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An empirical investigation into the effectiveness of genetic genealogy to identify individuals in the UK
Publication date: Available online 24 February 2020Source: Forensic Science International: GeneticsAuthor(s): Jim Thomson, Tim Clayton, John Cleary, Maurice Gleeson, Debbie Kennett, Michelle Leonard, Donna Rutherford (Source: Forensic Science International: Genetics)
Source: Forensic Science International: Genetics - February 25, 2020 Category: Forensic Medicine Source Type: research

How to choose sets of ancestry informative markers: A supervised feature selection approach
Publication date: Available online 15 February 2020Source: Forensic Science International: GeneticsAuthor(s): Peter Pfaffelhuber, Franziska Grundner-Culemann, Veronika Lipphardt, Franz BaumdickerAbstractInference of the Biogeographical Ancestry (BGA) of a person or trace relies on three ingredients: (1) A reference database of DNA samples including BGA information; (2) a statistical clustering method; (3) a set of loci which segregate dependent on geographical location, i.e. a set of so-called Ancestry Informative Markers (AIMs). We used the theory of feature selection from statistical learning in order to obtain AIMsets f...
Source: Forensic Science International: Genetics - February 17, 2020 Category: Forensic Medicine Source Type: research

Attribution of non-convoluted peaks in human STR markers and its possible microbial connection
Publication date: Available online 13 February 2020Source: Forensic Science International: GeneticsAuthor(s): Hirak Ranjan Dash (Source: Forensic Science International: Genetics)
Source: Forensic Science International: Genetics - February 14, 2020 Category: Forensic Medicine Source Type: research

Spanish allele and haplotype database for 32 X-chromosome Insertion-Deletion polymorphisms
Publication date: Available online 13 February 2020Source: Forensic Science International: GeneticsAuthor(s): Cláudia Gomes, José David Quintero-Brito, Jesús Martínez-Gómez, Rui Pereira, Carlos Baeza-Richer, Mercedes Aler Gay, Laura Díez-Juárez, Sara Palomo-Díez, Ana María López-Parra, Elena Labajo, Victor José Esteban-Ramos, Bernardo Perea-Pérez, Eduardo Arroyo-PardoAbstractX-chromosome markers have been proved to be decisive both complementing and solving kinship analysis, particularly when autosomal markers are not able to produce adequate likelihood ratios between different hypothesis. On the other hand, Pe...
Source: Forensic Science International: Genetics - February 14, 2020 Category: Forensic Medicine Source Type: research

Taxonomic classification and abundance estimation using 16S and WGS—A comparison using controlled reference samples
Publication date: May 2020Source: Forensic Science International: Genetics, Volume 46Author(s): Lusine Khachatryan, Rick H. de Leeuw, Margriet E.M. Kraakman, Nikos Pappas, Marije te Raa, Hailiang Mei, Peter de Knijff, Jeroen F.J. LarosAbstractThe assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated with 16S da...
Source: Forensic Science International: Genetics - February 12, 2020 Category: Forensic Medicine Source Type: research

Epigenetic age signatures in bones
In this study, we generated genome-wide DNA methylation profiles of bone samples from 32 identified skeletal remains with an age at death ranging from 31 to 96 years. Only 12 provided more than 800 K quality-filtered CpG methylation values using Illumina’s Infinium MethylationEPIC BeadChip array. Methylation ages of the bone samples calculated using a recently developed skin & blood clock composed of 391 CpG sites were found to be very similar to their actual ages (MAD = 6.4 years). However, the low success rate in methylation profiling of bone DNA samples may prevent researchers from applying the array to this typ...
Source: Forensic Science International: Genetics - February 10, 2020 Category: Forensic Medicine Source Type: research

Taxonomic classification and abundance estimation using 16S and WGS - a comparison using controlled reference samples
Publication date: Available online 5 February 2020Source: Forensic Science International: GeneticsAuthor(s): Lusine Khachatryan, Rick H de Leeuw, Margriet E M Kraakman, Nikos Pappas, Marije te Raa, Hailiang Mei, Peter de Knijff, Jeroen F J LarosAbstractThe assessment of microbiome biodiversity is the most common application of metagenomics. While 16S sequencing remains standard procedure for taxonomic profiling of metagenomic data, a growing number of studies have clearly demonstrated biases associated with this method. By using Whole Genome Shotgun sequencing (WGS) metagenomics, most of the known restrictions associated w...
Source: Forensic Science International: Genetics - February 6, 2020 Category: Forensic Medicine Source Type: research

Paternal and maternal mutations in X-STRs: a GHEP-ISFG collaborative study
Publication date: Available online 5 February 2020Source: Forensic Science International: GeneticsAuthor(s): Nádia Pinto, Vânia Pereira, Carmen Tomas, Silvia Loiola, Elizeu F. Carvalho, Nidia Modesti, Mariana Maxzud, Valeria Marcucci, Hortensia Cano, Regina Cicarelli, Bianca Januario, Ana Bento, Pedro Brito, Germán Burgos, Elius Paz-Cruz, Laura Díez-Juárez, Silvia Vannelli, Maria de Lurdes Pontes, Gabriela Berardi, Sandra FurfuroAbstractThe GHEP-ISFG organized a collaborative study to estimate mutation rates for the markers included in the Investigator Argus X-12 QS kit (Qiagen). A total of 16 laboratories gathered da...
Source: Forensic Science International: Genetics - February 6, 2020 Category: Forensic Medicine Source Type: research

A top-down approach to DNA mixtures
We present another approach, in which we target the contributors of the mixture in the order of their contribution. With this approach the calculation time now depends on how many contributors are queried. This means that any trace can be subjected to calculations of likelihood ratios in favour of being a relatively prominent contributor, and we can choose not to query it for all its contributors, e.g., if that is computationally not feasible, or not relevant for the case. We do so without using a quantitative peak height model, i.e., we do not define a peak height distribution. Instead, we work with subprofiles derived fr...
Source: Forensic Science International: Genetics - February 6, 2020 Category: Forensic Medicine Source Type: research

Forensically relevant phylogeographic evaluation of mitogenome variation in the Basque Country
In this study we present the full mitogenome sequences of 178 autochthonous Basque individuals that were carefully selected based on their familial descent and discuss the observed phylogenetic signals in the light of earlier published findings. We confirm the presence of Basque-specific mtDNA lineages and extend the knowledge of these lineages by providing data on their distribution in comparison to other Basque and non-Basque populations. This dataset improves our understanding of the Basque mtDNA phylogeny and serves as a high-quality dataset that is provided via EMPOP for forensic genetic purposes. (Source: Forensic Sc...
Source: Forensic Science International: Genetics - February 6, 2020 Category: Forensic Medicine Source Type: research

Successful STR Amplification of Post-Blast IED Samples by Fluorescent Visualisation and Direct PCR
This study presents data to support the use of direct PCR in the analysis of IED components post-detonation. VeriFiler™ Plus generated informative profiles, containing ≥ 12 autosomal alleles, from samples touched for a maximum of 15 seconds that were then exposed to a detonation from plastic explosive placed as close as 100 mm. Of the 37 recovered touched items or fragments, 28 contained autosomal alleles from the donor with 18 (49%) presenting informative profiles that matched the DNA donor. This compared with results following STR PCR post-extraction with one of 11 post-detonation touch DNA samples being informat...
Source: Forensic Science International: Genetics - January 29, 2020 Category: Forensic Medicine Source Type: research

Does Bonferroni correction “rescue” the deviation from Hardy-Weinberg equilibrium?
In conclusion, according to the purpose of forensic population research, applying BC to HWE tests is unnecessary; rather, an unadjusted α should be used. BC does not “rescue” the deviation from HWE. To “rescue” it indeed, directly discussing the possible explanation for each departure from HWE and simply describing what has been done sequentially and why should be enough for readers to reach a reasonable conclusion even without the help of Bonferroni methods. (Source: Forensic Science International: Genetics)
Source: Forensic Science International: Genetics - January 26, 2020 Category: Forensic Medicine Source Type: research

The evaluation of seven age-related CpGs for forensic purpose in blood from Chinese Han population
In this study, seven age-related CpG (AR-CpG) sites, cg02228185 (ASPA), cg09809672 (EDARADD), cg19283806 (CCDC102B), cg04208403 (ZNF423), chr17: 44,390,358 of GRCh38/hg38 (ITGA2B), cg14361627 (KLF14), and cg06639320 (FHL2), were selected and analyzed in 310 blood samples using a multiplex methylation SNaPshot assay to evaluate the value of selected AR-CpGs in age prediction in blood from Chinese Han population. The study confirmed the correlation of all the investigated markers with human age, and the correlation of cg19283806 with age is the highest while cg04208403 is the lowest in the Chinese Han population. Two differe...
Source: Forensic Science International: Genetics - January 26, 2020 Category: Forensic Medicine Source Type: research

Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives
In this study, we selected 30 microhaplotypes from 1000 genome projects, including one non-binary SNP and other six microhaplotypes from published studies containing only binary SNPs to established a panel of microhaplotypes for paternity testing. Most microhaplotypes generated a high effective number of alleles (Ae) with the harmonic mean value of Ae of 3.91 and the arithmetic mean value of heterozygosity of 0.74, respectively. We collected 54 unrelated individuals and 53 samples from six extended families. It was noting that 13 samples from six extended families were unrelated so they were also included in unrelated indi...
Source: Forensic Science International: Genetics - January 26, 2020 Category: Forensic Medicine Source Type: research

Forensic validation of a SNP and INDEL panel for individualisation of timber from bigleaf maple (Acer macrophyllum Pursch)
Publication date: Available online 24 January 2020Source: Forensic Science International: GeneticsAuthor(s): E.E. Dormontt, D.I. Jardine, K.-J. van Dijk, B.F. Dunker, R.R.M. Dixon, V.D. Hipkins, S. Tobe, A. Linacre, A.J. LoweAbstractIllegal logging is one of the largest illicit trades in the world, with high profits and generally low risks of detection and prosecution. Timber identification presents problems for law enforcement as traditionally used forensic methods such as wood anatomy and dendrochronology are often unable to confidently match wood evidence to the remains of illegally felled trees. Here we have developed ...
Source: Forensic Science International: Genetics - January 26, 2020 Category: Forensic Medicine Source Type: research