MarkerSet: a marker selection tool based on markers location and informativity in experimental designs.

BMC Research Notes
Olivier Demeure, Frédéric Lecerf

Abstract

The recent sequencing of full genomes has led to the availability of many SNP markers which are very useful for the mapping of complex traits. In livestock production, there are still no commercial arrays and many studies use home-made sets of SNPs. Thus, the current methodologies for SNP genotyping are still expensive and it is a crucial step to select the SNPs to use. Indeed, the main factors affecting the power of the linkage analyses are the density of the genetic map and the heterozygosity of markers in tested animal parents. This is why we have developed a PERL program selecting a defined number of markers based on their locations on the genome and their informativity in specific experimental designs. As an option, different experimental designs can be combined in order to select the best possible common marker set. The program has been tested using different conditions of marker informativity and density with both real and simulated datasets. The results show the efficiency of our program to select the most informative markers even if there is a wide range of informativity for whole genome scan mapping analyses. In case of combination of different experimental crosses, the multidesign mode can optimize the SNP markers se...Continue Reading

References

Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Dec 19, 2003·American Journal of Human Genetics·Christopher S CarlsonDeborah A Nickerson
Sep 17, 2004·Genetic Epidemiology·Daniel O Stram
Dec 14, 2004·Nature·Gane Ka-Shu WongUNKNOWN International Chicken Polymorphism Map Consortium
Jul 12, 2005·Human Genomics·Daniel O Stram
Jun 17, 2006·BMC Bioinformatics·Pierre NicolasLei M Li
Feb 3, 2007·Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society·Jingwu He, Alex Zelikovsky
Mar 31, 2007·IEEE Transactions on Nanobioscience·Jingwu He, Alexander Zelikovsky
Dec 1, 2007·International Journal of Bioinformatics Research and Applications·Jingwu HeAlexander Zelikovsky

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Citations

Feb 1, 2011·Molecular Genetics and Genomics : MGG·Fanny CalengeCatherine Beaumont
Apr 9, 2014·Genetics, Selection, Evolution : GSE·Thanh-Son TranSandrine Mignon-Grasteau
Aug 25, 2009·Neuroscience and Biobehavioral Reviews·A V KalueffJ R Homberg
Dec 6, 2017·The Pharmacogenomics Journal·J JackK L Richards

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Methods Mentioned

BETA
genotyping

Software Mentioned

config
PERL
pm
MarkerSet

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