Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.
Identifieur interne : 000046 ( OpenAccess/Analysis ); précédent : 000045; suivant : 000047Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.
Auteurs : A. Van Geystelen [Belgique] ; R. Decorte ; M H D. LarmuseauSource :
- Forensic science international. Genetics [ 1878-0326 ] ; 2013.
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Abstract
The Y-chromosomal phylogenetic tree has a wide variety of important forensic applications and therefore it needs to be state-of-the-art. Nevertheless, since the last 'official' published tree many publications reported additional Y-chromosomal lineages and other phylogenetic topologies. Therefore, it is difficult for forensic scientists to interpret those reports and use an up-to-date tree and corresponding nomenclature in their daily work. Whole genome sequencing (WGS) data is useful to verify and optimise the current phylogenetic tree for haploid markers. The AMY-tree software is the first open access program which analyses WGS data for Y-chromosomal phylogenetic applications. Here, all published information is collected in a phylogenetic tree and the correctness of this tree is checked based on the first large analysis of 747 WGS samples with AMY-tree. The obtained result is one phylogenetic tree with all peer-reviewed reported Y-SNPs without the observed recurrent and ambiguous mutations. Nevertheless, the results showed that currently only the genomes of a limited set of Y-chromosomal (sub-)haplogroups is available and that many newly reported Y-SNPs based on WGS projects are false positives, even with high sequencing coverage methods. This study demonstrates the usefulness of AMY-tree in the process of checking the quality of the present Y-chromosomal tree and it accentuates the difficulties to enlarge this tree based on only WGS methods.
DOI: 10.1016/j.fsigen.2013.03.010
PubMed: 23597787
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Decorte</name></author><author><name sortKey="Larmuseau, M H D" sort="Larmuseau, M H D" uniqKey="Larmuseau M" first="M H D" last="Larmuseau">M H D. 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Van Geystelen</name><affiliation wicri:level="1"><nlm:affiliation>UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Biology, Laboratory of Socioecology and Social Evolution, Leuven, Belgium.</nlm:affiliation><country xml:lang="fr">Belgique</country><wicri:regionArea>UZ Leuven, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium; KU Leuven, Department of Biology, Laboratory of Socioecology and Social Evolution, Leuven</wicri:regionArea><wicri:noRegion>Leuven</wicri:noRegion></affiliation></author><author><name sortKey="Decorte, R" sort="Decorte, R" uniqKey="Decorte R" first="R" last="Decorte">R. Decorte</name></author><author><name sortKey="Larmuseau, M H D" sort="Larmuseau, M H D" uniqKey="Larmuseau M" first="M H D" last="Larmuseau">M H D. Larmuseau</name></author></analytic><series><title level="j">Forensic science international. Genetics</title><idno type="eISSN">1878-0326</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosomes, Human, Y</term><term>Forensic Genetics</term><term>Haplotypes</term><term>Humans</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide (genetics)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosomes, Human, Y</term><term>Forensic Genetics</term><term>Haplotypes</term><term>Humans</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The Y-chromosomal phylogenetic tree has a wide variety of important forensic applications and therefore it needs to be state-of-the-art. Nevertheless, since the last 'official' published tree many publications reported additional Y-chromosomal lineages and other phylogenetic topologies. Therefore, it is difficult for forensic scientists to interpret those reports and use an up-to-date tree and corresponding nomenclature in their daily work. Whole genome sequencing (WGS) data is useful to verify and optimise the current phylogenetic tree for haploid markers. The AMY-tree software is the first open access program which analyses WGS data for Y-chromosomal phylogenetic applications. Here, all published information is collected in a phylogenetic tree and the correctness of this tree is checked based on the first large analysis of 747 WGS samples with AMY-tree. The obtained result is one phylogenetic tree with all peer-reviewed reported Y-SNPs without the observed recurrent and ambiguous mutations. Nevertheless, the results showed that currently only the genomes of a limited set of Y-chromosomal (sub-)haplogroups is available and that many newly reported Y-SNPs based on WGS projects are false positives, even with high sequencing coverage methods. This study demonstrates the usefulness of AMY-tree in the process of checking the quality of the present Y-chromosomal tree and it accentuates the difficulties to enlarge this tree based on only WGS methods.</div></front></TEI><affiliations><list><country><li>Belgique</li></country></list><tree><noCountry><name sortKey="Decorte, R" sort="Decorte, R" uniqKey="Decorte R" first="R" last="Decorte">R. Decorte</name><name sortKey="Larmuseau, M H D" sort="Larmuseau, M H D" uniqKey="Larmuseau M" first="M H D" last="Larmuseau">M H D. Larmuseau</name></noCountry><country name="Belgique"><noRegion><name sortKey="Van Geystelen, A" sort="Van Geystelen, A" uniqKey="Van Geystelen A" first="A" last="Van Geystelen">A. 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