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Nucleic Acids Research Advance Access published online on May 21, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp369
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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HomozygosityMapper—an interactive approach to homozygosity mapping

Dominik Seelow1,2,3,*, Markus Schuelke1,2, Friedhelm Hildebrandt4 and Peter Nürnberg3,5

1Department of Neuropaediatrics, 2NeuroCure Clinical Research Centre, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, D-13353 Berlin, 3Cologne Center for Genomics (CCG) and Institute for Genetics, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany, 4Department of Pediatrics, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0640, USA and 5Center for Molecular Medicine Cologne (CMMC), Universität zu Köln, Robert-Koch-Str. 21, D-50931 Köln, Germany

*To whom correspondence should be addressed. Tel: +49 30 4505 66263; Fax: +49 30 4505 66920; Email: dominik.seelow{at}charite.de

Received February 3, 2009. Revised April 14, 2009. Accepted April 24, 2009.

Homozygosity mapping is a common method for mapping recessive traits in consanguineous families. In most studies, applications for multipoint linkage analyses are applied to determine the genomic region linked to the disease. Unfortunately, these are neither suited for very large families nor for the inclusion of tens of thousands of SNPs. Even if less than 10 000 markers are employed, such an analysis may easily last hours if not days. Here we present a web-based approach to homozygosity mapping. Our application stores marker data in a database into which users can directly upload their own SNP genotype files. Within a few minutes, the database analyses the data, detects homozygous stretches and provides an intuitive graphical interface to the results. The homozygosity in affected individuals is visualized genome-wide with the ability to zoom into single chromosomes and user-defined chromosomal regions. The software also displays the underlying genotypes in all samples. It is integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. They can at any point restrict access to their data or make it public, allowing HomozygosityMapper to be used as a data repository for homozygosity-mapping studies. HomozygosityMapper is available at http://www.homozygositymapper.org/.


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