The effect of number of loci on geographical structuring and forensic applicability of Y-STR data in Finland

Palo, Jukka U.; Pirttimaa, Markus; Bengs, Auli; Johnsson, V.; Ulmanen, Ismo; Lukka, Matti; Udd, Bjarne; Sajantila, Antti

doi:10.1007/s00414-008-0250-6

Cited by 12 publications

(7 citation statements)

References 29 publications

(36 reference statements)

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“…Altogether, the newly developed typing methods applied to the Turku sample yielded results, which are in accordance with previous observations on Finnish Ychromosomal lineages [25,28,29,32,34]. Decreasing the volume of a SNP typing assay in the described manner leads to high-quality results comparable to those observed with conventional typing assays.…”

Section: Resultssupporting

confidence: 89%

“…However, western provinces have shown higher Y-chromosomal HT diversity than the middle and eastern parts [29], and it is still lower than in other Scandinavian [30] or in other European populations [31]. Analysis of a greater number of Y-STR loci has been shown to significantly increase the HT diversity and to lower the level of interregional differentiation in the Finnish population; nevertheless, discrimination power is relatively low [32]. The most common HT found in the Turku sample is abundant in the Uralic-Yukaghir metapopulation according to the Y chromosome haplotype reference database (YHRD) [33] and is also observed predominantly in the north and east of Europe, i.e., Norway, Sweden (Swedish Saami [30]), Estonia, Lithuania, Belarus, and the Russian Federation, but to a much lesser extent.…”

Section: Resultsmentioning

confidence: 90%

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Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes

et al. 2009

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Single-nucleotide extension is a widespread method for typing Y-chromosomal single-nucleotide polymorphisms. In our study, we validated a multiplex minisequencing assay in a reduced-volume and in a low-volume approach. A four-plex assay was performed in a 6-microL multiplex reaction in 96-well microtiter reaction plates, which can be directly used for capillary electrophoresis. In a second approach, a six-plex assay was performed on a chemically structured glass slide. Both techniques have proven to be highly sensitive as well as time- and cost-saving, which makes them a valuable option not only for forensic purposes but also for population genetic studies where large sample numbers have to be analyzed. In the present paper, both techniques are compared and applied to analyze a population sample from the area of Turku, Finland. The most common haplogroup was found to be N1c*, which is nearly absent in western and central European populations. Additionally, 11 short tandem repeat markers were analyzed to further discriminate Y-chromosomal lineages.

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Section: Resultssupporting

confidence: 89%

Section: Resultsmentioning

confidence: 90%

Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes

et al. 2009

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“…Because of environmental destruction and the scarcity of forensic samples, incomplete Y-STR profiles are often obtained from trace evidence material or mixed male/female samples in forensic casework. The DYS19, DYS389II, DYS448, and DYS635 loci have been reported to be among the most frequent noninformative loci, followed by DYS385a/b, DYS390, DYS392, DYS437, and DYS438 in the 17 Y-STRs system [6,14,15]. Loss of the signals will decrease the discrimination capacity.…”

Section: Introductionmentioning

confidence: 95%

“…Y haplotype distributions in different population groups and varied types of markers have been widely reported. Extensive large-scale population surveys have been carried out and are still ongoing to increase the forensic databases [3][4][5][6][7]. Population genetic diversity in relation to microsatellite heterogeneity has been investigated to trace human evolution and migration, and phylogenetic trees or multidimensional scaling (MDS) plots based on Y-STR have been described [6][7][8][9][10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Seventeen Y-chromosomal short tandem repeat haplotypes in seven groups of population living in Taiwan

Hwa

Tseng

Ko³

et al. 2010

Int J Legal Med

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The analysis of Y-chromosome short tandem repeat (Y-STR) loci is a powerful tool in forensic casework. The aim of this study was to present the 17 Y-STR loci haplotype distributions of groups of population living in Taiwan and to demonstrate genetic distances between the groups as well as multidimensional scaling plot based on Y-STR genotype data. Five hundred and fifteen DNA samples from unrelated males of seven groups of population, including Taiwanese Han, two groups of indigenous Taiwanese of Taiwan Island, Tao, mainland Chinese, Filipinos, and a group of people with European, Near Eastern, or South Asian ancestry, were analyzed using a commercial kit that co-amplifies 17 Y-STRs. A total of 471 different haplotypes with 440 unique haplotypes were identified. The overall haplotype diversity was 0.9995 +/- 0.0002. High haplotype diversity was observed in six groups of population, except the Tao. These Y-STRs revealed a low discrimination capacity in the Tao population (36.84%), which should be considered in forensic practice. The multidimensional scaling plot of these seven groups of population constructed based on the genetic distances according to 17 Y-STR loci presented a clear patrilineal genetic substructure in the area. Partial Y-STRs profiling reduced the discrimination capacity in most groups of population and distorted the multidimensional scaling plot.

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“…Some studies have shown (34) that commercially available kits like PowerPlex Y or Yfiler cannot provide a sufficient discrimination power to discern the haplotypes inside broad families, and a definition of a region-specific set of Y-STR loci is a must. The results of haplotype diversity of the population samples tested within this study (VALACH, VLIN, and CZE) revealed that the sampling in one close geographic region or inside a group of people that recognize themselves as members of a certain “clan” brings lower diversity.…”

Section: Discussionmentioning

confidence: 99%

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

Ehler

Vaněk²,

Stenzl³

et al. 2011

Croat Med J

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AimTo evaluate Y-chromosomal diversity of the Moravian Valachs of the Czech Republic and compare them with a Czech population sample and other samples from Central and South-Eastern Europe, and to evaluate the effects of genetic isolation and sampling.MethodsThe first sample set of the Valachs consisted of 94 unrelated male donors from the Valach region in northeastern Czech Republic border-area. The second sample set of the Valachs consisted of 79 men who originated from 7 paternal lineages defined by surname. No close relatives were sampled. The third sample set consisted of 273 unrelated men from the whole of the Czech Republic and was used for comparison, as well as published data for other 27 populations. The total number of samples was 3244. Y-short tandem repeat (STR) markers were typed by standard methods using PowerPlex® Y System (Promega) and Yfiler® Amplification Kit (Applied Biosystems) kits. Y-chromosomal haplogroups were estimated from the haplotype information. Haplotype diversity and other intra- and inter-population statistics were computed.ResultsThe Moravian Valachs showed a lower genetic variability of Y-STR markers than other Central European populations, resembling more to the isolated Balkan populations (Aromuns, Csango, Bulgarian, and Macedonian Roma) than the surrounding populations (Czechs, Slovaks, Poles, Saxons). We illustrated the effect of sampling on Valach paternal lineages, which includes reduction of discrimination capacity and variability inside Y-chromosomal haplogroups. Valach modal haplotype belongs to R1a haplogroup and it was not detected in the Czech population.ConclusionThe Moravian Valachs display strong substructure and isolation in their Y chromosomal markers. They represent a unique Central European population model for population genetics.

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The effect of number of loci on geographical structuring and forensic applicability of Y-STR data in Finland

Cited by 12 publications

References 29 publications

Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes

Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes

Seventeen Y-chromosomal short tandem repeat haplotypes in seven groups of population living in Taiwan

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

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