Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.
Identifieur interne : 000042 ( PubMed/Corpus ); précédent : 000041; suivant : 000043Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.
Auteurs : A. Van Geystelen ; R. Decorte ; M H D. LarmuseauSource :
- Forensic science international. Genetics [ 1878-0326 ] ; 2013.
English descriptors
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- MESH :
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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Larmuseau</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23597787</idno><idno type="pmid">23597787</idno><idno type="doi">10.1016/j.fsigen.2013.03.010</idno><idno type="wicri:Area/PubMed/Corpus">000042</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.</title><author><name sortKey="Van Geystelen, A" sort="Van Geystelen, A" uniqKey="Van Geystelen A" first="A" last="Van Geystelen">A. Van Geystelen</name><affiliation><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></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><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23597787</PMID><DateCreated><Year>2013</Year><Month>10</Month><Day>21</Day></DateCreated><DateCompleted><Year>2014</Year><Month>05</Month><Day>19</Day></DateCompleted><DateRevised><Year>2013</Year><Month>10</Month><Day>21</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1878-0326</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>6</Issue><PubDate><Year>2013</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Forensic science international. Genetics</Title><ISOAbbreviation>Forensic Sci Int Genet</ISOAbbreviation></Journal><ArticleTitle>Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs.</ArticleTitle><Pagination><MedlinePgn>573-80</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.fsigen.2013.03.010</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S1872-4973(13)00089-6</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Van Geystelen</LastName><ForeName>A</ForeName><Initials>A</Initials><AffiliationInfo><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.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Decorte</LastName><ForeName>R</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Larmuseau</LastName><ForeName>M H D</ForeName><Initials>MH</Initials></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>Apr</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Forensic Sci Int Genet</MedlineTA><NlmUniqueID>101317016</NlmUniqueID><ISSNLinking>1872-4973</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D041322" MajorTopicYN="Y">Chromosomes, Human, Y</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053803" MajorTopicYN="Y">Forensic Genetics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006239" MajorTopicYN="N">Haplotypes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bio-informatics</Keyword><Keyword MajorTopicYN="N">Haploid markers</Keyword><Keyword MajorTopicYN="N">Phylogenetic tree</Keyword><Keyword MajorTopicYN="N">Whole-genome SNP calling</Keyword><Keyword MajorTopicYN="N">Y-SNPs</Keyword><Keyword MajorTopicYN="N">Y-chromosome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>2</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>3</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>4</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>5</Month><Day>20</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23597787</ArticleId><ArticleId IdType="pii">S1872-4973(13)00089-6</ArticleId><ArticleId IdType="doi">10.1016/j.fsigen.2013.03.010</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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