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Genetically regulated gene expression underlies lipid traits in Hispanic cohorts

Author

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  • Angela Andaleon
  • Lauren S Mogil
  • Heather E Wheeler

Abstract

Plasma lipid levels are risk factors for cardiovascular disease, a leading cause of death worldwide. While many studies have been conducted in genetic variation underlying lipid levels, they mainly comprise individuals of European ancestry and thus their transferability to non-European populations is unclear. We performed genome-wide (GWAS) and imputed transcriptome-wide association studies of four lipid traits in the Hispanic Community Health Study/Study of Latinos cohort (HCHS/SoL, n = 11,103), replicated top hits in the Multi-Ethnic Study of Atherosclerosis (MESA, n = 3,855), and compared the results to the larger, predominantly European ancestry meta-analysis by the Global Lipids Genetics Consortium (GLGC, n = 196,475). In our GWAS, we found significant SNP associations in regions within or near known lipid genes, but in our admixture mapping analysis, we did not find significant associations between local ancestry and lipid phenotypes. In the imputed transcriptome-wide association study in multiple tissues and in different ethnicities, we found 59 significant gene-tissue-phenotype associations (P

Suggested Citation

  • Angela Andaleon & Lauren S Mogil & Heather E Wheeler, 2019. "Genetically regulated gene expression underlies lipid traits in Hispanic cohorts," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-21, August.
    • Handle: RePEc:plo:pone00:0220827
    DOI: 10.1371/journal.pone.0220827
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    References listed on IDEAS

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    1. Alvaro N. Barbeira & Scott P. Dickinson & Rodrigo Bonazzola & Jiamao Zheng & Heather E. Wheeler & Jason M. Torres & Eric S. Torstenson & Kaanan P. Shah & Tzintzuni Garcia & Todd L. Edwards & Eli A. St, 2018. "Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics," Nature Communications, Nature, vol. 9(1), pages 1-20, December.
    2. Lauren S Mogil & Angela Andaleon & Alexa Badalamenti & Scott P Dickinson & Xiuqing Guo & Jerome I Rotter & W Craig Johnson & Hae Kyung Im & Yongmei Liu & Heather E Wheeler, 2018. "Genetic architecture of gene expression traits across diverse populations," PLOS Genetics, Public Library of Science, vol. 14(8), pages 1-21, August.
    3. Alvaro N Barbeira & Milton Pividori & Jiamao Zheng & Heather E Wheeler & Dan L Nicolae & Hae Kyung Im, 2019. "Integrating predicted transcriptome from multiple tissues improves association detection," PLOS Genetics, Public Library of Science, vol. 15(1), pages 1-20, January.
    4. Claudia Giambartolomei & Damjan Vukcevic & Eric E Schadt & Lude Franke & Aroon D Hingorani & Chris Wallace & Vincent Plagnol, 2014. "Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics," PLOS Genetics, Public Library of Science, vol. 10(5), pages 1-15, May.
    5. Carl D. Langefeld & Hannah C. Ainsworth & Deborah S. Cunninghame Graham & Jennifer A. Kelly & Mary E. Comeau & Miranda C. Marion & Timothy D. Howard & Paula S. Ramos & Jennifer A. Croker & David L. Mo, 2017. "Transancestral mapping and genetic load in systemic lupus erythematosus," Nature Communications, Nature, vol. 8(1), pages 1-18, December.
    6. Andrés Moreno-Estrada & Simon Gravel & Fouad Zakharia & Jacob L McCauley & Jake K Byrnes & Christopher R Gignoux & Patricia A Ortiz-Tello & Ricardo J Martínez & Dale J Hedges & Richard W Morris & Cele, 2013. "Reconstructing the Population Genetic History of the Caribbean," PLOS Genetics, Public Library of Science, vol. 9(11), pages 1-19, November.
    7. Heather E Wheeler & Kaanan P Shah & Jonathon Brenner & Tzintzuni Garcia & Keston Aquino-Michaels & GTEx Consortium & Nancy J Cox & Dan L Nicolae & Hae Kyung Im, 2016. "Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues," PLOS Genetics, Public Library of Science, vol. 12(11), pages 1-23, November.
    8. Joseph Vijai & Zhaoming Wang & Sonja I. Berndt & Christine F. Skibola & Susan L. Slager & Silvia de Sanjose & Mads Melbye & Bengt Glimelius & Paige M. Bracci & Lucia Conde & Brenda M. Birmann & Sophia, 2015. "A genome-wide association study of marginal zone lymphoma shows association to the HLA region," Nature Communications, Nature, vol. 6(1), pages 1-7, May.
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