Publications by authors named "Sascha Willuweit"

31 Publications

DNA commission of the International Society of Forensic Genetics (ISFG): Recommendations on the interpretation of Y-STR results in forensic analysis.

Forensic Sci Int Genet 2020 09 4;48:102308. Epub 2020 Jun 4.

Institute of Legal Medicine and Forensic Sciences, Dept. Forensic Genetics, Charité - Universitätsmedizin Berlin, Germany.

Forensic genetic laboratories perform a large amount of STR analyses of the Y chromosome, in particular to analyze the male part of complex DNA mixtures. However, the statistical interpretation of evidence retrieved from Y-STR haplotypes is challenging. Due to the uni-parental inheritance mode, Y-STR loci are connected to each other and thus haplotypes show patterns of relationship on the familial and population level. This precludes the treatment of Y-STR loci as independently inherited variables and the application of the product rule. Instead, the dependency structure of Y-STRs needs to be included in the haplotype frequency estimation process affecting also the current paradigm of a random match probability that is in the autosomal case approximated by the population frequency assuming unrelatedness of sampled individuals. Information on the degree of paternal relatedness in the suspect population as well as on the familial network is however needed to interpret Y-chromosomal results in the best possible way. The previous recommendations of the DNA commission of the ISFG on the use of Y-STRs in forensic analysis published more than a decade ago [1] cover the interpretation issue only marginally. The current recommendations address a number of topics (frequency estimators, databases, metapopulations, LR formulation, triage, rapidly mutating Y-STRs) with relevance for the Y-STR statistics and recommend a decision-based procedure, which takes into account legal requirements as well as availability of population data and statistical methods.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2020.102308DOI Listing
September 2020

Inter-laboratory study on standardized MPS libraries: evaluation of performance, concordance, and sensitivity using mixtures and degraded DNA.

Int J Legal Med 2020 Jan 19;134(1):185-198. Epub 2019 Nov 19.

Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria.

We present results from an inter-laboratory massively parallel sequencing (MPS) study in the framework of the SeqForSTRs project to evaluate forensically relevant parameters, such as performance, concordance, and sensitivity, using a standardized sequencing library including reference material, mixtures, and ancient DNA samples. The standardized library was prepared using the ForenSeq DNA Signature Prep Kit (primer mix A). The library was shared between eight European laboratories located in Austria, France, Germany, The Netherlands, and Sweden to perform MPS on their particular MiSeq FGx sequencers. Despite variation in performance between sequencing runs, all laboratories obtained quality metrics that fell within the manufacturer's recommended ranges. Furthermore, differences in locus coverage did not inevitably adversely affect heterozygous balance. Inter-laboratory concordance showed 100% concordant genotypes for the included autosomal and Y-STRs, and still, X-STR concordance exceeded 83%. The exclusive reasons for X-STR discordances were drop-outs at DXS10103. Sensitivity experiments demonstrated that correct allele calling varied between sequencing instruments in particular for lower DNA amounts (≤ 125 pg). The analysis of compromised DNA samples showed the drop-out of one sample (FA10013B01A) while for the remaining three degraded DNA samples MPS was able to successfully type ≥ 87% of all aSTRs, ≥ 78% of all Y-STRs, ≥ 68% of all X-STRs, and ≥ 92% of all iSNPs demonstrating that MPS is a promising tool for human identity testing, which in return, has to undergo rigorous in-house validation before it can be implemented into forensic routine casework.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00414-019-02201-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6949318PMC
January 2020

Y-chromosome diversity of the three major ethno-linguistic groups in the Republic of North Macedonia.

Forensic Sci Int Genet 2019 09 11;42:165-170. Epub 2019 Jul 11.

Department Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany. Electronic address:

A total of 314 individuals representing the three major ethno-linguistic groups (ethnic Macedonians, Albanians and Turks) in the Republic of North Macedonia were analyzed for Y-SNPs and Y-STRs using minisequencing and fragment analysis. The haplogroup composition differed remarkably between the three groups with dominance of haplogroup I2 in ethnic Macedonians (28.1%), E1b in Albanians (35.3%) and J2a (34.9%) in Turks, respectively. The haplotype analysis using the YFilerPlus kit disclosed a significant reduction in diversity values (DC, GD) for the Turkish subgroup compared to the Macedonian and Albanian speaking populations. The Y-STR based population analysis revealed a similarity of ethnic Macedonians with neighboring Serbians and Bulgarians. The same holds true for the Albanian speakers from Macedonia and Albania, whereas the Turkish minority in North Macedonia stands apart from the population in Turkey.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2019.07.007DOI Listing
September 2019

Inter-laboratory validation study of the ForenSeq™ DNA Signature Prep Kit.

Forensic Sci Int Genet 2018 09 17;36:77-85. Epub 2018 May 17.

Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin Berlin, Germany.

The implementation of massively parallel sequencing (MPS) in forensic science revealed the advantages of the new method compared to the forensic benchmark in DNA-STR analysis, the capillary-electrophoresis (CE): Sequence information and the possibility to multiplex hundreds of markers in one multiplex PCR increase the discrimination power of a forensic (STR-) profile. The EU funded project DNASeqEx (DNA-STR Massive Sequencing & International Information Exchange) aims to evaluate MPS-based materials in their respective developmental stages using the two established platforms MiSeq FGx (Illumina) and Ion S5™ (Thermo Fisher Scientific). As part of this project, we present here an inter-laboratory validation of the Forenseq™ DNA Signature Prep Kit, focussing on STRs included in primer mix A. Our study comprises tests of concordance, reproducibility, sensitivity (1 ng, 500 pg, 250 pg, 125 pg, 63 pg, 31 pg) and mixtures (male-male and male-female at ratios of 1:1, 1:5, 1:10, 1:15, 1:20, 1:100, 1:500, 1:1000). Sequencing results found to be virtually concordant to CE results, to reference profiles and reproducible between duplicates and between both laboratories. We observed first locus drop-outs (LDO) at a DNA input of 63 pg (20 sample pool) and 125 pg (38 sample pool). Alleles were found to be well balanced at a DNA input of 250 pg or more. We found the kit to perform well on moderate mixtures (1:1-1:20).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2018.05.007DOI Listing
September 2018

Current state-of-art of STR sequencing in forensic genetics.

Electrophoresis 2018 11 4;39(21):2655-2668. Epub 2018 Jun 4.

Center for Human Identification, University of North Texas Health Science Center, TX, USA.

The current state of validation and implementation strategies of massively parallel sequencing (MPS) technology for the analysis of STR markers for forensic genetics use is described, covering the topics of the current catalog of commercial MPS-STR panels, leading MPS-platforms, and MPS-STR data analysis tools. In addition, the developmental and internal validation studies carried out to date to evaluate reliability, sensitivity, mixture analysis, concordance, and the ability to analyze challenged samples are summarized. The results of various MPS-STR population studies that showed a large number of new STR sequence variants that increase the power of discrimination in several forensically relevant loci are also presented. Finally, various initiatives developed by several international projects and standardization (or guidelines) groups to facilitate application of MPS technology for STR marker analyses are discussed in regard to promoting a standard STR sequence nomenclature, performing population studies to detect sequence variants, and developing a universal system to translate sequence variants into a simple STR nomenclature (numbers and letters) compatible with national STR databases.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/elps.201800030DOI Listing
November 2018

European survey on forensic applications of massively parallel sequencing.

Forensic Sci Int Genet 2017 07 26;29:e23-e25. Epub 2017 Apr 26.

Institute of Legal Medicine, Medical University of Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, PA, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2017.04.017DOI Listing
July 2017

Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes.

Hum Genet 2017 05 30;136(5):485-497. Epub 2017 Jan 30.

School of Forensic Medicine, China Medical University, Shenyang, People's Republic of China.

China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People's Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North-South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00439-017-1759-xDOI Listing
May 2017

Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.

Forensic Sci Int Genet 2016 May 21;22:54-63. Epub 2016 Jan 21.

Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain.

The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2016.01.009DOI Listing
May 2016

The new Y Chromosome Haplotype Reference Database.

Forensic Sci Int Genet 2015 Mar 3;15:43-8. Epub 2014 Dec 3.

Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité - Universitätsmedizin, Berlin, Germany.

After opening the first version of an internet-accessible worldwide reference database of Y chromosome profiles 14 years ago and six years after the last major relaunch the new YHRD 4.0 repository and website has been rolled-out. By November 2014 about 136k 9-locus haplotypes, among these 84k 17-locus haplotypes, 25k 23-locus haplotypes and 15k Y SNP profiles from 917 sampling locations in 128 countries have been submitted by more than 250 institutes and laboratories. In geographic terms, about 39% of the YHRD samples are from Europe, 32% from Asia, 16% from South America, 6% from North America, 4% from Africa and 2% from Oceania/Australia. Worldwide collaboration is the driving force for the rapid growth of the database and this, in turn, allows the evaluation and implementation of enhanced interpretation tools (variable frequency estimators, LR-based mixture and kinship analysis, Y-SNP-based ancestry assessment).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2014.11.024DOI Listing
March 2015

No shortcut solution to the problem of Y-STR match probability calculation.

Forensic Sci Int Genet 2015 Mar 24;15:69-75. Epub 2014 Oct 24.

Institut für Medizinische Informatik und Statistik, Kiel, Germany. Electronic address:

Match probability calculation is deemed much more intricate for lineage genetic markers, including Y-chromosomal short tandem repeats (Y-STRs), than for autosomal markers. This is because, owing to the lack of recombination, strong interdependence between markers is likely, which implies that haplotype frequency estimates cannot simply be obtained through the multiplication of allele frequency estimates. As yet, however, the practical relevance of this problem has not been studied in much detail using real data. In fact, such scrutiny appears well warranted because the high mutation rates of Y-STRs and the possibility of backward mutation should have worked against the statistical association of Y-STRs. We examined haplotype data of 21 markers included in the PowerPlex(®)Y23 set (PPY23, Promega Corporation, Madison, WI) originating from six different populations (four European and two Asian). Assessing the conditional entropies of the markers, given different subsets of markers from the same panel, we demonstrate that the PowerPlex(®)Y23 set cannot be decomposed into smaller marker subsets that would be (conditionally) independent. Nevertheless, in all six populations, >94% of the joint entropy of the 21 markers is explained by the seven most rapidly mutating markers. Although this result might render a reduction in marker number a sensible option for practical casework, the partial haplotypes would still be almost as diverse as the full haplotypes. Therefore, match probability calculation remains difficult and calls for the improvement of currently available methods of haplotype frequency estimation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2014.10.016DOI Listing
March 2015

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Forensic Sci Int Genet 2014 Sep 28;12:12-23. Epub 2014 Apr 28.

Forensische Genetik, Kantonsspital Aarau AG, Switzerland.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2014.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127773PMC
September 2014

Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jörg Jenatsch (1596-1639).

Forensic Sci Int Genet 2013 Dec 27;7(6):610-617. Epub 2013 Aug 27.

Institute of Medical Informatics and Statistics, Christian-Albrechts University of Kiel, Germany.

Jörg Jenatsch was a Swiss defender of independence and a fighter for liberty in the 17th century. With the help of three living male members of the Jenatsch family, we successfully identified a skeleton exhumed from Chur cathedral as the remains of Jörg Jenatsch. Our conclusion was based upon complete Y-STR and Y-SNP profiles that could be generated by replicate analyses of a bone sample available to us. The skeleton and the three living family members carried the same Y-SNP haplogroup, but were discordant at three of 23 Y-STR loci. This notwithstanding, conservative biostatistical evaluation of the data suggests that the Chur skeleton is at least 20 times more likely than not to be Jörg Jenatsch.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2013.08.006DOI Listing
December 2013

Multiple recurrent mutations at four human Y-chromosomal single nucleotide polymorphism sites in a 37 bp sequence tract on the ARSDP1 pseudogene.

Forensic Sci Int Genet 2013 Dec 27;7(6):593-600. Epub 2013 Jun 27.

Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany.

The male-specific region of the human Y chromosome (MSY) is passed down clonally from father to son and mutation is the single driving force for Y-chromosomal diversification. The geographical distribution of MSY variation is non-random. Therefore, Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are of forensic interest, as they can be utilized, e.g. for deducing the bio-geographical origin of biological evidence. This extra information can complement short tandem repeat data in criminal investigations. For forensic applications, however, any targeted marker has to be unequivocally interpretable. Here, we report findings for 17 samples from a population study comprising specimens from ∼3700 men living in Tyrol (Austria), indicating apparent homoplasic mutations at four Y-SNP loci on haplogroup R-M412/L51/S167, R-U152/S28, and L-M20 Y chromosomes. The affected Y-SNPs P41, P37, L202, and L203 mapped to a 37bp region on Yq11.21. Observing in multiple phylogenetic contexts up to four homoplasic mutations within such a short sequence tract is unlikely to result from a series of independent parallel mutations. Hence, we rather propose X-to-Y gene conversion as a more likely scenario. Practical implications arising from markers exhibiting paralogues on the Y chromosome or sites with a high propensity to recurrent mutation for database searches are addressed.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2013.05.010DOI Listing
December 2013

Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans.

PLoS Genet 2013 Apr 11;9(4):e1003460. Epub 2013 Apr 11.

Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.

Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1003460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623769PMC
April 2013

Estimating trace-suspect match probabilities for singleton Y-STR haplotypes using coalescent theory.

Forensic Sci Int Genet 2013 Feb 25;7(2):264-71. Epub 2012 Dec 25.

Department of Mathematical Sciences, Aalborg University, Aalborg East, Denmark.

Estimation of match probabilities for singleton haplotypes of lineage markers, i.e. for haplotypes observed only once in a reference database augmented by a suspect profile, is an important problem in forensic genetics. We compared the performance of four estimators of singleton match probabilities for Y-STRs, namely the count estimate, both with and without Brenner's so-called 'kappa correction', the surveying estimate, and a previously proposed, but rarely used, coalescent-based approach implemented in the BATWING software. Extensive simulation with BATWING of the underlying population history, haplotype evolution and subsequent database sampling revealed that the coalescent-based approach is characterized by lower bias and lower mean squared error than the uncorrected count estimator and the surveying estimator. Moreover, in contrast to the two count estimators, both the surveying and the coalescent-based approach exhibited a good correlation between the estimated and true match probabilities. However, although its overall performance is thus better than that of any other recognized method, the coalescent-based estimator is still computation-intense on the verge of general impracticability. Its application in forensic practice therefore will have to be limited to small reference databases, or to isolated cases of particular interest, until more powerful algorithms for coalescent simulation have become available.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2012.11.004DOI Listing
February 2013

Y-chromosomal STR analysis in the Pashtun population of Southern Afghanistan.

Forensic Sci Int Genet 2012 Jul 3;6(4):e103-5. Epub 2011 Dec 3.

DNA Typing Laboratory, Centre of Excellence in Molecular Biology CEMB, University of the Punjab, Lahore, Pakistan.

Afghanistan is a landlocked country in the heart of Asia and since the dawn of humankind Afghanistan has faced centuries of turmoil, strife, conflict, warfare, distress, social unrest, difficult climate, harsh terrain and due to its unique geostrategic position in Eurasia which has historically attracted commerce and conflict. It is an important stop along the Silk Road, connecting the far eastern civilizations to the western world. A 5000-year history of constant invasion. Afghanistan has been repeatedly invaded and conquered by rulers and super powers, neighboring interference in this conflict-tattered land for centuries yet rarely leading to the conquest of this rugged and challenging terrain nation. Afghans are not only shepherds, farmers and nomads but also intense fighters and fierce warriors. Currently very limited genetic studies have been performed in Afghan populations. 17 Y chromosomal short tandem repeats (Y-STRs) were analyzed in 125 unrelated Pashtun (in hindi: Pathan) males residing in the Kandahar region of Southern Afghanistan. A total of 92 unique haplotypes were observed. The predominant haplotype reached a frequency of 9.6%. The haplotype diversity was 0.987 and the discrimination capacity 73.6%. Analysis of molecular variance (AMOVA) reveals a considerable regional stratification within the country as well as between different Pashtun (Pathan) groups from Afghanistan, Pakistan and India.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2011.10.005DOI Listing
July 2012

Y-STR Frequency Surveying Method: A critical reappraisal.

Forensic Sci Int Genet 2011 Mar 19;5(2):84-90. Epub 2010 Nov 19.

Charité - Universitätsmedizin Berlin, Institute of Legal Medicine, Department of Forensic Science, Berlin, Germany.

Reasonable formalized methods to estimate the frequencies of DNA profiles generated from lineage markers have been proposed in the past years and were discussed in the forensic community. Recently, collections of population data on the frequencies of variations in Y chromosomal STR profiles have reached a new quality with the establishment of the comprehensive neatly quality-controlled reference database YHRD. Grounded on such unrivalled empirical material from hundreds of populations studies the core assumption of the Haplotype Frequency Surveying Method originally described 10 years ago can be tested and improved. Here we provide new approaches to calculate the parameters used in the frequency surveying method: a maximum likelihood estimation of the regression parameters (r(1), r(2), s(1) and s(2)) and a revised Frequency Surveying framework with variable binning and a database preprocessing to take the population sub-structure into account. We found good estimates for 11 metapopulations using both approaches and demonstrate that the statistical basis of the method is well supported and independent of the population under study. The results of the estimation process are reliable and robust if the underlying datasets are large and representative and show small average and pairwise genetic distances.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2010.10.014DOI Listing
March 2011

Geostatistical inference of main Y-STR-haplotype groups in Europe.

Forensic Sci Int Genet 2011 Mar;5(2):91-4

Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Sigmund-Freud-Str. 25, 53105 Bonn, Germany.

We examined the multifarious genetic heterogeneity of Europe and neighboring regions from a geographical perspective. We created composite maps outlining the estimated geographical distribution of major groups of genetically similar individuals on the basis of forensic Y-chromosomal markers. We analyzed Y-chromosomal haplotypes composed of 7 highly polymorphic STR loci, genotyped for 33,010 samples, collected at 249 sites in Europe, Western Asia and North Africa, deposited in the YHRD database (www.yhrd.org). The data set comprised 4176 different haplotypes, which we grouped into 20 clusters. For each cluster, the frequency per site was calculated. All geostatistical analysis was performed with the geographic information system GRASS-GIS. We interpolated frequency values across the study area separately for each cluster. Juxtaposing all 20 interpolated surfaces, we point-wisely screened for the highest cluster frequencies and stored it in parallel with the respective cluster label. We combined these two types of data in a composite map. We repeated this procedure for the second highest frequencies in Europe. Major groups were assigned to Northern, Western and Eastern Europe. North Africa built a separate region, Southeastern Europe, Turkey and Near East were divided into several regions. The spatial distribution of the groups accounting for the second highest frequencies in Europe overlapped with the territories of the largest countries. The genetic structure presented in the composite maps fits major historical geopolitical regions and is in agreement with previous studies of genetic frequencies, validating our approach. Our genetic geostatistical approach provides, on the basis of two composite maps, detailed evidence of the geographical distribution and relative frequencies of the most predominant groups of the extant male European population, examined on the basis of forensic Y-STR haplotypes. The existence of considerable genetic differences among geographic subgroups in Europe has important consequences for the statistical inference in forensic Y-STR haplotype analyses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2010.09.010DOI Listing
March 2011

Assembly of a large Y-STR haplotype database for the Czech population and investigation of its substructure.

Forensic Sci Int Genet 2010 Apr;4(3):e75-8

Laboratory for Molecular Genetics and Oncology, Genomac International, Ltd., Prague, Czech Republic.

Twelve Y-chromosomal short tandem repeats (Y-STR) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, and DYS439) included in the PowerPlex Y Kit (Promega Corporation, Madison, USA) were studied for 1750 unrelated males living in 14 regions of the Czech Republic. A total of 1148 different haplotypes were found. The overall haplotype diversity (HD) was determined as 0.998. Analysis of Molecular Variance (AMOVA) reveals non-significant distances between regions concerning their haplotype distribution, thus allowing to use the whole sample as a representative reference database of the Czech Republic. Median network analysis shows a remarkable bipartite composition of the Czech haplotypes, falling in distinct clusters with Eastern and Western European roots.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2009.06.005DOI Listing
April 2010

Y-chromosomal STRs haplotypes in the Taiwanese Paiwan population.

Int J Legal Med 2011 Jan 28;125(1):39-43. Epub 2010 Jan 28.

Department of Forensic Science, Investigation Bureau, Ministry of Justice, Taipei County, Taiwan, Republic of China.

The distribution of Y-chromosomal short tandem repeat (Y-STR) haplotypes was determined in a population of Taiwanese Paiwan aboriginals. Using 17 Y-STR markers, a total of 135 haplotypes were observed, 102 of which were unique. The overall haplotype diversity for the 17 Y-STR loci tested was 0.9922 and the discrimination capacity was 0.6490. In addition, three novel intermediate alleles at the DYS448 locus were also found.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00414-009-0416-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3016148PMC
January 2011

A Y-STR database of Iranian and Azerbaijanian minority populations.

Forensic Sci Int Genet 2009 Dec 5;4(1):e53-5. Epub 2009 Jun 5.

Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité, Universitätsmedizin Berlin, Hannoversche Strasse 6, 10115 Berlin, Germany.

Seventeen Y-chromosomal short tandem repeats (Y-STR) DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4 were studied in five minor linguistic groups from Iran (Arabs, Gilaki, Mazandarani, Bakhtiari and Southern Talysh) and one from Azerbaijan (Northern Talysh) with the goal of constructing of a representative Y-STR database for this region in Southwest Asia. Analysis of Molecular Variance (AMOVA) reveals non-significant or low genetic distances between the Iranian Gilaki, Mazandarani, Bakhtiari and non-Iranian Turkish, Azerbaijanian, Armenian and Kurd populations, but larger genetic distances to both Talysh populations, the Iranian Arabs, Georgian and Kazakh populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2009.05.002DOI Listing
December 2009

Y-STR variation among ethnic groups from Ecuador: Mestizos, Kichwas, Afro-Ecuadorians and Waoranis.

Forensic Sci Int Genet 2009 Jun 2;3(3):e83-91. Epub 2008 Oct 2.

Hospital Metropolitano, Quito, Ecuador.

Twelve Y-chromosomal short tandem repeats (STRs) DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438 and DYS439 were studied in the three major ethnic groups from Ecuador: Mestizos, Native Amerindians (Kichwas, Quichuas) and Afro-Ecuadorians aiming to construct a representative database for this region in Latin America. All three populations exhibit high haplotypes diversities. Analysis of molecular variance (AMOVA) reveals significant differentiation between the Mestizos, the Kichwas and the Afro-Ecuadorians. The analysis of a hunter-gatherer group of Native Amerindians from the Amazonian provinces of Ecuador, the Waoranis (Huaorani) revealed markedly reduced haplotypes variability and a large genetic distance to the major Ecuadorian populations.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2008.08.003DOI Listing
June 2009

A Colombian Caribbean population study of 16 Y-chromosome STR loci.

Forensic Sci Int Genet 2008 Mar 26;2(2):e5-8. Epub 2007 Nov 26.

Grupo de Genética Forense, Instituto Nacional de Medicina Legal y Ciencias Forenses, Bogotá, Colombia.

Allelic frequencies and haplotypic composition of 305 male unrelated individuals from the Caribbean Colombian states of Atlántico, Bolívar, Cesar, Córdoba, Guajira, Magdalena and Sucre, were determined using 16 Y-chromosome STR loci. Two hundred and ninety three (293) haplotypes were identified, of which 283 were unique and the other 10 were found twice or thrice in the Caribbean population tested. Haplotypic diversity surpassed the values obtained in other populations, ranging from 99.66% in the population of Sucre to 99.99% in the population of Córdoba. We also calculated the overall haplotypic diversity (99.97%) and the discrimination power of these haplotypes (96.1%) in these groups. Analysis of molecular variance (AMOVA) for 10 Colombian and Spanish populations (3139 haplotypes) reveals low differentiation between the Colombian populations of mainly European descent and large distance to Afroamerican populations living in Colombia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2007.09.005DOI Listing
March 2008

Boundaries and clines in the West Eurasian Y-chromosome landscape: insights from the European part of Russia.

Am J Phys Anthropol 2008 Sep;137(1):41-7

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Previous studies of Y chromosome variation have revealed that western Europe, the Volga-Ural region, and the Caucasus differ dramatically with respect to Y-SNP haplogroup composition. The European part of Russia is situated in between these three regions; to determine if these differences reflect clines or boundaries in the Y-chromosome landscape, we analyzed 12 Y-SNPs in 545 males from 12 populations from the European part of Russia. The majority of Russian Y chromosomes (from 74% to 94%) belong to three Y chromosomal lineages [I-M170, R1a1-M17, and N3-TAT] that are also frequent in the rest of east Europe, north Europe, and/or in the Volga-Ural region. We find significant but low correlations between haplogroup frequencies and the geographic location of populations, suggesting gradual change in the Y chromosome gene pool across western Eurasia. However, we also find some significant boundaries between populations, suggesting that both isolation and migration have influenced the Y chromosome landscape.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajpa.20838DOI Listing
September 2008

Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations.

Int J Legal Med 2008 May 29;122(3):219-23. Epub 2008 Jan 29.

Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Hannoversche Strasse 6, 10115 Berlin, Germany.

A total of 17 Y-specific STR loci were studied in 12 districts of the European part of Russia aiming to ascertain the amount of substructure required for the construction of a representative regional database. All groups exhibited high haplotype diversities but low inter-population variance as measured by an analysis of molecular variance. However, when Western Russia is taken as a whole, the genetic distances to the neighbouring populations were significant. Whereas gradual change in the Y chromosome pool exists between Russia and the Slavic-speaking populations to the West, remarkable discontinuities were observed with neighbouring populations in the East, North and South.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00414-007-0222-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755792PMC
May 2008

Y chromosome haplotype reference database (YHRD): update.

Forensic Sci Int Genet 2007 Jun 2;1(2):83-7. Epub 2007 Mar 2.

Department of Forensic Genetics, Institute of Legal Medicine, Charité-Universitätsmedizin, Berlin, Germany.

The freely accessible YHRD (Y Chromosome Haplotype Reference Database, www.yhrd.org) is designed to store Y chromosome haplotypes from global populations and had replaced three earlier database versions collecting European, Asian and US American Y chromosomes separately. The focus is to disseminate haplotype frequency data to forensic analysts, researchers, and to everyone who is interested in historical and family genetics. YHRD considers reduction of the available number of polymorphisms on the Y chromosome to a uniform data string of 11 highly variable Y-STR loci as an efficient way to rapidly screen many world populations and to make their Y chromosome profiles comparable. Typing of the YHRD 11-locus core set is facilitated by commercial products, namely diagnostic PCR kits, and endorsed by scientific and forensic analyst's societies as ISFG or SWGDAM. YHRD is structured by the assignment of each submitted population sample to a set of populations sharing a common linguistic, demographic, genetic or geographic background (metapopulations). This principle facilitates the statistical evaluation of haplotype matches due to a significant enlargement of sample sizes. With the rapid growth of the database the definition of homogeneous metapopulations is now also feasible solely on the basis of the genetic data as exemplified for the whole dataset of YHRD, release 19 (August 2006). Large sample numbers within genetically defined metapopulations also allows the development of biostatistical methods to estimate the frequency of unobserved or rare haplotypes ("haplotype frequency surveying method"). Essential for the YHRD project is its collaborative character relying on the engagement of individual laboratories to make their data accessible via YHRD and to share the YHRD standards regarding data quality.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fsigen.2007.01.017DOI Listing
June 2007

Y-chromosomal STR haplotypes in Kalmyk population samples.

Forensic Sci Int 2007 Dec 20;173(2-3):204-9. Epub 2007 Feb 20.

Institute of Legal Medicine, Charité, University Medicine Berlin, Hannoversche Str. 6, 10115 Berlin, Germany.

Seventeen Y-chromosomal short tandem repeats (STRs), DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, GATA-H4, DYS448, DYS456, DYS458, DYS635 were typed in DNA samples from the Kalmyk population (n=99). The population is characterized by a high proportion of duplicated DYS19 alleles and deletions of the locus DYS448 on the background of the Central Asian haplogroup C*. AMOVA analysis reveals a close vicinity to Mongolian and Kazakh populations and large genetic distance to geographical neighbours from Russia, Ukraine and the Caucasus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.forsciint.2006.11.013DOI Listing
December 2007

Signature of recent historical events in the European Y-chromosomal STR haplotype distribution.

Hum Genet 2005 Mar 20;116(4):279-91. Epub 2005 Jan 20.

Institute of Legal Medicine, Humboldt-University, Berlin, Germany.

Previous studies of human Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) established a link between the extant Y-SNP haplogroup distribution and the prehistoric demography of Europe. By contrast, our analysis of seven rapidly evolving Y-chromosomal short tandem repeat loci (Y-STRs) in over 12,700 samples from 91 different locations in Europe reveals a signature of more recent historic events, not previously detected by other genetic markers. Cluster analysis based upon molecular variance yields two clearly identifiable sub-clusters of Western and Eastern European Y-STR haplotypes, and a diverse transition zone in central Europe, where haplotype spectra change more rapidly with longitude than with latitude. This and other observed patterns of Y-STR similarity may plausibly be related to particular historical incidents, including, for example, the expansion of the Franconian and Ottoman Empires. We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00439-004-1201-zDOI Listing
March 2005

Y-chromosomal STR haplotypes in Macedonian population samples.

Forensic Sci Int 2005 Feb;148(1):69-73

Institute of Immunobiology and Human Genetics, Faculty of Medicine, 50 Divizija 6a, 1109 Skopje, P.O. Box 60, Republic of Macedonia.

Eleven Y-chromosomal short tandem repeats (STRs), DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439 were typed in DNA samples from Macedonian population (n = 150).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.forsciint.2004.04.067DOI Listing
February 2005

Asian online Y-STR Haplotype Reference Database.

Leg Med (Tokyo) 2003 Mar;5 Suppl 1:S160-3

Institute of Legal Medicine, University of Leipzig, Johannisallee 28, D-04103 Leipzig, Germany.

For several years Y-chromosomal microsatellites (short tandem repeats, STRs) have been well established in forensic practice. In this context, the genetic characteristics of the Y chromosome (i.e. its paternal inheritance and lack of recombination) render STRs particularly powerful. However, genetic differences between male populations appear to be larger for Y-STRs than for autosomal STRs, a fact that is most likely due to the higher sensitivity of Y-chromosomal lineages to genetic drift (Forensic Sci Int 118 (2001) 153). The assessment of probabilities for matches between haplotyped male persons or traces/persons requires the typing of a large number of haplotypes in the appropriate reference populations. The haplotype data of a large number of European as well as South and North American populations have been collected and are continuously published online (Y-STR Haplotype Reference Database--YHRD; http://www.ystr.org). The most recent multicentric effort has led to the establishment of an Asian YHRD (http://www.ystr.org/asia) which has been available since January 2002. All databases are maintained and curated at the Institute of Legal Medicine, Humboldt-University, Berlin and will soon be fused to a global repository including populations from all continents.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/s1344-6223(02)00100-1DOI Listing
March 2003
-->