Forensic Science International: Genetics RSS feed: Articles in Press. 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, illegal trade in endangered species evidences, and bioterrorism 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//inpress?rss=yesElsevier Inc.en © 2010 Elsevier Ireland Ltd. All rights reserved. Forensic Science International: Genetics1872-49732010-09-01 © 2010 Elsevier Ireland Ltd. All rights reserved. healthpermissions@elsevier.comhttp://www.fsigenetics.com/article/PIIS1872497310001183/abstract?rss=yesMitochondrial DNA has for several years provided a helpful tool for the forensic geneticists in cases with low amounts of DNA or in cases where the maternal lineage needs to be investigated. Several methods are available for typing of mitochondrial DNA markers. SNP typing assays typing SNPs from the coding region of the mitochondrial DNA has been developed to distinguish between individuals with similar control region sequences .Frequencies of 33 coding region mitochondrial SNPs in a Danish and a Turkish population - Corrected ProofMartin Mikkelsen, Eszter Rockenbauer, Hande Demir, Claus Børsting, Niels Morling10.1016/j.fsigen.2010.08.001Forensic Science International: Genetics (2010)2010-09-01Forensic Science International: Genetics2010-09-01LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310001195/abstract?rss=yesAbstract: A total of 166 males from three main ethnic linguistic groups (Bakongo, Kimbundo and Ovimbundo) in Angola population were typed for the Y-chromosome STRs DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439 and DYS385 with the PowerPlex Y Kit (Promega). In Angola population a total of 138 haplotypes were identified being 120 unique. The genetic diversity ranged from 0.1478 (DYS392) to 0.7010 (DYS389 II) and the haplotypes diversity for 11 loci was computed to be 0.9969. There are no significant differences between the three ethnic linguistic groups.Y-STR haplotypes in three ethnic linguistic groups of Angola population - Corrected ProofMiguel Manuel Melo, Mónica Carvalho, Virgínia Lopes, Maria João Anjos, Armando Serra, Duarte Nuno Vieira, Jorge Sequeiros, Francisco Corte-Real10.1016/j.fsigen.2010.08.002Forensic Science International: Genetics (2010)2010-09-01Forensic Science International: Genetics2010-09-01FORENSIC POPULATION GENETICS – LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS187249731000116X/abstract?rss=yesAbstract: DNA evidence is widely recognized as an invaluable tool in the process of investigation and identification, as well as one of the most sought after types of evidence for presentation to a jury. In the United States, the development of state and federal DNA databases has greatly impacted the forensic community by creating an efficient, searchable system that can be used to eliminate or include suspects in an investigation based on matching DNA profiles – the profile already in the database to the profile of the unknown sample in evidence. Recent changes in legislation have begun to allow for the possibility to expand the parameters of DNA database searches, taking into account the possibility of familial searches.This article discusses prospective positive outcomes of utilizing familial DNA searches and acknowledges potential negative outcomes, thereby presenting both sides of this very complicated, rapidly evolving situation.Forensic utilization of familial searches in DNA databases - Corrected ProofCassandra J. Gershaw, Andrew J. Schweighardt, Linda C. Rourke, Margaret M. Wallace10.1016/j.fsigen.2010.07.005Forensic Science International: Genetics (2010)2010-08-26Forensic Science International: Genetics2010-08-26REVIEWhttp://www.fsigenetics.com/article/PIIS1872497310001171/abstract?rss=yesAbstract: More than 2700 unrelated individuals from Europe, northern Africa and western Asia were analyzed for the marker M269, which defines the Y chromosome haplogroup R1b1b2. A total of 593 subjects belonging to this haplogroup were identified and further analyzed for two SNPs, U106 and U152, which define haplogroups R1b1b2g and R1b1b2h, respectively. These haplogroups showed quite different frequency distribution patterns within Europe, with frequency peaks in northern Europe (R1b1b2g) and northern Italy/France (R1b1b2h).Strong intra- and inter-continental differentiation revealed by Y chromosome SNPs M269, U106 and U152 - Corrected ProofFulvio Cruciani, Beniamino Trombetta, Cheyenne Antonelli, Roberto Pascone, Guido Valesini, Valentina Scalzi, Giuseppe Vona, Bela Melegh, Boris Zagradisnik, Guenter Assum, Georgi D. Efremov, Daniele Sellitto, Rosaria Scozzari10.1016/j.fsigen.2010.07.006Forensic Science International: Genetics (2010)2010-08-26Forensic Science International: Genetics2010-08-26FORENSIC POPULATION GENETICS – SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310001092/abstract?rss=yesAbstract: Disaster victim identification (DVI) can be aided by DNA-evidence, by comparing the DNA-profiles of unidentified individuals with those of surviving relatives. The DNA-evidence is used optimally when such a comparison is done by calculating the appropriate likelihood ratios. Though conceptually simple, the calculations can be quite involved, especially with large pedigrees, precise mutation models etc. In this article we describe a series of test cases designed to check if software designed to calculate such likelihood ratios computes them correctly. The cases include both simple and more complicated pedigrees, among which inbred ones. We show how to calculate the likelihood ratio numerically and algebraically, including a general mutation model and possibility of allelic dropout. In we show how to derive such algebraic expressions mathematically.We have set up these cases to validate new software, called Bonaparte, which performs pedigree likelihood ratio calculations in a DVI context. Bonaparte has been developed by SNN Nijmegen (The Netherlands) for the Netherlands Forensic Institute (NFI). It is available free of charge for non-commercial purposes (see www.dnadvi.nl for details). Commercial licenses can also be obtained. The software uses Bayesian networks and the junction tree algorithm to perform its calculations.Validation of DNA-based identification software by computation of pedigree likelihood ratios - Corrected ProofK. Slooten10.1016/j.fsigen.2010.06.005Forensic Science International: Genetics (2010)2010-08-23Forensic Science International: Genetics2010-08-23http://www.fsigenetics.com/article/PIIS1872497310001146/abstract?rss=yesAbstract: Interpretation rules for standard 28 cycle PCR have been described previously for the analysis of mixed STR profiles. In this study the same guidelines are applied to 200 mixtures derived from pairs of known donors combined in ratios of 1:1, 2:1 and 5:1 which have been profiled in duplicate with SGM Plus® at total inputs ranging from 1ng to 50pg. The paired profiles were distributed among 35 FSS (Forensic Science Service) reporting officers trained in low copy number (LCN) interpretation who analysed them blind following standard casework procedures. Based upon the results from initial duplicate 34 cycle PCR reactions, the reporting officers made appropriate decisions regarding the benefits of processing the reserved third aliquot. Using the combined results, 49 consensus profiles were successfully resolved into major and minor contributor peaks. This demonstrates the reliability of the interpretation rules used in standard 28 cycle SGM Plus analysis when applied to 34 cycle generated profiles by trained and experienced reporting officers. No minor contributor peaks were assigned to a major profile in the final reported results. Those profiles which did not show sufficiently marked and consistent differentiation into major and minor peaks would have been correctly resolved if the profile of one contributor (e.g. the “victim”) was known.Analysis and interpretation of mixed profiles generated by 34 cycle SGM Plus® amplification - Corrected ProofJon H. Wetton, John Lee-Edghill, Emily Archer, Valerie C. Tucker, Andrew J. Hopwood, Jonathan Whitaker, Gillian Tully10.1016/j.fsigen.2010.07.003Forensic Science International: Genetics (2010)2010-08-23Forensic Science International: Genetics2010-08-23http://www.fsigenetics.com/article/PIIS1872497310001158/abstract?rss=yesWe have typed 10 Standard Reference Materials (SRMs) from the National Institute of Standards and Technology (NIST) and four reference DNA samples commonly used by the forensic genetic community for 51 of the 52 SNPs in the SNPforID multiplex .SNP typing of the reference materials SRM 2391b 1–10, K562, XY1, XX74, and 007 with the SNPforID multiplex - Corrected ProofClaus Børsting, Carmen Tomas, Niels Morling10.1016/j.fsigen.2010.07.004Forensic Science International: Genetics (2010)2010-08-20Forensic Science International: Genetics2010-08-20FORENSIC POPULATION GENETICS - LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310001134/abstract?rss=yesWe determined the allele frequencies and forensic parameters for 21 STR autosomal loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA, D10S1248, D1S1656, D22S1045, D2S441, D12S391 and SE33). Blood samples were collected from 104 unrelated healthy Basque resident donors following informed consent. DNA was extracted by a standard phenol-chloroform extraction procedure and PCR amplifications were performed using the Identifiler and the PowerPlex ESX 17 kits according to the manufacturers’ recommendations. Amplified products were analyzed using an ABI 310 and allele designations were made according to recommendations of the DNA Commission of the ISFG with the aid of allelic ladders provided by the manufacturers.Allele frequencies and concordance study between the Identifiler and the PowerPlex ESX17 systems in the Basque Country population - Corrected ProofI. Yurrebaso, J.A. Ajuriagerra, A. Alday, I. Lezama, J.A. Pérez, E. Romón, I. Uriarte, O. García10.1016/j.fsigen.2010.07.002Forensic Science International: Genetics (2010)2010-08-05Forensic Science International: Genetics2010-08-05FORENSIC POPULATION GENETICS - LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310001122/abstract?rss=yesAbstract: STR profiling of animal species has a wide range of applications, including forensic identification, wildlife preservation, veterinary public health protection and food safety. We tested the efficacy of a multiplex PCR-based assay including 11 porcine-specific tetrameric STRs in a population sample of wild boars (n=142) originating from Piedmont (North West Italy). Multiple deviations from Hardy–Weinberg expectations were observed, mostly due to a reduction in observed heterozygosity indicative of a high degree of inbreeding. A value of θ of 0.046 and an inbreeding coefficient of 0.089 were estimated. Combined power of discrimination and probability of exclusion values for the STR panel were 0.9999999999996 and 0.99989. In order to test the suitability of the method for meat traceability purposes, a domestic pig reference sample (n=412), consisting of commercial lines commonly used in the meat production process, was also typed. A Bayesian cluster analysis carried out using the observed genotypes, showed a percentage of correct subspecies assignment of individual samples of 0.974 for wild boars and 0.991 for pigs, thus demonstrating the usefulness of the multiplex STR-typing system for discrimination purposes.Analysis of 11 tetrameric STRs in wild boars for forensic purposes - Corrected ProofStefano Caratti, Luca Rossi, Bruno Sona, Silvia Origlia, Silvana Viara, Giuseppe Martano, Carlo Torre, Carlo Robino10.1016/j.fsigen.2010.07.001Forensic Science International: Genetics (2010)2010-08-04Forensic Science International: Genetics2010-08-04FORENSIC POPULATION GENETICS—ORIGINAL RESEARCHhttp://www.fsigenetics.com/article/PIIS1872497310001109/abstract?rss=yesAbstract: To analyze DNA samples with very low DNA concentrations, various methods have been developed that sensitize short tandem repeat (STR) typing. Sensitized DNA typing is accompanied by stochastic amplification effects, such as allele drop-outs and drop-ins. Therefore low template (LT) DNA profiles are interpreted with care. One can either try to infer the genotype by a consensus method that uses alleles confirmed in replicate analyses, or one can use a statistical model to evaluate the strength of the evidence in a direct comparison with a known DNA profile. In this study we focused on the first strategy and we show that the procedure by which the consensus profile is assembled will affect genotyping reliability. In order to gain insight in the roles of replicate number and requested level of reproducibility, we generated six independent amplifications of samples of known donors. The LT methods included both increased cycling and enhanced capillary electrophoresis (CE) injection . Consensus profiles were assembled from two to six of the replications using four methods: composite (include all alleles), n−1 (include alleles detected in all but one replicate), n/2 (include alleles detected in at least half of the replicates) and 2× (include alleles detected twice). We compared the consensus DNA profiles with the DNA profile of the known donor, studied the stochastic amplification effects and examined the effect of the consensus procedure on DNA database search results. From all these analyses we conclude that the accuracy of LT DNA typing and the efficiency of database searching improve when the number of replicates is increased and the consensus method is n/2. The most functional number of replicates within this n/2 method is four (although a replicate number of three suffices for samples showing >25% of the alleles in standard STR typing). This approach was also the optimal strategy for the analysis of 2-person mixtures, although modified search strategies may be needed to retrieve the minor component in database searches. From the database searches follows the recommendation to specifically mark LT DNA profiles when entering them into the DNA database.Low template STR typing: Effect of replicate number and consensus method on genotyping reliability and DNA database search results - Corrected ProofCorina C.G. Benschop, Cornelis P. van der Beek, Hugo C. Meiland, Ankie G.M. van Gorp, Antoinette A. Westen, Titia Sijen10.1016/j.fsigen.2010.06.006Forensic Science International: Genetics (2010)2010-07-23Forensic Science International: Genetics2010-07-23FORENSIC POPULATION GENETICS—ORIGINAL RESEARCHhttp://www.fsigenetics.com/article/PIIS1872497310001110/abstract?rss=yesAbstract: The GenPlex™ HID System (Applied Biosystems – AB) offers typing of 48 of the 52 SNPforID SNPs and amelogenin. Previous studies have shown a high reproducibility of the GenPlex™ HID System using 250–500pg DNA of good quality. An international exercise was performed by 14 laboratories (9 in Europe and 5 in the US) in order to test the robustness and reliability of the GenPlex™ HID System on forensic samples. Three samples with partly degraded DNA and 10 samples with low amounts of DNA were analyzed in duplicates using various amounts of DNA. In order to compare the performance of the GenPlex™ HID System with the most commonly used STR kits, 500pg of partly degraded DNA from three samples was typed by the laboratories using one or more STR kits. The median SNP typing success rate was 92.3% with 500pg of partly degraded DNA. Three of the fourteen laboratories counted for more than two thirds of the locus dropouts. The median percentage of discrepant results was 0.2% with 500pg degraded DNA. An increasing percentage of locus dropouts and discrepant results were observed when lower amounts of DNA were used. Different success rates were observed for the various SNPs. The rs763869 SNP was the least successful. With the exception of the MiniFiler™ kit (AB), GenPlex™ HID performed better than five other tested STR kits. When partly degraded DNA was analyzed, GenPlex™ HID showed a very low mean mach probability, while all STR kits except MiniFiler™ had very limited discriminatory power.Autosomal SNP typing of forensic samples with the GenPlex™ HID System: Results of a collaborative study - Corrected ProofC. Tomas, G. Axler-DiPerte, Z.M. Budimlija, C. Børsting, M.D. Coble, A.E. Decker, A. Eisenberg, R. Fang, M. Fondevila, S. Frisk Fredslund, S. Gonzalez, A.J. Hansen, P. Hoff-Olsen, C. Haas, P. Kohler, A.K. Kriegel, B. Lindblom, F. Manohar, O. Maroñas, H.S. Mogensen, K. Neureuther, H. Nilsson, M.K. Scheible, P.M. Schneider, M.L. Sonntag, M. Stangegaard, D. Syndercombe-Court, C.R. Thacker, P.M. Vallone, A.A. Westen, N. Morling10.1016/j.fsigen.2010.06.007Forensic Science International: Genetics (2010)2010-07-23Forensic Science International: Genetics2010-07-23http://www.fsigenetics.com/article/PIIS1872497310001079/abstract?rss=yesAbstract: Pangolin scales are encountered in traditional East Asian medicines (TEAM) and the ever increasing demand for these scales has escalated the decline in the numbers of these mammals. The identification of protected pangolin species is necessary to enforce international and national legislation as well as assist with conservation measures. There is limited morphological feature on a pangolin scale thus requiring DNA analysis as a means of identification. We report on the isolation of DNA from pangolin scales and a strategy for obtaining the full length of the mitochondrial D-loop, being 1159bp. Primer sets creating five overlapping amplicons were designed to amplify sections of this mitochondrial DNA locus. DNA from the blood stain of nineteen Formosan pangolins (Manis pentadactyla pentadactyla) along with 145 scale samples that were suspected to have come from pangolins, was amplified and sequenced; leading to a total of 91 D-loop sequences being obtained. The 19 Formosan pangolin sequences produced 5 haplotypes and 72 of the 145 seized scales provided useable sequence classified as a further 38 haplotypes. The D-loop sequences from those scales suspected to be from a pangolin had a higher similarity to any of the 19 samples taken from M. p. pentadactyla compared to a D-loop sequence from Manis tetradactyla (the only pangolin D-loop sequence in GenBank, NC_004027). These 43 haplotypes were used to establish a local database for the D-loop sequence of pangolins and add to the data of Manis sp. held on GenBank. The PCR amplification strategy development in this study could be used in forensic DNA identification of scales suspected to be from protected pangolin species.Establishing the pangolin mitochondrial D-loop sequences from the confiscated scales - Corrected ProofHsing-Mei Hsieh, James Chun-I. Lee, Jane-Hong Wu, Chao-An Chen, Yen-Jean Chen, Guan-Bang Wang, Shih-Chien Chin, Lih-Chiann Wang, Adrian Linacre, Li-Chin Tsai10.1016/j.fsigen.2010.06.003Forensic Science International: Genetics (2010)2010-07-20Forensic Science International: Genetics2010-07-20http://www.fsigenetics.com/article/PIIS1872497310001055/abstract?rss=yesAbstract: Members of the National DNA Data Bank (NDDB) of Canada designed and searched two simulated mass disaster (MD) scenarios for User Acceptance Testing (UAT) of the Combined DNA Index System (CODIS) 6.0, developed by the Federal Bureau of Investigation (FBI) and the US Department of Justice. A simulated airplane MD and inland Tsunami MD were designed representing a closed and open environment respectively. An in-house software program was written to randomly generate DNA profiles from a mock Caucasian population database. As part of the UAT, these two MDs were searched separately using CODIS 6.0. The new options available for identity and pedigree searching in addition to the inclusion of mitochondrial DNA (mtDNA) and Y-STR (short tandem repeat) information in CODIS 6.0, led to rapid identification of all victims. A Joint Pedigree Likelihood Ratio (JPLR) was calculated from the pedigree searches and ranks were stored in Rank Manager providing confidence to the user in assigning an Unidentified Human Remain (UHR) to a pedigree tree. Analyses of the results indicated that primary relatives were more useful in Disaster Victim Identification (DVI) compared to secondary or tertiary relatives and that inclusion of mtDNA and/or Y-STR technologies helped to link family units together as shown by the software searches. It is recommended that UHRs have as many informative loci possible to assist with their identification. CODIS 6.0 is a valuable technological tool for rapidly and confidently identifying victims of mass disasters.Disaster victim investigation recommendations from two simulated mass disaster scenarios utilized for user acceptance testing CODIS 6.0 - Corrected ProofLaurie Bradford, Jennifer Heal, Jeff Anderson, Nichole Faragher, Kristin Duval, Sylvain Lalonde10.1016/j.fsigen.2010.05.005Forensic Science International: Genetics (2010)2010-07-12Forensic Science International: Genetics2010-07-12http://www.fsigenetics.com/article/PIIS1872497310001080/abstract?rss=yesDNA-based human identification has demonstrated reliability and robustness for easy resolution of the majority of forensic and paternity cases. The capacity to work successfully with minimal quantities and different types of biological samples (e.g., hair, saliva, teeth, bloodstains, etc.) allows unraveling a vast spectrum of special situations. For instance, DNA analysis of these samples permits to identify missing persons, to find relatives in mass disasters, and to clarify historical events and criminal cases, among others. For these purposes, a commercially available battery of molecular markers is employed worldwide at present, such as autosomal and Y-linked short tandem repeats (STRs), facilitating inter-laboratory comparison . Moreover, when these markers are applied to a relatively large number of individuals, important information has been obtained concerning past and current human populations that explain different aspects on their origin, geographic dispersion, and evolution . Nevertheless, this technology has been scarcely employed to investigate – at first glance – unexplained events within the religious context, which the majority of people formerly called “miracles”. To our knowledge, the origin and gender determination of dried blood on a statue of the Virgin Mary is the only published antecedent regarding this approach . However, in this study, only X and Y specific loci were employed to arrive at the conclusion of a human female origin of the sample.New approaches for forensic genetics: Breaking down “False Miracles” - Corrected ProofRangel-Villalobos Héctor10.1016/j.fsigen.2010.06.004Forensic Science International: Genetics (2010)2010-07-09Forensic Science International: Genetics2010-07-09LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310001043/abstract?rss=yesShort tandem repeat (STR) alleles are usually assigned by alleles comprising commercially produced allelic ladders. When large population samples are typed, variants which are absent from allelic ladder, are encountered. In the forensic casework, variant alleles can greatly increase the power of discrimination. In this regard, practitioners need to be aware of the possibility of rare variants and share information on the occurrence of these variants. We present here all off-ladder variants and instances of tri-allelic patterns that have been observed in STR profiles of 11,565 individuals in Korea.Variant alleles detected in a large Korean population using AmpFlSTR Profiler Plus - Corrected ProofEun Hae Cho, Eun Hee Lee, Su Hwa Kim, Eun Young Kim, Jong Won Kim10.1016/j.fsigen.2010.06.001Forensic Science International: Genetics (2010)2010-07-05Forensic Science International: Genetics2010-07-05LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310001067/abstract?rss=yesDear editor, The European Council resolution (9192/01) calls upon EU countries to use the European Standard Set (ESS) as a minimum to enable international comparison of DNA profiles. The ESS of loci presently contains only 7 loci which will not be sufficient for comparison purposes when massive exchanges of DNA profiles are undertaken.Allele distribution of the new European Standard Set (ESS) loci in the Hungarian population - Corrected ProofAliz Molnár, Andrea Zalán, Gergely Horváth, Horolma Pamjav10.1016/j.fsigen.2010.06.002Forensic Science International: Genetics (2010)2010-07-05Forensic Science International: Genetics2010-07-05LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310000864/abstract?rss=yesAbstract: In recent years there has been much attention to Argentinean population stratification. We were interested in assessing population stratification from a geographical perspective and summarizing it in form of maps. We mapped the genetic admixture of the extant male population in central and northern Argentina on the basis of forensic Y-chromosomal haplotypes. We addressed the question which group of genetically similar individuals is predominant in this area. Haplotypes containing seven Y-chromosomal short tandem repeat polymorphisms (Y-STRs), also known as microsatellites – DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 – were constructed for 145 individuals, recruited in 10 provinces. 97 distinct haplotypes were clustered into four clusters according to molecular distances. A genetic geostatistical analysis was conducted with the open-source geographical information system GRASS GIS. For each haplotype cluster, the according frequency was spatially interpolated over the total study area. Juxtaposing the interpolation surfaces, we screened point-wisely the maximal frequency as well as the label of the respective cluster. The screening results were combined in one summary map. We repeated this procedure for the second maximal frequencies. The resulting maps subdivide the study area into continuous regions comprising one predominant group of similar haplotypes. The first summary map divides the study area into three regions and the second summary map divides the area into four regions. The results of our analysis indicate that two groups of similar European haplotypes alternatively dominate the largest extension of the Argentinean territory. A third group, including South-American haplotypes, dominates the indigenous northwestern Argentinean area. The last group, including worldwide dispersed haplotypes, preponderates in frequency in second place in central Argentina. Our findings confirm a widespread European paternal ancestry, a substantial Amerindian contribution in the northwest, as well as a considerable proportion of diverse paternal lineages. In this work, we further discuss these findings in reference to ethno-historical, genetic, and demographic information.Spatial assessment of Argentinean genetic admixture with geographical information systems - Corrected ProofAmalia Diaz-Lacava, Maja Walier, Gustavo Penacino, Thomas F. Wienker, Max P. Baur10.1016/j.fsigen.2010.05.003Forensic Science International: Genetics (2010)2010-06-21Forensic Science International: Genetics2010-06-21http://www.fsigenetics.com/article/PIIS1872497310000876/abstract?rss=yesAbstract: We report a case study, where we have established the identity from a challenging biological sample of a deceased tigress by parentage analysis. A wildlife crime was committed in one of the zoological parks in India in the year 2000, where one young tigress was killed for its claws. This was of media interest for several days and remained an unsolved case for four years. A framed claw and decomposed tiger hide were seized from the accused in 2005. Biological samples of the victim tigress was not available for further forensics examination, therefore; DNA samples of the biological parents and a male sibling were used to establish the identity of the claw using STRs and mitochondrial DNA markers. Our analysis indicates that the seized claw belongs to the victim tigress.Establishing the identity of the massacred tigress in a case of wildlife crime - Corrected ProofSandeep Kumar Gupta, Jyotsna Bhagavatula, Kumarasamy Thangaraj, Lalji Singh10.1016/j.fsigen.2010.05.004Forensic Science International: Genetics (2010)2010-06-18Forensic Science International: Genetics2010-06-18CASE REPORThttp://www.fsigenetics.com/article/PIIS1872497310000852/abstract?rss=yesAbstract: This study reports sequence characteristics and population genetic data on a ‘new’ STR locus HumHUU (D16S3433) located in the non-coding region of chromosome 16q. Based on a population sample of 306 non-related Polish individuals 205 genotypes and 15 alleles with length range of 157–211bp were distinguished. No deviation from HWE was observed. The sequence analysis of each D16S3433 allele revealed a tetranucleotide repeat motif with a basic sequence structure (AAAA)0–1(AAAG)11–22(AAAAG)(AAAA)(AG)(AAAAAAG). The power of discrimination is 0.9538, showing a high degree of polymorphism. The presented results demonstrate that the D16S3433 is a useful genetic marker for forensic purposes and paternity testing.Population data and sequence analysis of a ‘new’ microsatellite locus HumHUU (D16S3433) - Corrected ProofMagdalena Konarzewska, Witold Pepinski, A. Jagiello, M. Spolnicka, I. Soltyszewski, A. Plucienniczak, J. Berent10.1016/j.fsigen.2010.03.018Forensic Science International: Genetics (2010)2010-06-16Forensic Science International: Genetics2010-06-16FORENSIC POPULATION GENETICS—SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310000840/abstract?rss=yesAbstract: Degraded forensic samples have proved difficult to analyze and interpret. New analysis techniques are constantly being discovered and improved but researchers have overlooked the structural properties that could prevent or slow the process of degradation. In theory, DNA that are bound to histones as nucleosomes are less prone to degradation, because nucleosomes prevent DNA from being exposed to degradative enzymes. In this study we determined the probability of 60 forensic DNA markers to be bound to histones based on their base sequence composition. Two web-based tools – NXSensor and nuScore – were used to analyze four hundred base pairs surrounding each DNA marker for properties that inhibit or promote the binding of DNA to histones. Our results showed that the majority of markers analyzed were likely to be bound as nucleosomes. Selection of the markers that are more protected to form a multiplex could increase the chance of obtaining a better balanced, easier to interpret DNA profile from degraded samples.Evaluation of nucleosome forming potentials (NFPs) of forensically important STRs - Corrected ProofPhuvadol Thanakiatkrai, Lindsey Welch10.1016/j.fsigen.2010.05.002Forensic Science International: Genetics (2010)2010-06-14Forensic Science International: Genetics2010-06-14http://www.fsigenetics.com/article/PIIS1872497310000839/abstract?rss=yesAbstract: This study provides population genetic data for individuals of Vitoria, Espirito Santo, Brazil, a location not yet characterized for STR frequencies used for genetic identification studies. Allelic frequencies and other population data analysis are reported for the 15 autosomal-STR loci included in the PowerPlex®16 kit (CSF1PO, D13S317, D16S539, D18S51, D21S11, D3S1358, D5S818, D7S820, D8S1179, FGA, Penta D, Penta E, TPOX, TH01 and vWA). Allele and haplotype frequencies, gene diversity and discrimination capacity were also estimated for the PowerPlex® Y System (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439). Blood samples were obtained from 226 unrelated volunteers (135 males and 91 females) residents in the city of Vitoria, representing a typical sample of the mixed ethnicity present in the Espirito Santo State, Brazil. Within the tested population, the total number of individuals typed for specific markers is: 226 for D13S317, D21S11, D3S1358, D7S820, D8S1179 and FGA; 225 for D16S539 and D5S818; 224 for D18S51; 223 for CSF1PO; 222 for Penta D and vWA; 220 for Penta E; 207 for TPOX and 142 for TH01. Y-STR haplotypes were analyzed for 102 unrelated males, being 71 of them present in the 135 autosomal-STR sample, and 31 new males tested only for Y-STR markers. All autosomal markers were in Hardy–Weinberg Equilibrium. Y-STR analysis identified 101 haplotypes, being 100 of them unique.Genetic analysis of 15 autosomal and 12 Y-STR loci in the Espirito Santo State population, Brazil - Corrected ProofEldamária de Vargas Wolfgramm, Beatriz Candida Silva, Vitor Resende da Costa Aguiar, Frederico Scott Varela Malta, Amanda Mafia de Castro, Alessandro Clayton de Souza Ferreira, Alessandra Nunes Loureiro Prezoti, Flavia de Paula, Iúri Drumond Louro10.1016/j.fsigen.2010.05.001Forensic Science International: Genetics (2010)2010-06-07Forensic Science International: Genetics2010-06-07FORENSIC POPULATION GENETICS—SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310000827/abstract?rss=yesAbstract: In cases of sexual assault where sperm are not present, preferential lysis fails to yield the DNA profile of the assailant. The Forensic Science Service® has developed a technique combining fluorescence in situ hybridisation and laser microdissection to enable the identification and isolation of male cells that may be present in azoospermic semen on vaginal swabs from victims of sexual assault. This technique has been used successfully by The Forensic Science Service® in a sexual assault case providing evidence for the assertion that the suspect had vaginal intercourse with the victim rather than he had not.The use of fluorescence in situ hybridisation and laser microdissection to identify and isolate male cells in an azoospermic sexual assault case - Corrected ProofColin McAlister10.1016/j.fsigen.2010.04.008Forensic Science International: Genetics (2010)2010-06-02Forensic Science International: Genetics2010-06-02CASE REPORThttp://www.fsigenetics.com/article/PIIS1872497310000815/abstract?rss=yesAbstract: Gelao ethnic group, an aboriginal population residing in southwest China, has undergone a long and complex evolutionary process. To investigate the genetic structure of this ancient ethnic group, mitochondrial DNA (mtDNA) polymorphisms of 102 Gelao individuals were collected and analyzed in this study. With the aid of the information extracted from control-region hypervariable segments (HVSs) I and II as well as some necessary coding-region segments, phylogenetic status of all mtDNAs under study were determined by means of classifying into various defined haplogroups. The southern-prevalent haplogroups B, R9, and M7 account for 45.1% of the gene pool, whereas northern-prevalent haplogroups A, D, G, N9, and M8 consist of 39.2%. Haplogroup distribution indicates that the Gelao bears signatures of southern populations and possesses some regional characters. In the PC map, Gelao clusters together with populations with Bai-Yue tribe origin as well as the local Han and the Miao. The results demonstrate the complexity of Gelao population and the data can well supplement the China mtDNA database.Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China - Corrected ProofChang Liu, Sha-Yan Wang, Mian Zhao, Zhi-Yong Xu, Yu-Hua Hu, Feng Chen, Ruan-Zhang Zhang, Guo-Feng Gao, Yue-Sheng Yu, Qing-Peng Kong10.1016/j.fsigen.2010.04.007Forensic Science International: Genetics (2010)2010-05-24Forensic Science International: Genetics2010-05-24FORENSIC POPULATION GENETICS—SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310000785/abstract?rss=yesAbstract: Objective: To genotype X-linked single nucleotide polymorphisms by TaqMan® SNP genotyping assay.Methods: 14 SNP markers on X chromosome were selected and genotyped by TaqMan® SNP genotyping assay in Chinese Han population samples.Results: According to the results of population studies, deviations from Hardy–Weinberg equilibrium could be found at rs1299087 SNP loci, no deviations from Hardy–Weinberg equilibrium could be found at the other 13 SNP loci. The 14 X-SNPs were high informative. The overall power of discrimination (CPD) in females and in males were 0.999998379 and 0.999899, respectively. The combined exclusion probability in paternity testing for trios and duos were 0.9983 and 0.9788, respectively.Conclusion: SNP typing by TaqMan® SNP genotyping assay is suitable for low-throughput application. The forensic efficiency parameters showed that the 14 X-linked SNPs are highly informative and seem to be useful for forensic genetics except rs1299087.Analysis of 14 highly informative SNP markers on X chromosome by TaqMan® SNP genotyping assay - Corrected ProofLi Li, Chengtao Li, Suhua Zhang, Shumin Zhao, Yan Liu, Yuan Lin10.1016/j.fsigen.2010.04.004Forensic Science International: Genetics (2010)2010-05-21Forensic Science International: Genetics2010-05-21FORENSIC POPULATION GENETICS - SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310000797/abstract?rss=yesAbstract: We propose to quantify the accuracy of a likelihood-based estimator that was recently proposed for the determination of the number of contributors to a DNA mixture, when genetic data alone is considered [H. Haned, L. Pène, J.R. Lobry, A.B. Dufour, D. Pontier, Estimating the number of contributors to forensic DNA mixtures: does maximum likelihood perform better than maximum allele count? J. Forensic Sci., in press]. Using Bayes’ theorem, we derive a formula for the calculation of the predictive value (PV) of the likelihood-based estimator. The PV gives the probability that a DNA stain contains the DNAs of i people given that the maximum likelihood estimator gave an estimate of i contributors for this stain. We illustrate the PV calculations for two different types of DNA evidence: traces and body fluids.The PV varied according to the number of contributors involved in the DNA stain. Setting the maximum number of possible contributors to five, the lowest predictive values were scored for five-person mixtures with a minimum value of 0.26 for traces, but values were always above 0.94 for stains comprising one, two or three contributors, for both traces and body fluids. Values remained relatively high for four-person mixtures with a minimum value of 0.69. These findings confirm that likelihood-maximization is a powerful approach for the determination of the number of contributors to forensic DNA mixtures.The predictive value of the maximum likelihood estimator of the number of contributors to a DNA mixture - Corrected ProofH. Haned, L. Pène, F. Sauvage, D. Pontier10.1016/j.fsigen.2010.04.005Forensic Science International: Genetics (2010)2010-05-20Forensic Science International: Genetics2010-05-20ORIGINAL RESEARCH PAPERhttp://www.fsigenetics.com/article/PIIS1872497310000803/abstract?rss=yesThe gender marker amelogenin is incorporated in almost all commercially available multiplex STR kits. It is widely used in forensic casework, DNA databasing, blood sample storage, for prenatal sex determination and in pre-implantation genetic diagnosis. As shown by several publications amplification of the homologous amelogenin part on the X and Y chromosome using these STR kits is not fully reliable and sometimes fails for different reasons, either due to translocation or deletion events or due to mutations in the amelogenin primer binding site. During routine paternity testing in our laboratories we observed two cases of amelogenin Y negative males. Further investigations revealed one XX male and a XY father son pair with a failure to amplify the homologous amelogenin part on the Y chromosome. Wrong sex determinations can result in misinterpretations and their forensic relevance should not be underestimated .A molecular analysis of three amelogenin negative males in two routine paternity tests - Corrected ProofKarl Zehethofer, Burkhard Rolf10.1016/j.fsigen.2010.04.006Forensic Science International: Genetics (2010)2010-05-20Forensic Science International: Genetics2010-05-20LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310000657/abstract?rss=yesAbstract: This paper presents a coherent probabilistic framework for taking account of allelic dropout, stutter bands and silent alleles when interpreting STR DNA profiles from a mixture sample using peak size information arising from a PCR analysis. This information can be exploited for evaluating the evidential strength for a hypothesis that DNA from a particular person is present in the mixture. It extends an earlier Bayesian network approach that ignored such artifacts. We illustrate the use of the extended network on a published casework example.Probabilistic expert systems for handling artifacts in complex DNA mixtures - Corrected ProofR.G. Cowell, S.L. Lauritzen, J. Mortera10.1016/j.fsigen.2010.03.008Forensic Science International: Genetics (2010)2010-05-10Forensic Science International: Genetics2010-05-10http://www.fsigenetics.com/article/PIIS1872497310000761/abstract?rss=yesAbstract: A review recently published in this journal on the future of single nucleotide polymorphisms (SNPs) in the forensic field raised important points, some of which deserve further analysis. A contribution to the discussion of relevant theoretical, methodological and technological aspects, as well as of some legal constraints is presented.A comment on “The hare and the tortoise: One small step for four SNPs, one giant leap for SNP-kind” - Corrected ProofAntónio Amorim10.1016/j.fsigen.2010.04.002Forensic Science International: Genetics (2010)2010-05-10Forensic Science International: Genetics2010-05-10COMMENTARYhttp://www.fsigenetics.com/article/PIIS1872497310000773/abstract?rss=yesAbstract: The possibility of introducing new sequencing technologies into forensic genetics raises questions that go beyond the choice between SNPs and STRs as the preferred genetic markers. We suggest that many of the novel methodological and technical issues could be incorporated into the likelihood ratio frameworks currently used by forensic scientists. However, changes to ethical and legal structures may be needed before the new information could be used.Response to the comment on “The hare and the tortoise: One small step for four SNPs, one giant leap for SNP-kind” - Corrected ProofYali Xue, Chris Tyler-Smith10.1016/j.fsigen.2010.04.003Forensic Science International: Genetics (2010)2010-05-10Forensic Science International: Genetics2010-05-10DISCUSSIONhttp://www.fsigenetics.com/article/PIIS1872497310000748/abstract?rss=yesAbstract: Forensim is a new package for the R statistical software that is dedicated to forensic DNA evidence interpretation. As far as we know, forensim is the first open-source tool that allows for the simulation of data encountered in forensic genetics studies. The package also implements common statistical methods used for reporting the weight of DNA evidence. Forensim is written in the R language and is freely available from http://forensim.r-forge.r-project.org. This paper presents an overview of the software's functionalities.Forensim: An open-source initiative for the evaluation of statistical methods in forensic genetics - Corrected ProofHinda Haned10.1016/j.fsigen.2010.03.017Forensic Science International: Genetics (2010)2010-05-06Forensic Science International: Genetics2010-05-06http://www.fsigenetics.com/article/PIIS187249731000075X/abstract?rss=yesAbstract: Inadequate sample quantities and qualities can commonly result in poor DNA amplification success rates for forensic case samples. In some instances, modifying the PCR protocol or components may assist profiling by overcoming inhibition, or reducing the threshold required for successful amplification and detection. Incorporation of locked nucleic acids (LNAs) into PCR primers has previously been shown to increase amplification success for a range of non-forensic sample types and applications. To investigate their use in a forensic context, the PCR primers for four commonly used STR loci have been redesigned to include LNA bases. The modified LNA primers provided significantly increased amplification success when compared to standard DNA primers, with both high-quality buccal samples and simulated forensic casework samples. Peak heights increased by as much as 5.75× for the singleplex amplifications. When incorporated into multiplexes, the LNA primers continued to outperform standard DNA primers, with increased ease of optimisation, and increased amplification success. The use of LNAs in PCR primers can greatly assist the profiling of a range of samples, and increase success rates from challenging forensic samples.Increased amplification success from forensic samples with locked nucleic acids - Corrected ProofKaye N. Ballantyne, Roland A.H. van Oorschot, R. John Mitchell10.1016/j.fsigen.2010.04.001Forensic Science International: Genetics (2010)2010-05-05Forensic Science International: Genetics2010-05-05http://www.fsigenetics.com/article/PIIS1872497310000682/abstract?rss=yesRecently Budowle et al. published an article entitled “Low copy number has yet to achieve “general acceptance.” This article is not peer reviewed. The proceedings of the ISFG Congress are prefaced by the message: “the manuscripts were neither reviewed nor edited in detail…The articles reflect the opinions of the authors.” It contains neither new data nor any novel scientific findings. Rather it represents public advocacy and is an expression of alternative opinion by the three authors concerning observations that are largely common ground. There is a place in the scientific literature for advocacy but it must be soundly based on proven facts.Further Comment on “Low copy number typing has yet to achieve “general acceptance”” by Budowle, B., et al, 2009. Forensic Sci. Int. Genetics: Supplement Series 2, 551–552 - Corrected ProofJohn Buckleton, Peter Gill10.1016/j.fsigen.2010.03.011Forensic Science International: Genetics (2010)2010-05-03Forensic Science International: Genetics2010-05-03DISCUSSIONhttp://www.fsigenetics.com/article/PIIS1872497310000724/abstract?rss=yesBruce Budowle, Arthur Eisenberg, and Angela van Daal recently authored an article entitled “Low Copy Number typing has yet to achieve ‘general acceptance”’ . We have concerns about both the title and the content of this article.Comment on “Low copy number typing has yet to achieve “general acceptance”” by Budowle, B., et al., 2009. Forensic Sci. Int. Genetics: Supplement Series 2, 551–552 - Corrected ProofTheresa Caragine, Mechthild Prinz10.1016/j.fsigen.2010.03.015Forensic Science International: Genetics (2010)2010-05-03Forensic Science International: Genetics2010-05-03DISCUSSIONhttp://www.fsigenetics.com/article/PIIS1872497310000645/abstract?rss=yesAbstract: The forensic use of Y-chromosomal markers can be hampered by reduced diversity and geographical subdivision in some populations. In Finland both of these confounding factors are well documented, but it is also shown that increase of data could resolve or at least alleviate these problems. In order to increase the forensic usability of Y-chromosomal data in Finland, we have here evaluated the diversity at a number of additional Y-STRs. A seven Y-STR locus panel (“FY7”: DYS449, DYS460, DYS505, DYS522, DYS576, DYS612 and DYS627) was found to reveal higher diversity levels among Finns than the substantially larger commercial multiplexes commonly in use. The Y-STR data augmented with the FY7 panel shows substantially higher discrimination capacity and lower levels of geographical structure among Finns. Amplifiable in one multiplex, this set of loci offers an informative and easy-to-use supplementary for the commercial Y-STR kits.Dissecting the Finnish male uniformity: The value of additional Y-STR loci - Corrected ProofM. Hedman, A.M. Neuvonen, A. Sajantila, J.U. Palo10.1016/j.fsigen.2010.03.007Forensic Science International: Genetics (2010)2010-04-30Forensic Science International: Genetics2010-04-30http://www.fsigenetics.com/article/PIIS1872497310000694/abstract?rss=yesGill and Buckleton, in their opinion article , say they “hope that our response has now clarified and will now end the so-called LCN ‘debate’.” Their response has not ended our concerns and we disagree with much of what they attempt to argue to justify avoiding the vagaries of LCN typing. Since these same arguments were also raised recently by Gill and Buckleton , instead of repeating the concerns we have we refer the readers to our response . This “debate” on LCN typing should continue until there are valid methods for interpreting and placing meaningful statistical weight on evidentiary results, and inherent biases are reduced (and if possible eliminated). We now know that the Forensic Science Service (FSS), for example, does not follow the often cited Gill et al. article (written by FSS employees) for statistical assessment of LCN evidence even a decade after its publication. The forensic science community does not know what the practices of LCN laboratories are and whether they are valid and reliable. Again we call for openness by these authors and in the case of Buckleton, who currently is employed by a LCN service laboratory (ESR), to provide his laboratory's protocols for LCN typing and interpretation and statistical analysis of LCN results. Gill and Buckleton end their opinion article with “LCN or LT-DNA is not a method or technique, it is a way of thinking.” LCN typing is not a way of thinking; it is an analytical tool with reproducibility issues that must be considered and properly addressed.Comment on “A universal strategy to interpret DNA profiles that does not require a definition of low copy number” by Peter Gill and John Buckleton, 2010, Forensic Sci. Int. Genetics 4, 221–227 - Corrected ProofBruce Budowle, Angela van Daal10.1016/j.fsigen.2010.03.012Forensic Science International: Genetics (2010)2010-04-30Forensic Science International: Genetics2010-04-30DISCUSSIONhttp://www.fsigenetics.com/article/PIIS1872497310000591/abstract?rss=yesAbstract: The goal of this paper was to examine and compare two different commercially available approaches to the determination of the relative quantities of autosomal and Y chromosomal DNA using real-time PCR. One, Quantifiler® Duo, utilizes a TaqMan® assay with single copy probes for both autosomal human and Y quantification. The other method, Plexor HY® utilizes a primer quenching assay with multi-copy probes for its quantification of autosomal human and Y chromosomal DNA. To test these approaches we have utilized the NIST Human DNA Quantitation Standard Reference Material 2372, a set of three different NIST human DNA quantification standards, to examine the precision, accuracy and sensitivity of the real-time PCR assays. We also examined data from both systems utilizing casework samples. The results show that both systems produced linear estimates for DNA quantity over a broad range of input DNA. However we did observe some apparent copy number effects when comparing the three different NIST standards which we attributed to issues with sequence variations in the different standards. Overall, the single copy approach provided better accuracy while the multi-copy approach produced better sensitivity. Thus the choice of which system to use should depend upon the goals of the user.An analysis of single and multi-copy methods for DNA quantitation by real-time polymerase chain reaction - Corrected ProofHeather E. LaSalle, George Duncan, Bruce McCord10.1016/j.fsigen.2010.03.002Forensic Science International: Genetics (2010)2010-04-26Forensic Science International: Genetics2010-04-26http://www.fsigenetics.com/article/PIIS1872497310000700/abstract?rss=yesAbstract: Allele frequencies for 10 short tandem repeats (STRs) were determined using the StockMarks® Dog Genotyping Kit (Applied Biosystems) from a pool of 668 unrelated dogs, consisting of 79 different breeds or breed variants from the Hungarian canine population. For the comparative statistical analysis, four pure bred, one mixed group – all individuals except from the four breeds – and considering to unequal representation of breeds the group of all pooled individuals (“All breeds”) were distinguished. The forensically informative values – Hardy–Weinberg equilibrium (HWE), observed heterozygosity (Hobs), polymorphism information content (PIC), power of discrimination (PD), power of paternity exclusion (PE), linkage disequilibrium (LD) and fixation index (F) were determined. The Hungarian pure bred dog populations could be distinguished by comparing the allele frequency values using G-statistics and calculating the FST indices with pair-wise comparisons of inter-population molecular variance (AMOVA). The results showed that these 10 loci can be adequate for individual identification in forensic cases even in relatively inbred dog populations.Population genetic study in Hungarian canine populations using forensically informative STR loci - Corrected ProofP. Zenke, B. Egyed, L. Zöldág, Z. Pádár10.1016/j.fsigen.2010.03.013Forensic Science International: Genetics (2010)2010-04-26Forensic Science International: Genetics2010-04-26ANNOUNCEMENT OF POPULATION DATAhttp://www.fsigenetics.com/article/PIIS1872497310000712/abstract?rss=yesAbstract: The PowerPlex® ESX 17 and ESI 17 Systems for short tandem repeat (STR) amplification were developed by the Promega Corporation to meet the European Network of Forensic Science Institutes (ENFSI) and the European DNA Profiling (EDNAP) Group recommendations for increasing the number of STR loci included in the European Standard Set (ESS). The PowerPlex ESX 17 and ESI 17 Systems utilize different PCR primer combinations to co-amplify the following 17 loci: D1S1656, D2S441, D2S1338, D3S1358, D8S1179, D10S1248, D12S391, D16S539, D18S51, D19S433, D21S11, D22S1045, FGA, TH01, vWA, SE33, and the sex-typing locus amelogenin. A total of 1443 U.S. population samples were evaluated with pre-commercialization versions of both kits. Stutter and heterozygote peak height ratios have been used to characterize kit performance. Typing results have been used to estimate the match probabilities provided by the chosen loci as well as in concordance studies. Full concordance between the typing results for the two kits was observed in 99.994% (49,055 out of 49,062) STR allele calls compared. All genotyping discrepancies were confirmed by DNA sequence analysis. As a result of these comparisons, a second forward primer for the D22S1045 locus has been added to the PowerPlex ESX 17 System to address a primer binding site mutation and the D1S1656 locus reverse primer in the PowerPlex ESI 17 System was modified to eliminate an amplification-efficiency reducing primer dimer.Concordance and population studies along with stutter and peak height ratio analysis for the PowerPlex® ESX 17 and ESI 17 Systems - Corrected ProofCarolyn R. Hill, David L. Duewer, Margaret C. Kline, Cynthia J. Sprecher, Robert S. McLaren, Dawn R. Rabbach, Benjamin E. Krenke, Martin G. Ensenberger, Patricia M. Fulmer, Douglas R. Storts, John M. Butler10.1016/j.fsigen.2010.03.014Forensic Science International: Genetics (2010)2010-04-23Forensic Science International: Genetics2010-04-23http://www.fsigenetics.com/article/PIIS187249731000061X/abstract?rss=yesAbstract: The interest of forensic researchers in single nucleotide polymorphism (SNP) has been attracted because of its potential advantages, such as low mutation rates, amenable to high-throughput automated platform and the improved application in the analysis of degraded samples. In this article, 29 highly informative insertion/deletion (InDel) polymorphism markers were selected from the dbSNP (http://www.ncbi.nlm.nih.gov/SNP/), according to the given criteria. Allele frequencies for the 29 InDels were determined in a sample of 109 unrelated individuals living in Shanghai in East China with an SNPlex genotyping system. The values of observed heterozygosity (Ho), power of discrimination (PD), power of exclusion (PE) and polymorphism information content (PIC) were calculated. The combined power of discrimination was 0.999999999990867 and the cumulative probability of exclusion (CPE) was 0.9930. All of the 29 InDel markers were in accordance with the Hardy–Weinberg equilibrium (P>0.0017, after Bonferroni correction for multiple testing). The obtained frequency distributions were compared with other previously reported population data.Genetic polymorphism of 29 highly informative InDel markers for forensic use in the Chinese Han population - Corrected ProofChengtao Li, Shumin Zhao, Suhua Zhang, Li Li, Yan Liu, Jinzhong Chen, Jinglun Xue10.1016/j.fsigen.2010.03.004Forensic Science International: Genetics (2010)2010-04-20Forensic Science International: Genetics2010-04-20ANNOUNCEMENT OF POPULATION DATAhttp://www.fsigenetics.com/article/PIIS1872497310000633/abstract?rss=yesAbstract: A set of 52 autosomal single nucleotide polymorphism (SNP) loci was analyzed in 46 unrelated individuals from the East Timor population using the forensic assay previously described by Sanchez et al. (2006) [J.J. Sanchez, C. Phillips, C. Børsting, K. Balogh, M. Bogus, M. Fondevila, C.D. Harrison, E. Musgrave-Brown, A. Salas, D. Syndercombe Court, PM. Schneider, Á. Carracedo, N. Morling, A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis 27 (2006) 1713–1724]. Allele frequencies are presented for the 52 SNPs with all loci in Hardy–Weinberg equilibrium for the study population. Comparison with African, European, East Asian and Oceanian populations of the CEPH human genome diversity panel (CEPH-HGDP) revealed significant differences in allele frequency distributions between East Timor and each of the above population groups. Statistical parameters measuring forensic informativeness were also calculated and the values obtained reached comparable levels to those previously described for the other global population groups. This is the first study of variability in these SNPs in an Oceanian population outside of the CEPH-HGDP.A study of East Timor variability using the SNPforID 52-plex SNP panel - Corrected ProofC. Santos, C. Phillips, M. Fondevila, L. Porras-Hurtado, Á. Carracedo, L. Souto, M.V. Lareu10.1016/j.fsigen.2010.03.006Forensic Science International: Genetics (2010)2010-04-20Forensic Science International: Genetics2010-04-20ANNOUNCEMENT OF POPULATION DATAhttp://www.fsigenetics.com/article/PIIS1872497310000669/abstract?rss=yesAllele frequencies and resulting statistical parameters of the five miniSTR loci D1S1656, D2S441, D10S1248, D12S391 and D22S1045 (“European recommended loci”) were obtained from a sample of 404 unrelated individuals from South Germany. No deviations from Hardy–Weinberg equilibrium were observed. Amplification was done simultaneously in a PCR-multiplex reaction with a maximum fragment size of less than 175bp. Due to the small amplicon length this multiplex is particularly suitable for the analysis of degraded DNA samples.Allele frequencies of the five miniSTR loci D1S1656, D2S441, D10S1248, D12S391 and D22S1045 in a German population sample - Corrected ProofT. Seider, R. Fimmers, P. Betz, T. Lederer10.1016/j.fsigen.2010.03.009Forensic Science International: Genetics (2010)2010-04-20Forensic Science International: Genetics2010-04-20LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310000736/abstract?rss=yesIn response to Caragine and Prinz we have held the position for many years that there are serious concerns about the application of low copy number (LCN) typing. These concerns have always been about the scientific issues related to LCN typing and are not brought on by a recent activity in the legal system as they intimate. The issues raised in Budowle et al. and other publications are about validity and reliability and such a discussion should be welcomed as part of a healthy debate by the forensic scientific community. Attempts to dismiss the discussion on LCN typing on non-scientific bases are detrimental to the forensic science field. Our hope is that by open discussion of its potential problems and limitations, and with continued research in this area, that some day LCN typing will enjoy the robustness seen with other DNA typing procedures. We address the scientific issues related to LCN typing herein, but unfortunately must also address the non-scientific issues raised by Caragine and Prinz to set the record straight. We urge the community to continue a dialogue on the validity and reliability of LCN typing focused on the science.Response to Comment on “Low copy number typing has yet to achieve “general acceptance”” (Budowle et al., 2009. Forensic Sci. Int. Genetics: Supplement Series 2, 551–552) by Theresa Caragine, Mechthild Prinz - Corrected ProofBruce Budowle, Arthur J. Eisenberg, Angela van Daal10.1016/j.fsigen.2010.03.016Forensic Science International: Genetics (2010)2010-04-20Forensic Science International: Genetics2010-04-20DISCUSSIONhttp://www.fsigenetics.com/article/PIIS1872497310000621/abstract?rss=yesAbstract: Traditionally, DNA extracts from biological evidence items have been concentrated and rinsed using microdialysis filtration units, including the Centricon® and Microcon® centrifugal filter devices. As an alternative to microdialysis filtration, we present an optimized method for using NucleoSpin® XS silica columns to concentrate and clean-up aqueous extracts from the organic extraction of DNA from biological samples. The method can be used with standard organic extraction and dithiothreitol (DTT)-based differential extraction methods with no modifications to these methods prior to the concentration and clean-up step. Extracts from laboratory-prepared bloodstains, saliva and semen stains have been successfully amplified with both qPCR and STR assays. Finally, the total time to process a set of samples with the NucleoSpin® XS column is approximately 30min vs. approximately 1.5h with the Centricon® YM-100 filter device.The NucleoSpin® DNA Clean-up XS kit for the concentration and purification of genomic DNA extracts: An alternative to microdialysis filtration - Corrected ProofWilliam R. Hudlow, Robert Krieger, Markus Meusel, Joshua C. Sehhat, Mark D. Timken, Martin R. Buoncristiani10.1016/j.fsigen.2010.03.005Forensic Science International: Genetics (2010)2010-04-16Forensic Science International: Genetics2010-04-16SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310000670/abstract?rss=yesAbstract: Angola is located in the African continent, in the area of southern Africa and has a population of approximately 14 million inhabitants. The Angola population has origin from Occidental and Southern Bantu people that came from the great lakes region, creating the most ever known African migration of our days.Allele frequencies for the 15 STRs loci in the AmpFlSTR Identifiler kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, HUMTH01, D13S317, D16S539, D2S1338, D19S433, HUMVWA, TPOX, D18S51, D5S818, HUMFIBRA/FGA and including the segment of the X-Y homologous gene amelogenin) were studied for Angola population.The genotype frequency of the 15 STR loci showed no significant deviations from Hardy–Weinberg equilibrium expectations and great values for the combined power of discrimination and combined power of a priori exclusion validate the application of these markers in forensic genetics. Comparative analyses between Angola population data and other relevant population database from Africa, Europe and American are presented.Genetic study of 15 STRs loci of Identifiler system in Angola population - Corrected ProofMiguel Manuel Melo, Mónica Carvalho, Virgínia Lopes, Maria João Anjos, Armando Serra, Duarte Nuno Vieira, Jorge Sequeiros, Francisco Corte-Real10.1016/j.fsigen.2010.03.010Forensic Science International: Genetics (2010)2010-04-16Forensic Science International: Genetics2010-04-16FORENSIC POPULATION GENETICS—LETTER TO THE EDITORhttp://www.fsigenetics.com/article/PIIS1872497310000554/abstract?rss=yesAbstract: Mitochondrial DNA (mtDNA) testing in the forensic context requires appropriate, high quality population databases for estimating the rarity of questioned haplotypes. Currently, however, available forensic mtDNA reference databases only include information from the mtDNA control region. While this information is obviously strengthening the foundation upon which current mtDNA identification efforts are based, these data do not adequately prepare the field for recent and rapid advancements in mtDNA typing technologies. Novel tools that quickly and easily permit access to mtDNA coding region data for increased discrimination are now available in the form of single nucleotide polymorphism assays, sequence specific oligonucleotide probes, mass spectrometry instrumentation and next generation sequencing technologies. However, the randomly sampled entire mtGenome reference population data required for statistical interpretation of coding region data are lacking. As a result, in the near future, it seems that routine use of mtDNA coding region data in forensic case work will depend more upon the availability of high-quality entire mtGenome population reference data than the ease with which coding region data can be generated from evidence specimens. Until mtGenome reference databases are available, the utility of novel mtDNA typing technologies and the benefits of recovering mtDNA coding region information from forensic specimens will be limited. Thus, future mtDNA databasing efforts are needed for the development of entire mtDNA genome reference population data suitable for forensic comparisons.mtGenome reference population databases and the future of forensic mtDNA analysis - Corrected ProofJodi A. Irwin, Walther Parson, Michael D. Coble, Rebecca S. Just10.1016/j.fsigen.2010.02.008Forensic Science International: Genetics (2010)2010-04-15Forensic Science International: Genetics2010-04-15SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310000608/abstract?rss=yesAbstract: Amylase testing has been used as a presumptive test for crime scene saliva for over three decades, mainly to locate saliva stains on surfaces. We have developed a saliva screening application for crime scene trace swabs, utilising an amylase sensitive paper (Phadebas® Forensic Press test). Positive results were obtained for all tested dried saliva stains (0.5–32μL) with high or intermediate amylase activity (840 and 290kU/L). Results were typically obtained within 5min, and all samples that produced DNA profiles were positive. However, salivary amylase activities, as well as DNA concentrations, vary significantly between individuals. We show that there is no correlation between amylase activity and amount of DNA in fresh saliva. Even so, a positive amylase result indicates presence of saliva, and thereby presence of DNA. Amylase testing may be useful for screening in investigations where the number of DNA analyses is limited due to cost, e.g., in volume crime.Evaluation of amylase testing as a tool for saliva screening of crime scene trace swabs - Corrected ProofJohannes Hedman, Erik Dalin, Birgitta Rasmusson, Ricky Ansell10.1016/j.fsigen.2010.03.003Forensic Science International: Genetics (2010)2010-04-09Forensic Science International: Genetics2010-04-09http://www.fsigenetics.com/article/PIIS187249731000058X/abstract?rss=yesAbstract: Illegal trade of snake skin and uncontrolled hunting have instigated the extermination of many endangered snake species. Efforts to check illegal trade are often impeded due to lack of proper species identification methods. Hence, conservation strategies demand for authentic and quick identification techniques to trace the origin of the seized samples. This study employs DNA mini-barcoding as a method to identify some endangered snake species of India. We have designed two sets of novel primers for targeting regions within the mitochondrial Cytochrome Oxidase I gene to produce 175bp and 245bp amplicons. 175bp fragment was amplified in all 11 snake species studied while the 245bp amplicon was obtained in 10 species. DNA mini-barcodes recovered from these amplicons enabled the identification of snake species by retrieving the sequences available in public databases. The similarity scores ranging from 98 to 100% (98% taken as threshold value for species identification) signify the consistency of these mini-barcodes in snake species identification. Moreover, the results of the validation study confirm the effectiveness of the technique in forensic perspective, where the diagnostic morphological features of the seized sample are often missing.DNA mini-barcoding: An approach for forensic identification of some endangered Indian snake species - Corrected ProofBhawna Dubey, P.R. Meganathan, Ikramul Haque10.1016/j.fsigen.2010.03.001Forensic Science International: Genetics (2010)2010-04-08Forensic Science International: Genetics2010-04-08http://www.fsigenetics.com/article/PIIS1872497310000207/abstract?rss=yesAbstract: This report describes a re-examination of the remains of a young male child recovered in the Northwest Atlantic following the loss of the Royal Mail Ship Titanic in 1912 and buried as an unknown in Halifax, Nova Scotia shortly thereafter. Following exhumation of the grave in 2001, mitochondrial DNA (mtDNA) hypervariable region 1 sequencing and odontological examination of the extremely limited skeletal remains resulted in the identification of the child as Eino Viljami Panula, a 13-month-old Finnish boy. This paper details recent and more extensive mitochondrial genome analyses that indicate the remains are instead most likely those of an English child, Sidney Leslie Goodwin. The case demonstrates the benefit of targeted mtDNA coding region typing in difficult forensic cases, and highlights the need for entire mtDNA sequence databases appropriate for forensic use.Titanic's unknown child: The critical role of the mitochondrial DNA coding region in a re-identification effort - Corrected ProofRebecca S. Just, Odile M. Loreille, J. Eldon Molto, D. Andrew Merriwether, Scott R. Woodward, Carney Matheson, Jennifer Creed, Stacey E. McGrath, Kimberly Sturk-Andreaggi, Michael D. Coble, Jodi A. Irwin, Alan Ruffman, Ryan L. Parr10.1016/j.fsigen.2010.01.012Forensic Science International: Genetics (2010)2010-04-05Forensic Science International: Genetics2010-04-05SHORT COMMUNICATIONhttp://www.fsigenetics.com/article/PIIS1872497310000323/abstract?rss=yesAbstract: A new era of ‘DNA intelligence’ is arriving in forensic biology, due to the impending ability to predict externally visible characteristics (EVCs) from biological material such as those found at crime scenes. EVC prediction from forensic samples, or from body parts, is expected to help concentrate police investigations towards finding unknown individuals, at times when conventional DNA profiling fails to provide informative leads. Here we present a robust and sensitive tool, termed IrisPlex, for the accurate prediction of blue and brown eye colour from DNA in future forensic applications. We used the six currently most eye colour-informative single nucleotide polymorphisms (SNPs) that previously revealed prevalence-adjusted prediction accuracies of over 90% for blue and brown eye colour in 6168 Dutch Europeans. The single multiplex assay, based on SNaPshot chemistry and capillary electrophoresis, both widely used in forensic laboratories, displays high levels of genotyping sensitivity with complete profiles generated from as little as 31pg of DNA, approximately six human diploid cell equivalents. We also present a prediction model to correctly classify an individual's eye colour, via probability estimation solely based on DNA data, and illustrate the accuracy of the developed prediction test on 40 individuals from various geographic origins. Moreover, we obtained insights into the worldwide allele distribution of these six SNPs using the HGDP-CEPH samples of 51 populations. Eye colour prediction analyses from HGDP-CEPH samples provide evidence that the test and model presented here perform reliably without prior ancestry information, although future worldwide genotype and phenotype data shall confirm this notion. As our IrisPlex eye colour prediction test is capable of immediate implementation in forensic casework, it represents one of the first steps forward in the creation of a fully individualised EVC prediction system for future use in forensic DNA intelligence.IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information - Corrected ProofSusan Walsh, Fan Liu, Kaye N. Ballantyne, Mannis van Oven, Oscar Lao, Manfred Kayser10.1016/j.fsigen.2010.02.004Forensic Science International: Genetics (2010)2010-03-29Forensic Science International: Genetics2010-03-29http://www.fsigenetics.com/article/PIIS1872497310000359/abstract?rss=yesAbstract: Six case work examples are presented, where the individuals were typed for 15 autosomal short tandem repeats (STRs) and 49 autosomal single nucleotide polymorphisms (SNPs). The 15 STRs were typed with the AmpFlSTR Identifiler PCR Amplification Kit and the 49 SNPs were typed with the SNPforID multiplex assay. The six cases included two duos, two trios and two cases, where the alleged father was not available for testing and one or two of his close relatives were tested instead. The SNP investigation was more informative than the STR investigation in all six cases. In two cases, the alleged father would have been falsely included based on the STR results, while the SNP results showed that the alleged father was not the true parent. These case work examples underline the importance of performing supplementary investigations in selected cases and demonstrate the usefulness of the SNPforID multiplex assay.Mutations and/or close relatives? Six case work examples where 49 autosomal SNPs were used as supplementary markers - Corrected ProofClaus Børsting, Niels Morling10.1016/j.fsigen.2010.02.007Forensic Science International: Genetics (2010)2010-03-19Forensic Science International: Genetics2010-03-19CASE REPORT