The interpretation of short tandem repeat (STR) profiles can be challenging when, for example, alleles are masked due to allele sharing among contributors and/or when they are subject to drop-out,... Show moreThe interpretation of short tandem repeat (STR) profiles can be challenging when, for example, alleles are masked due to allele sharing among contributors and/or when they are subject to drop-out, for instance from sample degradation. Mixture interpretation can be improved by increasing the number of STRs and/or loci with a higher discriminatory power. Both capillary electrophoresis (CE, 6-dye) and massively parallel sequencing (MPS) provide a platform for analysing relatively large numbers of autosomal STRs. In addition, MPS enables distinguishing between sequence variants, resulting in enlarged discriminatory power. Also, MPS allows for small amplicon sizes for all loci as spacing is not an issue, which is beneficial with degraded DNA. Altogether, MPS has the potential to increase the weights of evidence for true contributors to (complex) DNA profiles. In this study, likelihood ratio (LR) calculations were performed using STR profiles obtained with two different MPS systems and analysed using different settings: 1) MPS PowerSeqTM Auto System profiles analysed using FDSTools equipped with optimized settings such as noise correction, 2) ForenSeqTM DNA Signature Prep Kit profiles analysed using the default settings in the Universal Analysis Software (UAS), and 3) ForenSeqTM DNA Signature Prep Kit profiles analysed using FDSTools empirically adapted to cope with one-directional reads and provisional, basic settings. The LR calculations used genotyping data for two- to four-person mixtures varying for mixture proportion, level of drop-out and allele sharing and were generated with the continuous model EuroForMix. The LR results for the over 2000 sets of propositions were affected by the variation for the number of markers and analysis settings used in the three approaches. Nevertheless, trends for true and non-contributors, effects of replicates, assigned number of contributors, and model validation results were comparable for the three MPS approaches and alike the trends known for CE data. Based on this analogy, we regard the probabilistic interpretation of MPS STR data fit for forensic DNA casework. In addition, guidelines were derived on when to apply LR calculations to MPS autosomal STR data and report the corresponding results. Show less
Altena, E.; Smeding, R.; Gaag, K.J. van der; Larmuseau, M.H.D.; Decorte, R.; Lao, O.; ... ; Knijff, P. de 2020
Previous studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data... Show morePrevious studies indicated existing, albeit limited, genetic-geographic population substructure in the Dutch population based on genome-wide data and a lack of this for mitochondrial SNP based data. Despite the aforementioned studies, Y-chromosomal SNP data from the Netherlands remain scarce and do not cover the territory of the Netherlands well enough to allow a reliable investigation of genetic-geographic population substructure. Here we provide the first substantial dataset of detailed spatial Y-chromosomal haplogroup information in 2085 males collected across the Netherlands and supplemented with previously published data from northern Belgium. We found Y-chromosomal evidence for genetic-geographic population substructure, and several Y-haplogroups demonstrating significant clinal frequency distributions in different directions. By means of prediction surface maps we could visualize (complex) distribution patterns of individual Y-haplogroups in detail. These results highlight the value of a micro-geographic approach and are of great use for forensic and epidemiological investigations and our understanding of the Dutch population history. Moreover, the previously noted absence of genetic-geographic population substructure in the Netherlands based on mitochondrial DNA in contrast to our Y-chromosome results, hints at different population histories for women and men in the Netherlands. Show less
Currently, Forensic DNA research is conducted almost exclusively using capillary electrophoresis to determine the length of fragments containing Short Tandem Repeats (STRs). Over the past decade,... Show moreCurrently, Forensic DNA research is conducted almost exclusively using capillary electrophoresis to determine the length of fragments containing Short Tandem Repeats (STRs). Over the past decade, developments in MPS (Massively Parallel Sequencing techniques, also known as Next Generation Sequencing) offered new possibilities for forensic DNA research. This thesis focusses on the preparation, validation and implementation of MPS and the accompanying data analysis. By MPS, the exact DNA sequence of STRs is determined often revealing additional variation on top of the fragment length resulting in an even more unique DNA profile. Sequence information provides more insight on the DNA molecules comprising a conventional DNA profile. With this information, a software could be developed to make a better distinction between genuine alleles and noise offering possibilities for analysis of unbalanced DNA mixtures which are often encountered in forensic casework.As alternative DNA marker to STRs, research was conducted to select microhaplotypes (multiple variable positions in a small fragment). The statistical power of a profile generated from these microhaplotypes turned out to be almost as strong as that of STRs without suffering from the known STR-artefacts thereby offering possibilities for interpretation of DNA mixtures. Show less
Gaag, K.J. van der; Leeuw, R.H. de; Laros, J.F.J.; Dunnen, J.T. den; Knijff, P. de 2018
The current U.S. population represents an amalgam of individuals originating mainly from four continental regions (Africa, Europe, Asia and America). To study the genetic ancestry and compare with... Show moreThe current U.S. population represents an amalgam of individuals originating mainly from four continental regions (Africa, Europe, Asia and America). To study the genetic ancestry and compare with self-declared ancestry we have analyzed paternally, maternally and bi-parentally inherited DNA markers sensitive for indicating continental genetic ancestry in all four major U.S. American groups. We found that self-declared U.S. Hispanics and U.S. African Americans tend to show variable degrees of continental genetic admixture among the three genetic systems, with evidence for a marked sex-biased admixture history. Moreover, for these two groups we observed significant regional variation across the country in genetic admixture. In contrast, self-declared U.S. European and U.S. Asian Americans were genetically more homogeneous at the continental ancestry level. Two autosomal ancestry-sensitive markers located in skin pigmentation candidate genes showed significant differences in self-declared U.S. African Americans or U.S. European Americans, relative to their assumed parental populations from Africa or Europe. This provides genetic support for the importance of skin color in the complex process of ancestry identification. Show less
Lemmers, R.J.L.F.; Vliet, P.J. van der; Gaag, K.J. van der; Zuniga, S.; Frants, R.R.; Knijff, P. de; Maarel, S.M. van der 2010
Subtelomeres are dynamic structures composed of blocks of homologous DNA sequences. These so-called duplicons are dispersed over many chromosome ends. We studied the human 4q and 10q subtelomeres,... Show moreSubtelomeres are dynamic structures composed of blocks of homologous DNA sequences. These so-called duplicons are dispersed over many chromosome ends. We studied the human 4q and 10q subtelomeres, which contain the polymorphic macrosatellite repeat D4Z4 and which share high sequence similarity over a region of, on average, >200 kb. Sequence analysis of four polymorphic markers in the African, European, and Asian HAPMAP panels revealed 17 subtelomeric 4q and eight subtelomeric 10qter haplotypes. Haplotypes that are composed of a mixture of 4q and 10q sequences were detected at frequencies >10% in all three populations, seemingly supporting a mechanism of ongoing interchromosomal exchanges between these chromosomes. We constructed an evolutionary network of most haplotypes and identified the 4q haplotype ancestral to all 4q and 10q haplotypes. According to the network, all subtelomeres originate from only four discrete sequence-transfer events during human evolution, and haplotypes with mixtures of 4q- and 10q-specific sequences represent intermediate structures in the transition from 4q to 10q subtelomeres. Haplotype distribution studies on a large number of globally dispersed human DNA samples from the HGDP-CEPH panel supported our findings and show that all haplotypes were present before human migration out of Africa. D4Z4 repeat array contractions on the 4A161 haplotype cause Facioscapulohumeral muscular dystrophy (FSHD), whereas contractions on most other haplotypes; are nonpathogenic. We propose that the limited occurrence of interchromosomal sequence transfers results in an accumulation of haplotype-specific polymorphisms that can explain the unique association of FSHD with D4Z4 contractions in a single 4q subtelomere. Show less
