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TOP STORY OF THE MONTH (April, 2014)

Wed April 23, 14

Collaborative EDNAP exercise on the IrisPlex system for DNA-based prediction of human eye colour - Accepted Manuscript - Forensic article feed - RSS
Highlights: Abstract: The IrisPlex system is a DNA-based test system for the prediction of human eye colour from biological samples and consists of a single forensically validated multiplex genotyping assay together with a statistical prediction model that is based on genotypes and phenotypes from thousands of individuals. IrisPlex predicts blue and brown human eye colour with, on average,>94% precision accuracy using six of the currently most eye colour informative single nucleotide polymorphisms (HERC2 rs12913832, OCA2 rs1800407, SLC24A4 rs12896399, SLC45A2 (MATP) rs16891982, TYR rs1393350, and IRF4 rs12203592) according to a previous study, while the accuracy in predicting non-blue and non-brown eye colours is considerably lower. In an effort to vigorously assess the IrisPlex system at the international level, testing was performed by 21 laboratories in the context of a collaborative exercise divided into three tasks and organized by the European DNA Profiling (EDNAP) Group of the International Society of Forensic Genetics (ISFG). Task 1 involved the assessment of 10 blood and saliva samples provided on FTA cards by the organising laboratory together with eye colour phenotypes; 99.4% of the genotypes were correctly reported and 99% of the eye colour phenotypes were correctly predicted. Task 2 involved the assessment of 5 DNA samples extracted by the host laboratory from simulated casework samples, artificially degraded, and provided to the participants in varying DNA concentrations. For this task, 98.7% of the genotypes were correctly determined and 96.2% of eye colour phenotypes were correctly inferred. For Tasks 1 and 2 together, 99.2% (1875) of the 1890 genotypes were correctly generated and of the 15 (0.8%) incorrect genotype calls, only 2 (0.1%) resulted in incorrect eye colour phenotypes. The voluntary Task 3 involved participants choosing their own test subjects for IrisPlex genotyping and eye colour phenotype inference, while eye photographs were provided to the organising laboratory and judged; 96% of the eye colour phenotypes were inferred correctly across 100 samples and 19 laboratories. The high success rates in genotyping and eye colour phenotyping clearly demonstrate the reproducibility and the robustness of the IrisPlex assay as well as the accuracy of the IrisPlex model to predict blue and brown eye colourfrom DNA. Additionally, this study demonstrates the ease with which the IrisPlex system is implementable and applicable across forensic laboratories around the world with varying pre-existing experiences.
Mon April 21, 14

Evidential evaluation of DNA profiles using a discrete statistical model implemented in the DNA LiRa software - Accepted Manuscript - Forensic article feed - RSS
Abstract: The high sensitivity of the technology for producing profiles means that it has become routine to produce profiles from relatively small quantities of DNA. The profiles obtained from low template DNA (LTDNA) are affected by several phenomena which must be taken into consideration when interpreting and evaluating this evidence. Furthermore, many of the same phenomena affect profiles from higher amounts of DNA (e.g. where complex mixtures has been revealed). In this article we present a statistical model, which forms the basis of software DNA LiRa, and that is able to calculate likelihood ratios where one to four donors are postulated and for any number of replicates. The model can take into account dropin and allelic dropout for different contributors, template degradation and uncertain allele designations. In this statistical model unknown parameters are treated following the Empirical Bayesian paradigm. The performance of LiRa is tested using examples and the outputs are compared with those generated using two other statistical software packages likeLTD and LRmix. The concept of ban efficiency is introduced as a measure for assessing model sensitivity.
Fri April 18, 14

Analysis of allelic drop-out using the Identifiler ® and PowerPlex® 16 forensic STR typing systems - Accepted Manuscript - Forensic article feed - RSS
Highlights: Abstract: Low-template (LT) DNA profiles continue to present interpretational challenges to the forensic community. Whether the LT contribution comprises the main profile, or whether it is present as the minor component of a mixture, ambiguity arises from the possibility that alleles present in the biological sample may not be detected in the resulting DNA profile. This phenomenon is known as allelic drop-out. This ambiguity complicates both the assessment of the potential number of contributors and estimation of the weight of the DNA evidence for or against specific propositions. One solution to estimating the weight of the evidence is to use a likelihood ratio (LR) that incorporates the probability of allelic drop-out P(DO) estimated for the specific evidence sample under consideration. However, although a vast repository of data exists, few empirical studies to determine allelic drop-out probabilities have been performed to date. Here we characterized patterns of allelic drop-out in single-source samples using both universal and run-specific analytical thresholds. Not surprisingly, we found fewer instances of apparent drop-out when using a lower (run-specific) detection threshold. Also, unsurprisingly, a positive correlation exists between allele drop-out and allele length, even in good quality samples. We used logistic regression to model the fraction of alleles that dropped out of a profile as a function of the average height of the detected peaks. The equation derived from the logistic regression model allowed us to estimate the expected drop-out probability for an evidentiary sample based on the average peak height of the profile. We show that the LRs calculated using the estimated drop-out probabilities were similar to those calculated using the benchmark drop-out probabilities, suggesting that the estimates of the drop-out probability are accurate and useful. This trend holds even when using the data from the PowerPlex ® 16 typing system to estimate the drop-out probability for an Identifiler ® profile, and vice versa. Thus we demonstrate that use of a LR that incorporates empirically estimated allelic drop-out probabilities provides a reliable means for extracting additional information from LT forensic DNA profiles.

Concordance study and population frequencies for 16 autosomal STRs analyzed with PowerPlex® ESI 17 and AmpF?STR® NGMSelect™ in Somalis, Danes and Greenlanders - Accepted Manuscript - Forensic article feed - RSS
Highlights: Abstract: A concordance study of the results of PowerPlex® ESI 17 and AmpF?STR® NGMSelect™ kits obtained from 591 individuals from Somalia (N=198), Denmark (N=199) and Greenland (N=194) was performed. Among 9,456 STR types, seven discordant results were found with the two kits: one observed in the D19S433 system in an individual from Denmark and six in the SE33 system in six individuals from Somalia. Sequencing of SE33 in the six samples with discordant results, showed G>A transition 15bp downstream of the repeat unit in three of the individuals, and G>A transition 68bp downstream of the repeat unit in the other three individuals. Population data for 16 autosomal STR systems analyzed in 989 individuals from Somalia, Denmark and Greenland are also presented. The highest mean heterozygosity was observed in Danes (82.5%). With the exception of D8S1179 in Danes, no significant deviations from Hardy-Weinberg expectations were observed. Only one pair of systems (D12S391 and D18S51) showed significant allelic association in Greenlanders (after Holm- Šidák correction). A MDS plot drawn from pairwise FST values calculated between 21 populations showed a clear displacement of the Greenlandic population versus the other ones included in the analyses. The highest combined chance of exclusion and power of discrimination was observed for Danes reaching values of 99.9999987% and 1 in 1.8×1021, respectively.
Mon April 14, 14

Cluster analysis of European Y-chromosomal STR haplotypes using the discrete Laplace method - Accepted Manuscript - Forensic article feed - RSS
Highlights: Abstract: The European Y-chromosomal short tandem repeat (STR) haplotype distribution has previously been analysed in various ways. Here, we introduce a new way of analysing population substructure using a new method based on clustering within the discrete Laplace exponential family that models the probability distribution of the Y-STR haplotypes. Creating a consistent statistical model of the haplotypes enables us to perform a wide range of analyses. Previously, haplotype frequency estimation using the discrete Laplace method has been validated. In this paper we investigate how the discrete Laplace method can be used for cluster analysis to further validate the discrete Laplace method. A very important practical fact is that the calculations can be performed on a normal computer.We identified two sub-clusters of the Eastern and Western European Y-STR haplotypes similar to results of previous studies. We also compared pairwise distances (between geographically separated samples) with those obtained using the AMOVA method and found good agreement. Further analyses that are impossible with AMOVA were made using the discrete Laplace method: analysis of the homogeneity in two different ways and calculating marginal STR distributions. We found that the Y-STR haplotypes from e.g. Finland were relatively homogeneous as opposed to the relatively heterogeneous Y-STR haplotypes from e.g. Lublin, Eastern Poland and Berlin, Germany. We demonstrated that the observed distributions of alleles at each locus were similar to the expected ones.We also compared pairwise distances between geographically separated samples from Africa with those obtained using the AMOVA method and found good agreement.

Population genetics of 30 insertion–deletion polymorphisms in two Chinese populations using Qiagen Investigator® DIPplex kit - Accepted Manuscript - Forensic article feed - RSS
Abstract: Insertion-deletion polymorphisms (INDELs) are short length diallelic polymorphisms caused by the insertion or deletion of several bases. INDEL markers can serve as useful supplementary or stand-alone assays for human identification. The Qiagen Investigator® DIPplex kit multiplexes 30 autosomal INDELs plus Amelogenin for forensic use. The objective of this study was to estimate genetic diversity of 30 INDEL markers in the Han (the largest ethnic group of China, n=565) and She population (almost the smallest ethnic group of China, n=119), and to evaluate their usefulness in forensic genetics. In the Han and She, the mean observed heterozygosity values were 0.4133 and 0.3896, and the combined matching probability values were 1.80×10?11 and 3.17×10?11, respectively. Furthermore, the allele frequencies for each locus were compared with those in other reported Chinese subpopulations, and the forensic efficacy was compared between this kit and in-house developed INDEL assay. This study demonstrates that the Investigator® DIPplex kit can be used as a supplementary tool for human identity testing in China.

A substantially lower frequency of uninformative matches between 23 versus 17 Y-STR haplotypes in north western Europe - Accepted Manuscript - Forensic article feed - RSS
Abstract: The analysis of human short tandem repeats of the Y-chromosome (Y-STRs) provides a powerful tool in forensic cases for male sex identification, male lineage identification and identification of the geographical origin of male lineages. As the commonly used 12 and 17 Y-STR multiplexes do not discriminate between some unrelated males, additional Y-STRs were implemented in the PowerPlex® Y23 System to supplement the existing commercial Y-STR kits. Until today, the forensic value of a (near) 23 versus 17 Y-STR haplotype match between an unknown DNA donor and a certain biological sample in a database is not yet well studied. This will be of huge interest for cases where an autosomal DNA profile yields no match to a DNA database and the database is used for familial searching (male relative(s) of the offender) or for the estimation of the geographical origin of the offender. In order to value (near) 23 Y-STR haplotype matches in a local sample from Western Europe, we selected the region of Flanders (Belgium) due to the already present knowledge on its Y-chromosomal variants. Many Y-chromosomes of this region were previously genotyped with Y-SNPs at a high resolution of the most recently updated Y-chromosomal tree and the deep-rooted genealogy of each DNA donor was already established. By comparing (near) matches of 23 versus 17 Y-STR haplotypes between patrilineal-unrelated males, a substantial lower number of uninformative (near) 23 Y-STR haplotype matches has been observed compared to 17 Y-STR haplotypes. Furthermore, the use of SNP data was informative to discriminate >60% of unrelated males with an (near) identical 17 Y-STR match while SNP data was only necessary to discriminate about 10% of unrelated males with a 23 Y-STR haplotype that differed at only two Y-STRs. This shows the higher value of the Y23 haplotype within familial DNA searching and the estimation of the geographical origin of a DNA donor. Therefore, the use of the PowerPlex® Y23 System instead of the commonly used 12 and 17 Y-STRs by the forensic community is recommended as it will increase the efficiency of Y-STRs in forensic casework.
Thu April 10, 14

Population data of 16 autosomal STR loci of the Powerplex ESX 17 System in a Brazilian Population from the State of São Paulo - Accepted Manuscript - Forensic article feed - RSS
Abstract: The State of São Paulo is the most populous state in Brazil, including approximately one fifth of the population of the country. In addition to a strong economy, the state has relatively good social indicators when compared with the rest of the country. The capital city, also called São Paulo, is the sixth largest city in the world. Its population is considered the most multicultural and racially mixed in Brazil. Currently, the largest populations in São Paulo are of Italian, Lebanese, Spanish and Japanese origin, and the state has the largest number of Northeasterners outside of the Northeast region. This population structure may lead to a particular genotype frequency. In this context, the formation of a new database containing the allele frequencies of five new genetic markers (D2S441, D10S1248, D22S1045, D1S1656 and D12S391) in a sample population is relevant.The allele frequencies of 16 STR loci, including the five new European Standard Set (ESS) loci, were calculated in a sample of 1088-1098 unrelated individuals, who geographically represent the Capital city.
Tue April 8, 14

Massively parallel pyrosequencing 454 methodology of the mitochondrial genome in forensic genetics - Accepted Manuscript - Forensic article feed - RSS
Highlights: Abstract: Sequencing of the mitochondrial genome using Sanger sequencing has for many years been the golden standard in forensic genetics and the method has undergone extensive validations. With the introduction of the second generation sequencing platforms, the forensic community needs to understand and validate these new technologies in order to provide valid and high quality results. We carried out a range of different experiment investigating the performance of the second generations system (SGS) 454 from Roche comparing mtDNA sequencing results to those of Sanger sequencing, the ability to sequence homopolymer regions, ability to detect mixtures (heteroplasmy), ability to reproduce results and what depth of coverage (DOC) to aim for. We found close to full concordance between the mtDNA sequences of 26 samples (compromising 72,942 sites) sequenced with both Sanger and 454 sequencing using a DOC>100. However, manual interpretation of the sequencing results was needed to avoid mapping artefacts. We found full reproducibility between samples sequenced twice. When sequencing homopolymeric regions, the 454 sequencing was able to sequence 95% of the reads correctly in homopolymers up to 4 bases; up to 5-6 bases could also be sequenced with careful inspection of the alignment data. We found that the 454 technology was able to detect mixtures above 10%. We detected unreported heteroplasmy in the GM9947A component of the NIST SRM-2392 standard. However, the correlation between the observed heteroplasmy and expected heteroplasmy is not strong.

Stochastic Sampling Effects in STR Typing: Implications for Analysis and Interpretation - Accepted Manuscript - Forensic article feed - RSS
Highlights: Abstract: The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increasedstochastic effects. These effects are typically observed as reducedheterozygous peak-height balance and increased frequency of undetected alleles (allelic “dropout”). To investigate the origins of these effects, a study was performed using the AmpFlSTR® Identifiler Plus® and MiniFiler® kits to amplify replicates from a dilution series of NIST human DNA quantitation standard (SRM® 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies.
Last updated : Thu April 24, 14 - 03:00:01




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