Original message: From david.machughucd.ie Fri Nov 12 07:54:34 2010 From: David MacHugh <david.machughucd.ie> To: Multiple Recipients of <angenmapanimalgenome.org> Subject: Linkage mapping software for SNP chip data in pedigrees Date: Fri, 12 Nov 2010 07:54:34 -0600 Hi everyone, We currently trying to find suitable software for linkage mapping of a sheep monogenic trait using 54K Illumina SNP chip data. The backcross pedigree consists of approximately 80 animals and further details can be found in the following paper: http://www.ncbi.nlm.nih.gov/pubmed/17242863 We are finding it difficult to identify suitable software that can handle dense SNP marker data in conventional pedigree linkage analyses. Therefore, I would be grateful if anyone could suggest software packages that can handle SNP chip data from conventional genetic linkage mapping pedigree experiments. Most of the recent software development seems to be geared towards genetic association studies. Also, we would be interested in collaborating on these linkage analyses if anyone is able to help. Best wishes, David. David MacHugh, Ph.D. Associate Professor of Genomics, Animal Genomics Laboratory, University College Dublin. www.animalgenomics.ucd.ie/dmachugh.php

From david.machughucd.ie Mon Nov 22 13:12:16 2010 From: David MacHugh <david.machughucd.ie> To: Multiple Recipients of <angenmapanimalgenome.org> Subject: Summary of responses to question on linkage analyses using ovine SNP chip data Date: Mon, 22 Nov 2010 13:12:16 -0600 Dear colleagues, As requested I have prepared a summary of the responses I received regarding my question about using SNP chip data to map a monogenic trait in a sheep pedigree we have been working on for the last number of years. I have placed a PDF summary of the responses at the following link: https://files.me.com/davidmachugh/odz1eu If anyone has any further queries or suggestions, please don't hesitate to email me. Best regard and thanks again for your help with this question. David. Responses: Ikhide Imumorin at Cornell (www.ansci.cornell.edu/faculty/imumorin.html) suggested the list of programs available from The Laboratory of Statistical Genetics at the Rockefeller University (http://linkage.rockefeller.edu/soft). This list is regularly updated and the most recent update was on 7th October 2010). The software packages that may be useful for our problem are: ALLEGRO from Decode Genetics; ALOHOMORA from the Max Belbruck Center for Molecular Medicine in Berlin; DCHIP LINKAGE from Stanford University (www.dchip.org); EAGLET from Columbia University; EASYLINKAGE from the Institute of Human Genetics, Charitéirchow Campus Berlin (compbio.charite.de/genetik/hoffmann/easyLINKAGE); GENEHUNTER software package available from the Broad Institute and elsewhere; The GLUE web interface to multiple linkage analysis programs; GRIDQTL (www.gridqtl.org.uk); LAMP (www.sph.umich.edu/csg/abecasis/LAMP); MENDEL from UCLA – can import PLINK files and do linkage analyses (www.genetics.ucla.edu/software); MERLIN from the University of Michigan (www.sph.umich.edu/csg/abecasis/Merlin); MORGAN from the University of Washington (www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml); SNPLINK from the Institute for Cancer Research in the UK (tinyurl.com/3973lg2); SOLAR from the Southwest Foundation for Biomedical Research (www.sfbr.org/Departments/genetics_detail.aspx?p=37); Cord Drogemuller at the Institute of Genetics at the University of Berne suggested the use of MERLIN and possibly PLINK for homozygosity mapping of affected animals only on the chromosome where linkage had been previously detected (OAR5). Juan Pedro Steibel at Michigan State University suggested the use of QXPAK v. 5.02 available from the Catalan Institution for Research and Advanced Studies (www.icrea.cat/Web/OtherSectionViewer.aspx?key=485&titol=Software:%20Qxpak&researcher=255). Dorian Garrick at Iowa State suggested identify by descent (IBD) methods to pinpoint the most likely homozygous stretch of SNPs in the genome scan data from the homozygous recessive individuals in the pedigree. Robert Schnabel at the University of Missouri suggested using the latest re-written version of CRI-MAP available from Jill Maddox at the University of Melbourne. Jules Hernandez at IRTA in Catalonia suggested using the GenABEL package in R. However, he indicated that there may be some glitches in the software. Also, this software is geared specifically towards GWAS-type projects. Chris Haley at the Roslin Institute suggested using the following software packages and also indicated that this is a problem that other people are struggling with. Alohomora: http://bioinformatics.oxfordjournals.org/content/21/9/2123.full SNPLink: http://bioinformatics.oxfordjournals.org/content/21/9/2123.full SNPHiTLink: http://www.biomedcentral.com/1471-2105/10/121 Jill Maddox also suggested the use of the up-dated version of CRI-MAP. David Henderson suggested using the R/QTL package (www.rqtl.org). Mark Fife at the Institute of Animal Health suggested using GRIDQTL (www.gridqtl.org.uk). Jens Tetens at the Christian-Albrechts-University, Kiel suggested using MERLIN with some modifications that involve a haplotype approach. James Kijas at CSIRO also suggested using the modified version of CRI-MAP available from Jill Maddox. Helene Gilbert at INRA suggested the QTLMap software package (dga7.jouy.inra.fr/qtlmap/index.html#Presentation). John McEwan at the University of Otago suggested using the modified version of CRI-MAP and also doing analyses of homozygosity and FST across the chromosome between affected and control animals. Ricardo Pong-Wong at the Roslin provided a very detailed response and suggested using QTL Express with reduced numbers of SNPs on the target chromosome. He also suggested using homozygosity mapping.

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