Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities

Dense single nucleotide polymorphism (SNP) panels are widely used for genome-wide association studies (GWAS). In these panels, SNPs within a genomic segment tend to be highly correlated. Thus, association studies based on testing the significance of single SNPs are not very effective, and genomic-wi...

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Autores principales: Li, Jinghui, Wang, Zigui, Fernando, Rohan, Cheng, Hao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Short Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157676/
https://www.ncbi.nlm.nih.gov/pubmed/34039266
http://dx.doi.org/10.1186/s12711-021-00638-x
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author Li, Jinghui
Wang, Zigui
Fernando, Rohan
Cheng, Hao
author_facet Li, Jinghui
Wang, Zigui
Fernando, Rohan
Cheng, Hao
author_sort Li, Jinghui
collection PubMed
description Dense single nucleotide polymorphism (SNP) panels are widely used for genome-wide association studies (GWAS). In these panels, SNPs within a genomic segment tend to be highly correlated. Thus, association studies based on testing the significance of single SNPs are not very effective, and genomic-window based tests have been proposed to address this problem. However, when the SNP density on the genotype panel is not homogeneous, genomic-window based tests can lead to the detection of spurious associations by declaring effects of genomic windows that explain a large proportion of genetic variance as significant. We propose two methods to solve this problem.
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spelling pubmed-81576762021-05-28 Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities Li, Jinghui Wang, Zigui Fernando, Rohan Cheng, Hao Genet Sel Evol Short Communication Dense single nucleotide polymorphism (SNP) panels are widely used for genome-wide association studies (GWAS). In these panels, SNPs within a genomic segment tend to be highly correlated. Thus, association studies based on testing the significance of single SNPs are not very effective, and genomic-window based tests have been proposed to address this problem. However, when the SNP density on the genotype panel is not homogeneous, genomic-window based tests can lead to the detection of spurious associations by declaring effects of genomic windows that explain a large proportion of genetic variance as significant. We propose two methods to solve this problem. BioMed Central 2021-05-26 /pmc/articles/PMC8157676/ /pubmed/34039266 http://dx.doi.org/10.1186/s12711-021-00638-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Short Communication
Li, Jinghui
Wang, Zigui
Fernando, Rohan
Cheng, Hao
Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities
title Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities
title_full Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities
title_fullStr Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities
title_full_unstemmed Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities
title_short Tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous SNP densities
title_sort tests of association based on genomic windows can lead to spurious associations when using genotype panels with heterogeneous snp densities
topic Short Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157676/
https://www.ncbi.nlm.nih.gov/pubmed/34039266
http://dx.doi.org/10.1186/s12711-021-00638-x
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