Haploscope: a tool for the graphical display of haplotype structure in populations
Version of Record online: 6 DEC 2011
© 2011 Wiley Periodicals, Inc.
Volume 36, Issue 1, pages 17–21, January 2012
How to Cite
San Lucas, F. A., Rosenberg, N. A. and Scheet, P. (2012), Haploscope: a tool for the graphical display of haplotype structure in populations. Genet. Epidemiol., 36: 17–21. doi: 10.1002/gepi.20640
- Issue online: 29 DEC 2011
- Version of Record online: 6 DEC 2011
- Manuscript Accepted: 21 SEP 2011
- Manuscript Revised: 14 SEP 2011
- Manuscript Received: 27 JUN 2011
- NIH. Grant Numbers: R01 GM081441, U01 GM 92666, R01 HG005855, 5R03-CA143982
- The Schissler Foundation, Burroughs Wellcome Fund
- linkage disequilibrium;
Patterns of linkage disequilibrium are often depicted pictorially by using tools that rely on visualizations of raw data or pairwise correlations among individual markers. Such approaches can fail to highlight some of the more interesting and complex features of haplotype structure. To enable natural visual comparisons of haplotype structure across subgroups of a population (e.g. isolated subpopulations or cases and controls), we propose an alternative visualization that provides a novel graphical representation of haplotype frequencies. We introduce Haploscope, a tool for visualizing the haplotype cluster frequencies that are produced by statistical models for population haplotype variation. We demonstrate the utility of our technique by examining haplotypes around the LCT gene, an example of recent positive selection, in samples from the Human Genome Diversity Panel. Haploscope, which has flexible options for annotation and inspection of haplotypes, is available for download at http://scheet.org/software.