Prediction of people’s origin from degraded DNA—presentation of SNP assays and calculation of probability

Poetsch, Micaela; Blöhm, Rowena; Harder, Melanie; Inoue, Hiromasa; Wurmb‐Schwark, Nicole von; Freitag‐Wolf, Sandra

doi:10.1007/s00414-012-0728-0

Cited by 10 publications

(10 citation statements)

References 22 publications

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“…15 The structures of the Y-chromosomal STR loci is illustrated by phylogenetic analysis, which was performed by Network 2.0 with the median joining (MJ)-network method. 20 Two different colourings were applied to the networks according to Y haplotype groups and population differentiation SNPs based on correspondence analysis similarities of Y chromosome and mtDNA haplogroup frequencies from African, Asian and European populations are summarised in two-dimensional graphics with the R paket ca.…”

Section: Discussionmentioning

confidence: 99%

“…Sixteen SNPs in two SNaPshot assays (assay PD-1 comprises SNPs rs885479, rs2228478, rs1545397, rs12913832, rs6119471, rs1426654, rs16891982 and rs1800407, and assay PD-2 comprises rs885479, rs1800404, rs16891982, rs1528460, rs10843344, rs2814778, rs730570, rs1321333, rs5030240, rs4540055) were amplified as described before. 15 2. Forty-four SNPs from the Y chromosome were analysed to differentiate nine major Y-chromosomal haplogroups and their subgroups.…”

Section: Snp Analysismentioning

confidence: 99%

“…The population affiliation to one of the seven populations, which were included in the original project (West Africa, Northern Africa, Near East, Turkey, Balkan states, Northern Europe and East Asia (Japan)) was calculated as described before 15 (see Supplementary Table S4 for calculation results). This assay has been predominantly designed to distinguish African and European/Eurasian populations by phenotype, it is not as powerful in the differentiation of Asian populations.…”

Section: Population Differentiation Snpsmentioning

confidence: 99%

“…[4][5][6][7] The various ethnic groups on Madagascar are generally classified into two main subgroups: the Highlanders (HL), considered being more Asian in culture and phenotype, and the people from the coasts (CT), thought to be more African. 8 The determination of the phenotype, for example, eye colour, hair colour or skin colour, or the population origin from DNA has been an important research field in recent years, in which considerable progress has been accomplished (see for example [9][10][11][12][13][14][15] ). These techniques have already been applied successfully in the characterisation of ancient skeletal human remains.…”

Section: Introductionmentioning

confidence: 99%

“…16,17 Regarding these results, we were interested in how the Malagasy would perform in such an assay for the determination of the phenotype or the population affiliation. We applied our recently published assays for population differentiation 15 in addition to a large set of well known and commonly used binary markers as well as short tandem repeats (STRs) from the Y chromosome and mtDNA single-nucleotide polymorphisms (SNPs) to 168 unrelated individuals from Madagascar.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

Poetsch¹,

Wiegand²,

Harder³

et al. 2013

Eur J Hum Genet

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Y-chromosomal and mitochondrial DNA (mtDNA) polymorphisms have been used for population studies for a long time. However, there is another possibility to define the origin of a population: autosomal single-nucleotide polymorphisms (SNPs) whose allele frequencies differ considerably in different populations. In an attempt to compare the usefulness of these approaches we studied a population from Madagascar using all the three mentioned approaches. Former investigations of Malagasy maternal (mtDNA) and paternal (Y chromosome) lineages have led to the assumption that the Malagasy are an admixed population with an African and Asian-Indonesian heritage. Our additional study demonstrated that more than two-third of the Malagasy investigated showed clearly a West African genotype regarding only the autosomal SNPs despite the fact that 64% had an Asian mtDNA and more than 70% demonstrated an Asian-Indonesian heritage in either mtDNA or Y-chromosomal haplogroup or both. Nonetheless, the admixture of the Malagasy could be confirmed. A clear African or Asian-Indonesian heritage according to all the three DNA approaches investigated was only found in 14% and 1% of male samples, respectively. Not even the European or Northern African influences, detected in 9% of males (Y-chromosomal analysis) and 11% of samples (autosomal SNPs) were consistent. No Malagasy in our samples showed a European or Northern African origin in both categories. So, the analysis of autosomal SNPs could confirm the admixed character of the Malagasy population, even if it pointed to a greater African influence as detectable by Y-chromosomal or mtDNA analysis.

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Section: Discussionmentioning

confidence: 99%

Section: Snp Analysismentioning

confidence: 99%

Section: Population Differentiation Snpsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

Poetsch¹,

Wiegand²,

Harder³

et al. 2013

Eur J Hum Genet

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Improving the analysis of Y‐SNP haplogroups by a single highly informative 16 SNP multiplex PCR‐minisequencing assay

et al. 2013

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The SNP haplogroups of the Y-chromosome are nonrandomly distributed among human populations. They are used for tracing the phylogeographical history of paternal lineages of male individuals and can be a useful tool for approaching the patrilineal bio-geographic ancestry of unknown forensic evidences. With the aim of facilitating the inference of the principal informative worldwide Y-SNP haplogroups, we have selected the minimum possible number of key Y-SNPs to be amplified in a sensitive single multiplex PCR and detected by minisequencing. This assay, that includes 16 Y-SNPs, was tested for male human specificity, sensitivity, and reproducibility. Its effectiveness was assessed in a set of degraded DNA samples and in a panel of male individuals from different worldwide populations. All these tests demonstrated the convenience of this assay for assigning the major Y haplogroups to forensic evidences by one single PCR-minisequencing reaction.

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Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations

Yun

Rajeevan

et al. 2014

Int J Legal Med

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DNA-based prediction for externally visible characteristics such as eye color is already a useful tool in forensic criminal investigations. The IrisPlex system, consisting of six single nucleotide polymorphisms (SNPs) and a prediction model, was developed based on individuals from several European populations. Other recent studies have developed a different prediction model, also based on European populations. In this study, we compared two prediction models using the data for the six IrisPlex SNPs genotyped on 905 individuals from 12 different Eurasian populations. All SNPs showed significant differences in allele frequencies among three groups of populations: European, genetically intermediate (Khanty, Uygur, and Yakut), and East Asian. The two prediction models, the FROG-kb calculation based on the formula of Walsh et al. (2011) and the Snipper calculation from Ruiz et al. (2013), gave identical predictions of brown eye color for the four East Asian populations with complete data but did not give concordant predictions for many individuals in the seven intermediate and European populations. Inconsistencies were mainly conclusive prediction by one model but not the other. Of the 714 individuals with complete 6-locus genotypes, the two models gave 22 % inconsistent predictions. Eliminating the 306 individuals in the Korean and three Chinese populations, in which the predictions were always consistent for brown eye color, the inconsistencies (among the remaining 408 individuals) were 38.7 %. We conclude that more attention should be paid to predictive uncertainty/error. Implementation of both prediction models in future forensic casework is one immediate way to highlight uncertainty.

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Prediction of people’s origin from degraded DNA—presentation of SNP assays and calculation of probability

Cited by 10 publications

References 22 publications

Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

Determination of population origin: a comparison of autosomal SNPs, Y-chromosomal and mtDNA haplogroups using a Malagasy population as example

Improving the analysis of Y‐SNP haplogroups by a single highly informative 16 SNP multiplex PCR‐minisequencing assay

Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations

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