AMY-tree: software SNP calling Y chromosomal applications

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Joined: Mon Apr 23, 2012 6:15 pm
PostPosted: Sat Feb 16, 2013 5:16 pm
This tool could be interesting for usage on Geno2 and Y-sequence SNP readouts. A more thorough reading and publication of the final paper and software link is needed. Hope I can follow up.

AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications

Anneleen Van Geystelen, Ronny Decorte and Maarten HD Larmuseau

Abstract (provisional)
Background
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.

Results
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.

Conclusions
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.

http://www.biomedcentral.com/1471-2164/14/101/abstract
The complete article is available as a provisional PDF. The fully formatted PDF and HTML versions are in production.

BMC Genomics 2013, 14:101 doi:10.1186/1471-2164-14-101
Published: 13 February 2013
DNA/Admixture Central Europe (Alps, Tyrol, Dolomites, Raetia); Y-DNA J2a-L1064, J2a-L210, R1a-M17, R1b-U106 (L48-); mtDNA J1b1b, J1c1d, U5a2b2, U5b1b1. Projects : J2-M172, J2a-PF5197, Alpine DNA, ISOGG Wiki

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