Discovering weaker genetic associations guided by known associations
Abstract Background The current understanding of the genetic basis of complex human diseases is that they are caused and affected by many common and rare genetic variants. A considerable number of the disease-associated variants have been identified by Genome Wide Association Studies, however, they...
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doaj-5d60ea56fad74227b5b416b8e9fdc00d2021-04-02T14:45:36ZengBMCBMC Medical Genomics1755-87942020-02-0113S311010.1186/s12920-020-0667-4Discovering weaker genetic associations guided by known associationsHaohan Wang0Michael M. Vanyukov1Eric P. Xing2Wei Wu3Language Technologies Institute, School of Computer Science, Carnegie Mellon UniversityDepartment of Pharmaceutical Sciences, Departments of Psychiatry, and Human Genetics, University of PittsburghLanguage Technologies Institute, School of Computer Science, Carnegie Mellon UniversityComputational Biology Department, School of Computer Science, Carnegie Mellon UniversityAbstract Background The current understanding of the genetic basis of complex human diseases is that they are caused and affected by many common and rare genetic variants. A considerable number of the disease-associated variants have been identified by Genome Wide Association Studies, however, they can explain only a small proportion of heritability. One of the possible reasons for the missing heritability is that many undiscovered disease-causing variants are weakly associated with the disease. This can pose serious challenges to many statistical methods, which seems to be only capable of identifying disease-associated variants with relatively stronger coefficients. Results In order to help identify weaker variants, we propose a novel statistical method, Constrained Sparse multi-locus Linear Mixed Model (CS-LMM) that aims to uncover genetic variants of weaker associations by incorporating known associations as a prior knowledge in the model. Moreover, CS-LMM accounts for polygenic effects as well as corrects for complex relatednesses. Our simulation experiments show that CS-LMM outperforms other competing existing methods in various settings when the combinations of MAFs and coefficients reflect different scenarios in complex human diseases. Conclusions We also apply our method to the GWAS data of alcoholism and Alzheimer’s disease and exploratively discover several SNPs. Many of these discoveries are supported through literature survey. Furthermore, our association results strengthen the belief in genetic links between alcoholism and Alzheimer’s disease.http://link.springer.com/article/10.1186/s12920-020-0667-4Weak associationLinear mixed modelGWAS |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Haohan Wang Michael M. Vanyukov Eric P. Xing Wei Wu |
spellingShingle |
Haohan Wang Michael M. Vanyukov Eric P. Xing Wei Wu Discovering weaker genetic associations guided by known associations BMC Medical Genomics Weak association Linear mixed model GWAS |
author_facet |
Haohan Wang Michael M. Vanyukov Eric P. Xing Wei Wu |
author_sort |
Haohan Wang |
title |
Discovering weaker genetic associations guided by known associations |
title_short |
Discovering weaker genetic associations guided by known associations |
title_full |
Discovering weaker genetic associations guided by known associations |
title_fullStr |
Discovering weaker genetic associations guided by known associations |
title_full_unstemmed |
Discovering weaker genetic associations guided by known associations |
title_sort |
discovering weaker genetic associations guided by known associations |
publisher |
BMC |
series |
BMC Medical Genomics |
issn |
1755-8794 |
publishDate |
2020-02-01 |
description |
Abstract Background The current understanding of the genetic basis of complex human diseases is that they are caused and affected by many common and rare genetic variants. A considerable number of the disease-associated variants have been identified by Genome Wide Association Studies, however, they can explain only a small proportion of heritability. One of the possible reasons for the missing heritability is that many undiscovered disease-causing variants are weakly associated with the disease. This can pose serious challenges to many statistical methods, which seems to be only capable of identifying disease-associated variants with relatively stronger coefficients. Results In order to help identify weaker variants, we propose a novel statistical method, Constrained Sparse multi-locus Linear Mixed Model (CS-LMM) that aims to uncover genetic variants of weaker associations by incorporating known associations as a prior knowledge in the model. Moreover, CS-LMM accounts for polygenic effects as well as corrects for complex relatednesses. Our simulation experiments show that CS-LMM outperforms other competing existing methods in various settings when the combinations of MAFs and coefficients reflect different scenarios in complex human diseases. Conclusions We also apply our method to the GWAS data of alcoholism and Alzheimer’s disease and exploratively discover several SNPs. Many of these discoveries are supported through literature survey. Furthermore, our association results strengthen the belief in genetic links between alcoholism and Alzheimer’s disease. |
topic |
Weak association Linear mixed model GWAS |
url |
http://link.springer.com/article/10.1186/s12920-020-0667-4 |
work_keys_str_mv |
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1721561459201146880 |