dorsal/arxiv
View SchemaTowards the Human Genotope
| Authors | Peter Huggins, Lior Pachter, Bernd Sturmfels |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611032 |
| URL | https://arxiv.org/abs/q-bio/0611032 |
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 towards 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.
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"abstract": "The human genotope is the convex hull of all allele frequency vectors that\ncan be obtained from the genotypes present in the human population. In this\npaper we take a few initial steps towards a description of this object, which\nmay be fundamental for future population based genetics studies. Here we use\ndata from the HapMap Project, restricted to two ENCODE regions, to study a\nsubpolytope of the human genotope. We study three different approaches for\nobtaining informative low-dimensional projections of this subpolytope. The\nprojections are specified by projection onto few tag SNPs, principal component\nanalysis, and archetypal analysis. We describe the application of our geometric\napproach to identifying structure in populations based on single nucleotide\npolymorphisms.",
"arxiv_id": "q-bio/0611032",
"authors": [
"Peter Huggins",
"Lior Pachter",
"Bernd Sturmfels"
],
"categories": [
"q-bio.PE",
"math.ST",
"q-bio.QM",
"stat.TH"
],
"title": "Towards the Human Genotope",
"url": "https://arxiv.org/abs/q-bio/0611032"
},
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