AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications
<p>Abstract</p> <p>Background</p> <p>Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phy...
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| Format: | Article |
| Language: | English |
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BMC
2013-02-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://www.biomedcentral.com/1471-2164/14/101 |
| _version_ | 1818753821762912256 |
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| author | Van Geystelen Anneleen Decorte Ronny Larmuseau Maarten HD |
| author_facet | Van Geystelen Anneleen Decorte Ronny Larmuseau Maarten HD |
| author_sort | Van Geystelen Anneleen |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.</p> <p>Results</p> <p>We present an automated approach, ‘AMY-tree’, which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.</p> <p>Conclusions</p> <p>Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.</p> |
| first_indexed | 2024-12-18T05:13:27Z |
| format | Article |
| id | doaj.art-fdb9cc8aadeb4963b8adb01a10fc2822 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-18T05:13:27Z |
| publishDate | 2013-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-fdb9cc8aadeb4963b8adb01a10fc28222022-12-21T21:19:50ZengBMCBMC Genomics1471-21642013-02-0114110110.1186/1471-2164-14-101AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applicationsVan Geystelen AnneleenDecorte RonnyLarmuseau Maarten HD<p>Abstract</p> <p>Background</p> <p>Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.</p> <p>Results</p> <p>We present an automated approach, ‘AMY-tree’, which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.</p> <p>Conclusions</p> <p>Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.</p>http://www.biomedcentral.com/1471-2164/14/101Haploid markerPhylogenyNext-generation sequencingSNP callingY-SNP mutationsY chromosome haplogroups |
| spellingShingle | Van Geystelen Anneleen Decorte Ronny Larmuseau Maarten HD AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications BMC Genomics Haploid marker Phylogeny Next-generation sequencing SNP calling Y-SNP mutations Y chromosome haplogroups |
| title | AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications |
| title_full | AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications |
| title_fullStr | AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications |
| title_full_unstemmed | AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications |
| title_short | AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications |
| title_sort | amy tree an algorithm to use whole genome snp calling for y chromosomal phylogenetic applications |
| topic | Haploid marker Phylogeny Next-generation sequencing SNP calling Y-SNP mutations Y chromosome haplogroups |
| url | http://www.biomedcentral.com/1471-2164/14/101 |
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