Towards the Human Genotope
- Creators
- Huggins, Peter
- Pachter, Lior
- Sturmfels, Bernd
Abstract
The human genotope is the convex hull of all allele frequency vectors that can be obtained from the genotypes present in the human population. In this paper, we take a few initial steps toward a description of this object, which may be fundamental for future population based genetics studies. Here we use data from the HapMap Project, restricted to two ENCODE regions, to study a subpolytope of the human genotope. We study three different approaches for obtaining informative low-dimensional projections of this subpolytope. The projections are specified by projection onto few tag SNPs, principal component analysis, and archetypal analysis. We describe the application of our geometric approach to identifying structure in populations based on single nucleotide polymorphisms.
Additional Information
© 2007 Society for Mathematical Biology. Received: 10 January 2007 / Accepted: 15 June 2007 / Published online: 15 September 2007. This work was supported by in part by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0057.Attached Files
Submitted - 0611032.pdf
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Additional details
- Eprint ID
- 74837
- DOI
- 10.1007/s11538-007-9244-7
- Resolver ID
- CaltechAUTHORS:20170307-095818473
- HR0011-05-1-0057
- Defense Advanced Research Projects Agency (DARPA)
- Created
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2017-03-07Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field