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.
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.
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.
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.
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.
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.
Abstract: The effect of masking on the assignment of the number of contributors is assessed for the European Standard Set of loci by simulation. The risk that a two person mixture presents as single source is assessed as 2.6×10?13, a three person mixture presents as a two person 6.7×10?4 and a four person mixture presents as a three person 0.165.
Dear Editor, The objective of an ideal species-specific PCR assay (also known as allele-specific PCR) is to always provide a positive result whenever DNA from the target species is present and a negative outcome when it is absent, even in the presence of DNA from other species . PCR primers must be designed in DNA regions where the sequence varies significantly between the target and other species, reliably excluding those that might contaminate casework samples. Under suitable PCR conditions, such primers generate a fragment that can be visualized by conventional gel or capillary electrophoresis. However, poor design of the screening method may lead either to a failure in the PCR in the presence of DNA from the target species (a false negative or Type II error) or positive PCR amplification in the absence of the target species’ DNA (false positive or Type I error). In general, an incorrectly assigned result may occur if the PCR primers are not sufficiently selective, the annealing temperature is not adequately stringent or too many amplification cycles are used in the PCR .