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Towards the Human Genotope

Huggins, Peter and Pachter, Lior and Sturmfels, Bernd (2007) Towards the Human Genotope. Bulletin of Mathematical Biology, 69 (8). pp. 2723-2735. ISSN 0092-8240. doi:10.1007/s11538-007-9244-7. https://resolver.caltech.edu/CaltechAUTHORS:20170307-095818473

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1007/s11538-007-9244-7DOIArticle
https://link.springer.com/article/10.1007%2Fs11538-007-9244-7PublisherArticle
http://rdcu.be/pSRAPublisherFree ReadCube access
https://arxiv.org/abs/q-bio/0611032arXivDiscussion Paper
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
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.
Funders:
Funding AgencyGrant Number
Defense Advanced Research Projects Agency (DARPA)HR0011-05-1-0057
Subject Keywords:ENCODE project · Genotope · Human variation · Polytope · Single nucleotide polymorphism
Issue or Number:8
DOI:10.1007/s11538-007-9244-7
Record Number:CaltechAUTHORS:20170307-095818473
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170307-095818473
Official Citation:Huggins, P., Pachter, L. & Sturmfels, B. Bull. Math. Biol. (2007) 69: 2723. doi:10.1007/s11538-007-9244-7
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74837
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Mar 2017 18:01
Last Modified:11 Nov 2021 05:30

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