The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratification
Genome-wide association (GWA) studies have become a standard approach for discovering and validating genomic polymorphisms putatively associated with phenotypes of interest. Accounting for population structure in GWA studies is critical to attain unbiased parameter measurements and control Type I er...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2012-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00301/full |
| _version_ | 1819060620792692736 |
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| author | Robert eMakowsky Qi eYan Howard W Wiener Michael eSandel Brahim eAissani Hemant K Tiwari Sadeep eShrestha |
| author_facet | Robert eMakowsky Qi eYan Howard W Wiener Michael eSandel Brahim eAissani Hemant K Tiwari Sadeep eShrestha |
| author_sort | Robert eMakowsky |
| collection | DOAJ |
| description | Genome-wide association (GWA) studies have become a standard approach for discovering and validating genomic polymorphisms putatively associated with phenotypes of interest. Accounting for population structure in GWA studies is critical to attain unbiased parameter measurements and control Type I error. One common approach to accounting for population structure is to include several principal components derived from the entire autosomal dataset, which reflects population structure signal. However, knowing which components to include is subjective and generally not conclusive. We examined how phylogenetic signal from mitochondrial DNA (mtDNA) and chromosome Y (chr:Y) markers is concordant with principal component data based on autosomal markers to determine whether mtDNA and chr:Y phylogenetic data can help guide principal component selection. Using HAPMAP and other original data from individuals of multiple ancestries, we examined the relationships of mtDNA and chr:Y phylogenetic signal with the autosomal PCA using best subset logistic regression. We show that while the two approaches agree at times, this is independent of the component order and not completely represented in the Eigen values. Additionally, we use simulations to demonstrate that our approach leads to a slightly reduced Type I error rate compared to the standard approach. This approach provides preliminary evidence to support the theoretical concept that mtDNA and chr:Y data can be informative in locating the PCs that are most associated with evolutionary history of populations that are being studied, although the utility of such information will depend on the specific situation. |
| first_indexed | 2024-12-21T14:29:54Z |
| format | Article |
| id | doaj.art-3ff65220e15849418a6cd64732e7412f |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-21T14:29:54Z |
| publishDate | 2012-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-3ff65220e15849418a6cd64732e7412f2022-12-21T19:00:32ZengFrontiers Media S.A.Frontiers in Genetics1664-80212012-12-01310.3389/fgene.2012.0030136458The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratificationRobert eMakowsky0Qi eYan1Howard W Wiener2Michael eSandel3Brahim eAissani4Hemant K Tiwari5Sadeep eShrestha6University of Alabama at BirminghamUniversity of Alabama at BirminghamUniversity of Alabama at BirminghamUniversity of Alabama at BirminghamUniversity of Alabama at BirminghamUniversity of Alabama at BirminghamUniversity of Alabama at BirminghamGenome-wide association (GWA) studies have become a standard approach for discovering and validating genomic polymorphisms putatively associated with phenotypes of interest. Accounting for population structure in GWA studies is critical to attain unbiased parameter measurements and control Type I error. One common approach to accounting for population structure is to include several principal components derived from the entire autosomal dataset, which reflects population structure signal. However, knowing which components to include is subjective and generally not conclusive. We examined how phylogenetic signal from mitochondrial DNA (mtDNA) and chromosome Y (chr:Y) markers is concordant with principal component data based on autosomal markers to determine whether mtDNA and chr:Y phylogenetic data can help guide principal component selection. Using HAPMAP and other original data from individuals of multiple ancestries, we examined the relationships of mtDNA and chr:Y phylogenetic signal with the autosomal PCA using best subset logistic regression. We show that while the two approaches agree at times, this is independent of the component order and not completely represented in the Eigen values. Additionally, we use simulations to demonstrate that our approach leads to a slightly reduced Type I error rate compared to the standard approach. This approach provides preliminary evidence to support the theoretical concept that mtDNA and chr:Y data can be informative in locating the PCs that are most associated with evolutionary history of populations that are being studied, although the utility of such information will depend on the specific situation.http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00301/fullMitochondriaY ChromosomephylogenyPCApopulation sub-structure |
| spellingShingle | Robert eMakowsky Qi eYan Howard W Wiener Michael eSandel Brahim eAissani Hemant K Tiwari Sadeep eShrestha The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratification Frontiers in Genetics Mitochondria Y Chromosome phylogeny PCA population sub-structure |
| title | The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratification |
| title_full | The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratification |
| title_fullStr | The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratification |
| title_full_unstemmed | The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratification |
| title_short | The utility of mitochondrial and Y chromosome phylogenetic data to improve correction for population stratification |
| title_sort | utility of mitochondrial and y chromosome phylogenetic data to improve correction for population stratification |
| topic | Mitochondria Y Chromosome phylogeny PCA population sub-structure |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00301/full |
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