| Ancestral informative marker selection and population structure visualization using sparse laplacian eigenfunctions. | |
| | |
MedLine Citation:
|
PMID: 21079796 Owner: NLM Status: In-Process |
Abstract/OtherAbstract:
|
Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA) has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs) without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM) to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference. |
| | |
Authors:
|
Jun Zhang |
Related Documents
:
|
22444166 - Polymorphism identification, rh mapping and association of placental lactogen gene with... 3746136 - Examples of the effect of genetic variation on competing species. 17956396 - Effective population size associated with self-fertilization: lessons from temporal cha... 22325926 - Genetic improvement of reproductive efficiency of sheep and goats. 11812126 - Mistranslation induced by streptomycin provokes a recabc/ruvabc-dependent mutator pheno... 1488746 - Mutations of p53 gene in human colorectal tumor in japan: molecular epidemiological asp... |
Publication Detail:
|
Type: Journal Article Date: 2010-11-04 |
Journal Detail:
|
Title: PloS one Volume: 5 ISSN: 1932-6203 ISO Abbreviation: PLoS ONE Publication Date: 2010 |
Date Detail:
|
Created Date: 2010-11-16 Completed Date: - Revised Date: - |
Medline Journal Info:
|
Nlm Unique ID: 101285081 Medline TA: PLoS One Country: United States |
Other Details:
|
Languages: eng Pagination: e13734 Citation Subset: IM |
Affiliation:
|
Department of Radiology, The University of Chicago, Chicago, Illinois, United States of America. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
|
|
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: A voltage-sensitive dye-based assay for the identification of differentiated neurons derived from em...
Next Document: Anti-tumor effect in human lung cancer by a combination treatment of novel histone deacetylase inhib...