obtained from different protocols. This protocol has also been adjusted for the QIAcube platform.Automatable full demineralization DNA extraction procedure from degraded skeletal remainsSylvain Amory, René Huel, Ana Bilić, Odile Loreille, Thomas J. Parsons10.1016/j.fsigen.2011.08.004Forensic Science International: Genetics 6, 3 (2012)2011-09-02Forensic Science International: Genetics2011-09-0263S1872-4973(12)X0003-6Research Articles398406http://www.fsigenetics.com/article/PIIS1872497311001803/abstract?rss=yesAbstract: Direct PCR generates DNA profiles from samples without using the extraction process. During sample extraction, DNA may be lost due to the methods used, which can affect the quality of the DNA profile obtained. This is not the case with direct PCR, where the sample is transferred directly into the PCR tube. Here, we report on the ability of direct PCR to generate DNA profiles from low amounts of control DNA retrieved from various surfaces using PowerPlex 16 HS. A comparison is made with samples undergoing a preliminary extraction stage using QiaAmp DNA Micro kits. Samples subjected to direct PCR generated DNA profiles with higher peak heights and lower allele dropout on all the different substrates tested when compared to the samples subjected to extraction. The amount of DNA retrieved from each substrate also varied even though the same amount of starting material was deposited, proving that the type of substrate can affect the retrieval of DNA.A comparison between direct PCR and extraction to generate DNA profiles from samples retrieved from various substratesYuvaneswari Chandramoulee Swaran, Lindsey Welch10.1016/j.fsigen.2011.08.007Forensic Science International: Genetics 6, 3 (2012)2011-09-19Forensic Science International: Genetics2011-09-1963S1872-4973(12)X0003-6Research Articles407412http://www.fsigenetics.com/article/PIIS1872497311001542/abstract?rss=yesAbstract: Fourteen Y-STR loci (DYS458, DYS439, Y-GATA H4, DYS576, DYS447, DYS460, DYS456, YGATA A10, DYS437, DYS449, DYS570, DYS635 or Y-GATA C4, DYS448 and DYS438) were analysed in 873 males from eight northern Brazil populations: Belém (N=400), Santarém (N=69), Manaus (N=75), Macapá (N=65), Palmas (N=30), Rio Branco (N=32), Porto Velho (N=135) and Boa Vista (N=67). A total of 871 different haplotypes were identified, of which 869 were unique. The panel's estimated total haplotype diversity (HD) is 0.9988, and its discrimination capacity (DC) is 0.9980. The lowest estimates of genetic diversity correspond to markers Y-GATA H4 (0.550) and DYS460 (0.581), and the greatest (above 0.700) to markers DYS458, DYS576, DYS447, YS449, DYS570 and DYS635. The genetic parameters obtained were higher for the 14-Y-STR panel than that for the minimum haplotype set (HD=0.9969; DC=0.76) and the parameters were similar to those obtained with the panel of 17 YSTR of YHRD (HD=0.9987; DC=0. 9870). The analysis of molecular variance (AMOVA) indicated that most of the genetic variance is found within populations and a smaller, but significant part, is found among populations (RST=0.027, p value=0.009). The data when compared with those from African, Amerindian and European populations have shown no significant genetic distance between northern Brazil populations and Europeans, but there is a significant genetic distance when compared to Africans and Amerindians. The discrimination capacity of the markers shows a high potential for forensic analysis.Fourteen short tandem repeat loci Y chromosome haplotypes: Genetic analysis in populations from northern BrazilTeresinha Palha, Elzemar Ribeiro-Rodrigues, Ândrea Ribeiro-dos-Santos, Sidney Santos10.1016/j.fsigen.2011.08.003Forensic Science International: Genetics 6, 3 (2012)2011-08-29Forensic Science International: Genetics2011-08-2963S1872-4973(12)X0003-6Short Communications413418http://www.fsigenetics.com/article/PIIS1872497311001815/abstract?rss=yesAbstract: MicroRNAs (miRNAs, 18–25 bases in length) are small, non-coding RNAs that regulate gene expression at the post-transcriptional level. MiRNA expression patterns, including presence and relative abundance of particular miRNA species, provide cell- and tissue-specific information that can be used for body fluid identification. Recently, two published studies reported that a number of body fluid-specific miRNAs had been identified. However, the results were inconsistent when different technology platforms and statistical methods were applied. To further study the role of miRNAs in identification of body fluids, this study sets out to develop an accurate and reliable model for data analysis of miRNA expression. To that end, the relative expression levels of three miRNAs were studied using the mirVana™ miRNA Isolation Kit, high-specificity stem-loop reverse transcription (RT) and high-sensitivity hydrolysis probes (TaqMan) quantitative real-time polymerase chain reaction (qPCR) in forensically relevant biological fluids, including venous blood, vaginal secretions, menstrual blood, semen and saliva. Accurate quantification of miRNAs requires not only a highly sensitive and specific detection platform for experiment operation, but also a reproducible methodology with an adequate model for data analysis. In our study, the efficiency-calibrated model that incorporated the impact of the quantification cycle (Cq) values and PCR efficiencies of target and reference genes was developed to calculate the relative expression ratio of miRNAs in forensically relevant body fluids. Our results showed that venous blood was distinguished from other body fluids according to the relative expression ratio of miR16 using as little as 50pg of total RNA, while the expression level of miR658 was unstable and that of miR205 was nonspecific among different body fluids. Collectively, the findings may constitute a basis for future miRNA-based research on body fluid identification and show miRNAs as a promising biomarker in forensic identification of body fluids.A model for data analysis of microRNA expression in forensic body fluid identificationZheng Wang, Haibo Luo, Xiongfei Pan, Miao Liao, Yiping Hou10.1016/j.fsigen.2011.08.008Forensic Science International: Genetics 6, 3 (2012)2011-09-07Forensic Science International: Genetics2011-09-0763S1872-4973(12)X0003-6Short Communications419423http://www.fsigenetics.com/article/PIIS1872497311001372/abstract?rss=yesAbstract: The thirteen autosomal STR loci of the CODIS system were typed from DNA of 732 unrelated male individuals sampled from different locations in Chile. This is the first report of allele frequencies for the thirteen STRs loci defined in the CODIS system from the Chilean population.Autosomal STR allele frequencies for the CODIS system from a large random population sample in ChileIsmael A. Vergara, Pamela Villouta, Sandra Herrera, Francisco Melo10.1016/j.fsigen.2011.07.002Forensic Science International: Genetics 6, 3 (2012)2011-08-03Forensic Science International: Genetics2011-08-0363S1872-4973(12)X0003-6Letters to the Editore83e85http://www.fsigenetics.com/article/PIIS1872497311001384/abstract?rss=yesAutosomal short tandem repeats (STRs) are effective tools for human identification. The amplicon size of the conventional STR markers used for the forensic casework ranges from 75 to 450bp. Due to fragmented DNA template or PCR inhibitors present in the samples, often loss of signal or partial profiles are observed for the conventional STR markers. Previous studies have demonstrated utility of size-reduced amplicons (miniSTRs) for the analysis of highly degraded DNA by choosing primers close to the repeat regions . European DNA profiling group (EDNAP) recommended five new European Standard Set (ESS) markers D10S1248, D2S441, D22S1045, D1S1656 and D12S391 for the forensic casework and database . Evaluating polymorphisms of these miniSTR markers in the Indian population would enable their efficient use for the forensic casework. Hence, a pentaplex for the simultaneous analysis of these five miniSTR loci was optimized and their polymorphisms was studied in 11 endogamous populations of India belonging to four linguistic (Indo-European, Dravidian, Tibeto-Burman and Austro-Asiatic), six geographic (north, east, central, west, south and north-east) and two socio-cultural (caste and tribe) groups.Pentaplex typing of new European Standard Set (ESS) STR loci in Indian populationD. Kalpana, Tania Ghosh, Sanjukta Mukerjee, Meeta Mukherjee, Anil Kumar Sharma10.1016/j.fsigen.2011.07.003Forensic Science International: Genetics 6, 3 (2012)2011-08-03Forensic Science International: Genetics2011-08-0363S1872-4973(12)X0003-6Letters to the Editore86e89http://www.fsigenetics.com/article/PIIS1872497311001396/abstract?rss=yesThe highly polymorphic short tandem repeat (STR) loci in the human genome are widely used for forensic and paternity testing as well as for population genetic studies. Introducing set of STR loci as observed markers made marvels progress in this field of forensic science . Nowadays, in response to the ENFSI and EDNAP groups’ call for new STR multiplexes for Europe, Promega developed a suite of four new DNA profiling kits. One of them is PowerPlex ESI 17 that we have used in this study.Allele frequencies of the new European Standard Set (ESS) loci plus SE33 locus in a population from the Republic of MacedoniaZlatko Jakovski, Ksenija Nikolova, Renata Jankova-Ajanovska, Biljana Janeska, Naris Pojskic, Damir Marjanovic10.1016/j.fsigen.2011.07.004Forensic Science International: Genetics 6, 3 (2012)2011-07-29Forensic Science International: Genetics2011-07-2963S1872-4973(12)X0003-6Letters to the Editore90e92http://www.fsigenetics.com/article/PIIS1872497311001414/abstract?rss=yesWe undertook research that investigated the genetic diversity of the population of the city of Benghazi. This city is located in the northeast of Libya, on the Gulf of Sidra, a part of the Mediterranean Sea. Libya became independent in 1951 after a brief period as an Italian colony; it was invaded by Italy in 1911. In February 2011, there was an uprising against the Libyan government initiated in the city of Benghazi which led to a revolution that is ongoing. Benghazi is the second largest city in Libya, and the most dominating in the eastern Cyrenaica region, and is the capital of the district of Benghazi. The population of Benghazi was 500, 120 in the 1995 census and increased to 670,797 in the 2006 census. Throughout its history, Benghazi has developed with a certain level of independence from the more Maghreb (west) oriented capital, Tripoli. This has influenced the city and, as such, the cultural atmosphere in Benghazi is more Arab in nature than that in Tripoli. The city of Benghazi was first inhabited by Berbers, followed by Phoenicians, Greeks, Romans, Arabs and Ottomans. An influx of African, Egyptian, Iraqi, Palestinian, Sudanese and Syrian immigrants has also influenced the city's culture to a certain extent in recent years. This history of different waves of migration (genetic influx) makes Benghazi an interesting city for studies of intrapopulation genetic diversity. The main aim of the this study was to determine the genetic structure of the population of the city of Benghazi using 15 autosomal short tandem repeats (STR) loci and to evaluate the usefulness of these loci for forensic genetic purposes.Genetic data provided by 15 autosomal STR loci in the Libyan population living in BenghaziSamir Elmrghni, Ron A. Dixon, Yvette M. Coulson-Thomas, D. Ross Williams10.1016/j.fsigen.2011.07.006Forensic Science International: Genetics 6, 3 (2012)2011-07-29Forensic Science International: Genetics2011-07-2963S1872-4973(12)X0003-6Letters to the Editore93e94http://www.fsigenetics.com/article/PIIS1872497311001827/abstract?rss=yesX chromosome STR studies have a curious role in forensic and population genetics. These markers are present as a single copy in males and as double copies in females. Analysis of X-chromosomal loci can be beneficial in deficient paternity cases, when the offspring is female and the alleged father is missing, or in maternity cases . So far, a very limited number of X recombination and linkage disequilibrium studies (LD) has been published . Hering et al. have analyzed three-generation family studies and Inturri et al. have studied two-generation families in the past. Inturri et al. stated that two-generation family studies are less accurate than three-generation studies, as the unavailability of the maternal grandfather does not allow a direct count of recombinant chromosomes. Furthermore, only Tillmar et al. performed the LD test using data of male haplotypes for 8 X-STR loci, but not for 12 X-STR loci.X chromosomal recombination study in three-generation families in HungaryHorolma Pamjav, Renáta Kugler, Andrea Zalán, Antónia Völgyi, Zsuzsa Straky, Paula Endrédy, Zsolt Kozma10.1016/j.fsigen.2011.08.009Forensic Science International: Genetics 6, 3 (2012)2011-09-14Forensic Science International: Genetics2011-09-1463S1872-4973(12)X0003-6Letters to the Editore95e96http://www.fsigenetics.com/article/PIIS1872497311001840/abstract?rss=yesThis letter is an update to a recent publication in the Forensic Science International Genetics journal, “Quantitative real-time PCR (qPCR) assay for human–dog–cat species identification and nuclear DNA quantification”: S. Kanthaswamy, A. Premasuthan, et al. This triplex qPCR assay quantifies and identifies the presence of as little as 0.4pg of human, feline and canine DNA in a mixed sample . The assay did not include an Internal Positive Control (IPC) due to the three-dye limit in the Applied Biosystems 7300 machine. The assay is now modified to include an IPC using the 7500 Fast Real Time PCR system ().Quadriplex real-time PCR (qPCR) assay for human–canine–feline species identification and nuclear DNA quantificationS. Kanthaswamy, A. Premasuthan10.1016/j.fsigen.2011.09.001Forensic Science International: Genetics 6, 3 (2012)2011-10-03Forensic Science International: Genetics2011-10-0363S1872-4973(12)X0003-6Letters to the Editore97e98