Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Barbeira, Alvaro N.; Dickinson, Scott P.; Bonazzola, Rodrigo; Zheng, Jiamao; Wheeler, Heather E.; Torres, Jason M.; Torstenson, Eric S.; Shah, Kaanan P.; Garcia, Tzintzuni; Edwards, Todd L.; Stahl, Eli A.; Huckins, Laura M.; GTEx Consortium; Laboratory, Data Analysis & Coordinating Center (LDACC)—Analysis Working Group; Aguet, François; Ardlie, Kristin G.; Cummings, Beryl B.; Gelfand, Ellen T.; Getz, Gad; Hadley, Kane; Handsaker, Robert E.; Huang, Katherine H.; Kashin, Seva; Karczewski, Konrad J.; Lek, Monkol; Li, Xiao; MacArthur, Daniel G.; Nedzel, Jared L.; Nguyen, Duyen T.; Noble, Michael S.; Segrè, Ayellet V.; Trowbridge, Casandra A.; Tukiainen, Taru; Statistical Methods groups—Analysis Working Group; Abell, Nathan S.; Balliu, Brunilda; Barshir, Ruth; Basha, Omer; Battle, Alexis; Bogu, Gireesh K.; Brown, Andrew; Brown, Christopher D.; Castel, Stephane E.; Chen, Lin S.; Chiang, Colby; Conrad, Donald F.; Damani, Farhan N.; Davis, Joe R.; Delaneau, Olivier; Dermitzakis, Emmanouil T.

doi:10.1038/s41467-018-03621-1

Cited by 69Genetic Associations and EpidemiologyBioinformatics and Genomic NetworksGenetic Mapping and Diversity in Plants and Animals

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Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

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Barbeira, Alvaro N., Dickinson, Scott P., Bonazzola, Rodrigo, Zheng, Jiamao, Wheeler, Heather E., Torres, Jason M., Torstenson, Eric S., Shah, Kaanan P., Garcia, Tzintzuni, Edwards, Todd L., Stahl, Eli A., Huckins, Laura M., GTEx Consortium, Laboratory, Data Analysis & Coordinating Center (LDACC)—Analysis Working Group, Aguet, François, Ardlie, Kristin G., Cummings, Beryl B., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Karczewski, Konrad J., Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segrè, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, Statistical Methods groups—Analysis Working Group, Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Castel, Stephane E., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frésard, Laure, Gamazon, Eric R., Garrido-Martín, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muñoz-Aguirre, Manuel, Ndungu, Anne W., Nobel, Andrew B., Oliva, Meritxell, Ongen, Halit, Palowitch, John J., Panousis, Nikolaos, Papasaikas, Panagiotis, Park, YoSon, Parsana, Princy, Payne, Anthony J., Peterson, Christine B., Quan, Jie, Reverter, Ferran, Sabatti, Chiara, Saha, Ashis, Sammeth, Michael, Scott, Alexandra J., Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Strober, Benjamin J., Sul, Jae Hoon, Tsang, Emily K., Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zappala, Zachary, Zaugg, Judith B., Zhou, Yi-Hui, Enhancing GTEx (eGTEx) groups, Akey, Joshua M., Bates, Daniel, Chan, Joanne, Chen, Lin S., Claussnitzer, Melina, Demanelis, Kathryn, Diegel, Morgan, Doherty, Jennifer A., Feinberg, Andrew P., Fernando, Marian S., Halow, Jessica, Hansen, Kasper D., Haugen, Eric, Hickey, Peter F., Hou, Lei, Jasmine, Farzana, Jian, Ruiqi, Jiang, Lihua, Johnson, Audra, Kaul, Rajinder, Kellis, Manolis, Kibriya, Muhammad G., Lee, Kristen, Li, Jin Billy, Li, Qin, Li, Xiao, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Montgomery, Stephen B., Nelson, Jemma, Neri, Fidencio J., Oliva, Meritxell, Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Stranger, Barbara E., Tang, Hua, Tsang, Emily K., Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, NIH Common Fund, Nierras, Concepcion R., NIH/NCI, Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., NIH/NHGrI, Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, NIH/NIMH, Addington, Anjene M., Koester, Susan E., NIH/NIDA, Little, A. Roger, Biospecimen Collection Source Site—NDrI, Brigham, Lori E., Hasz, Richard, Hunter, Marcus, Johns, Christopher, Johnson, Mark, Kopen, Gene, Leinweber, William F., Lonsdale, John T., McDonald, Alisa, Mestichelli, Bernadette, Myer, Kevin, Roe, Brian, Salvatore, Michael, Shad, Saboor, Thomas, Jeffrey A., Walters, Gary, Washington, Michael, Wheeler, Joseph, Biospecimen Collection Source Site—rPCI, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Biospecimen Core resource—VArI, Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Brain Bank repository—University of Miami Brain Endowment Bank, Davis, David A., Mash, Deborah C., Leidos Biomedical—Project Management, Undale, Anita H., Smith, Anna M., Tabor, David E., Roche, Nancy V., McLean, Jeffrey A., Vatanian, Negin, Robinson, Karna L., Sobin, Leslie, Barcus, Mary E., Valentino, Kimberly M., Qi, Liqun, Hunter, Steven, Hariharan, Pushpa, Singh, Shilpi, Um, Ki Sung, Matose, Takunda, Tomaszewski, Maria M., ELSI Study, Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Genome Browser Data Integration & Visualization—EBI, Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Genome Browser Data Integration & Visualization—UCSC Genomics Institute, University of California Santa Cruz, Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Nicolae, Dan L., Cox, Nancy J., Im, Hae Kyung·2018·Nature Communications

DOI 10.1038/s41467-018-03621-1PMC PMC5940825

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Abstract

Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. Colocalized significant associations in unexpected tissues underscore the need for an agnostic scanning of multiple contexts to improve our ability to detect causal regulatory mechanisms. Monogenic disease genes are enriched among significant associations for related traits, suggesting that smaller alterations of these genes may cause a spectrum of milder phenotypes.

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Authors: Barbeira, A. N., Dickinson, S. P., Bonazzola, R., Zheng, J., Wheeler, H. E., Torres, J. M., Torstenson, E. S., Shah, K. P., Garcia, T., Edwards, T. L., Stahl, E. A., Huckins, L. M., GTEx Consortium, Laboratory, D. A. &. C. C. (. W. G., Aguet, F., Ardlie, K. G., Cummings, B. B., Gelfand, E. T., Getz, G., Hadley, K., Handsaker, R. E., Huang, K. H., Kashin, S., Karczewski, K. J., Lek, M., Li, X., MacArthur, D. G., Nedzel, J. L., Nguyen, D. T., Noble, M. S., Segrè, A. V., Trowbridge, C. A., Tukiainen, T., Statistical Methods groups—Analysis Working Group, Abell, N. S., Balliu, B., Barshir, R., Basha, O., Battle, A., Bogu, G. K., Brown, A., Brown, C. D., Castel, S. E., Chen, L. S., Chiang, C., Conrad, D. F., Damani, F. N., Davis, J. R., Delaneau, O., Dermitzakis, E. T., Engelhardt, B. E., Eskin, E., Ferreira, P. G., Frésard, L., Gamazon, E. R., Garrido-Martín, D., Gewirtz, A. D. H., Gliner, G., Gloudemans, M. J., Guigo, R., Hall, I. M., Han, B., He, Y., Hormozdiari, F., Howald, C., Jo, B., Kang, E. Y., Kim, Y., Kim-Hellmuth, S., Lappalainen, T., Li, G., Li, X., Liu, B., Mangul, S., McCarthy, M. I., McDowell, I. C., Mohammadi, P., Monlong, J., Montgomery, S. B., Muñoz-Aguirre, M., Ndungu, A. W., Nobel, A. B., Oliva, M., Ongen, H., Palowitch, J. J., Panousis, N., Papasaikas, P., Park, Y., Parsana, P., Payne, A. J., Peterson, C. B., Quan, J., Reverter, F., Sabatti, C., Saha, A., Sammeth, M., Scott, A. J., Shabalin, A. A., Sodaei, R., Stephens, M., Stranger, B. E., Strober, B. J., Sul, J. H., Tsang, E. K., Urbut, S., van de Bunt, M., Wang, G., Wen, X., Wright, F. A., Xi, H. S., Yeger-Lotem, E., Zappala, Z., Zaugg, J. B., Zhou, Y.-H., groups, E. G. (., Akey, J. M., Bates, D., Chan, J., Chen, L. S., Claussnitzer, M., Demanelis, K., Diegel, M., Doherty, J. A., Feinberg, A. P., Fernando, M. S., Halow, J., Hansen, K. D., Haugen, E., Hickey, P. F., Hou, L., Jasmine, F., Jian, R., Jiang, L., Johnson, A., Kaul, R., Kellis, M., Kibriya, M. G., Lee, K., Li, J. B., Li, Q., Li, X., Lin, J., Lin, S., Linder, S., Linke, C., Liu, Y., Maurano, M. T., Molinie, B., Montgomery, S. B., Nelson, J., Neri, F. J., Oliva, M., Park, Y., Pierce, B. L., Rinaldi, N. J., Rizzardi, L. F., Sandstrom, R., Skol, A., Smith, K. S., Snyder, M. P., Stamatoyannopoulos, J., Stranger, B. E., Tang, H., Tsang, E. K., Wang, L., Wang, M., Van Wittenberghe, N., Wu, F., Zhang, R., Fund, N. C., Nierras, C. R., NIH/NCI, Branton, P. A., Carithers, L. J., Guan, P., Moore, H. M., Rao, A., Vaught, J. B., NIH/NHGrI, Gould, S. E., Lockart, N. C., Martin, C., Struewing, J. P., Volpi, S., NIH/NIMH, Addington, A. M., Koester, S. E., NIH/NIDA, Little, A. R., Site—NDrI, B. C. S., Brigham, L. E., Hasz, R., Hunter, M., Johns, C., Johnson, M., Kopen, G., Leinweber, W. F., Lonsdale, J. T., McDonald, A., Mestichelli, B., Myer, K., Roe, B., Salvatore, M., Shad, S., Thomas, J. A., Walters, G., Washington, M., Wheeler, J., Site—rPCI, B. C. S., Bridge, J., Foster, B. A., Gillard, B. M., Karasik, E., Kumar, R., Miklos, M., Moser, M. T., resource—VArI, B. C., Jewell, S. D., Montroy, R. G., Rohrer, D. C., Valley, D. R., Brain Bank repository—University of Miami Brain Endowment Bank, Davis, D. A., Mash, D. C., Leidos Biomedical—Project Management, Undale, A. H., Smith, A. M., Tabor, D. E., Roche, N. V., McLean, J. A., Vatanian, N., Robinson, K. L., Sobin, L., Barcus, M. E., Valentino, K. M., Qi, L., Hunter, S., Hariharan, P., Singh, S., Um, K. S., Matose, T., Tomaszewski, M. M., Study, E., Barker, L. K., Mosavel, M., Siminoff, L. A., Traino, H. M., Visualization—EBI, G. B. D. I. &., Flicek, P., Juettemann, T., Ruffier, M., Sheppard, D., Taylor, K., Trevanion, S. J., Zerbino, D. R., Genome Browser Data Integration & Visualization—UCSC Genomics Institute, U. O. C. S. C., Craft, B., Goldman, M., Haeussler, M., Kent, W. J., Lee, C. M., Paten, B., Rosenbloom, K. R., Vivian, J., Zhu, J., Nicolae, D. L., Cox, N. J., & Im, H. K.
Affiliations: University of Chicago (US)
Loyola University Chicago (US)
Vanderbilt University (US)
Vanderbilt University Medical Center (US)
Broad Institute (US)
Stanford University (US)
Ben-Gurion University of the Negev (IL)
Johns Hopkins University (US)
Universitat Pompeu Fabra (ES)
University of Geneva (CH)
University of Pennsylvania (US)
Columbia University Irving Medical Center (US)
Washington University in St. Louis (US)
Princeton University (US)
University of California, Los Angeles (US)
Universidade do Porto (PT)
Amsterdam UMC Location University of Amsterdam (NL)
Asan Medical Center (KR)
Columbia University (US)
Centre for Human Genetics (GB)
Duke University (US)
University of North Carolina at Chapel Hill (US)
The University of Texas MD Anderson Cancer Center (US)
Pfizer (United States) (US)
Universidade Federal do Rio de Janeiro (BR)
University of Utah (US)
University of Michigan (US)
North Carolina State University (US)
European Molecular Biology Laboratory (DE)
Altius Institute for Biomedical Sciences (US)
University of Washington (US)
NYU Langone Health (US)
National Institutes of Health (US)
National Cancer Institute (US)
National Institute of Dental and Craniofacial Research (US)
National Human Genome Research Institute (US)
Lifenet Health (US)
National Disease Research Interchange (US)
University at Buffalo, State University of New York (US)
Roswell Park Comprehensive Cancer Center (US)
Van Andel Institute (US)
University of Miami (US)
Leidos Biomedical Research Inc. (United States) (US)
Temple University (US)
Virginia Commonwealth University (US)
European Bioinformatics Institute (GB)
University of California, Santa Cruz (US)
Corresponding author: Im, Hae Kyung
ORCID: Barbeira, Alvaro N.
Bonazzola, Rodrigo
Wheeler, Heather E.
Torstenson, Eric S.
Edwards, Todd L.
Stahl, Eli A.
Huckins, Laura M.
Aguet, François
Ardlie, Kristin G.
Cummings, Beryl B.
Getz, Gad
Hadley, Kane
Handsaker, Robert E.
Huang, Katherine H.
Kashin, Seva
Karczewski, Konrad J.
Lek, Monkol
MacArthur, Daniel G.
Nedzel, Jared L.
Noble, Michael S.
Segrè, Ayellet V.
Tukiainen, Taru
Abell, Nathan S.
Balliu, Brunilda
Barshir, Ruth
Basha, Omer
Battle, Alexis
Bogu, Gireesh K.
Castel, Stephane E.
Conrad, Donald F.
Davis, Joe R.
Delaneau, Olivier
Dermitzakis, Emmanouil T.
Engelhardt, Barbara E.
Eskin, Eleazar
Frésard, Laure
Gamazon, Eric R.
Garrido-Martín, Diego
Gewirtz, Ariel D. H.
Gloudemans, Michael J.
Hall, Ira M.
Han, Buhm
Jo, Brian
Kim-Hellmuth, Sarah
Lappalainen, Tuuli
Li, Xin
Liu, Boxiang
Mangul, Serghei
McDowell, Ian C.
Mohammadi, Pejman
Monlong, Jean
Muñoz-Aguirre, Manuel
Nobel, Andrew B.
Ongen, Halit
Palowitch, John J.
Panousis, Nikolaos
Papasaikas, Panagiotis
Park, YoSon
Parsana, Princy
Payne, Anthony J.
Peterson, Christine B.
Quan, Jie
Sabatti, Chiara
Sammeth, Michael
Scott, Alexandra J.
Shabalin, Andrey A.
Strober, Benjamin J.
Sul, Jae Hoon
Urbut, Sarah
Wang, Gao
Wen, Xiaoquan
Wright, Fred A.
Xi, Hualin S.
Zappala, Zachary
Zaugg, Judith B.
Zhou, Yi-Hui
Akey, Joshua M.
Bates, Daniel
Chan, Joanne
Claussnitzer, Melina
Feinberg, Andrew P.
Hansen, Kasper D.
Haugen, Eric
Hickey, Peter F.
Jasmine, Farzana
Jian, Ruiqi
Jiang, Lihua
Kellis, Manolis
Lee, Kristen
Li, Jin Billy
Li, Qin
Lin, Shin
Liu, Yaping
Maurano, Matthew T.
Nelson, Jemma
Park, Yongjin
Pierce, Brandon L.
Rinaldi, Nicola J.
Rizzardi, Lindsay F.
Sandstrom, Richard
Smith, Kevin S.
Snyder, Michael P.
Stamatoyannopoulos, John
Tang, Hua
Wang, Li
Wang, Meng
Zhang, Rui
Branton, Philip A.
Struewing, Jeffery P.
Volpi, Simona
Addington, Anjene M.
Hasz, Richard
Foster, Barbara A.
Gillard, Bryan M.
Moser, Michael T.
Jewell, Scott D.
Rohrer, Daniel C.
Davis, David A.
Mash, Deborah C.
Tabor, David E.
Singh, Shilpi
Matose, Takunda
Mosavel, Maghboeba
Siminoff, Laura A.
Juettemann, Thomas
Ruffier, Magali
Sheppard, Dan
Trevanion, Stephen J.
Zerbino, Daniel R.
Craft, Brian
Haeussler, Maximilian
Paten, Benedict
Rosenbloom, Kate R.
Nicolae, Dan L.
Cox, Nancy J.
Im, Hae Kyung
Venue: Nature Communications
Publisher: Springer Science and Business Media LLC
Published: 2018-05-08
Volume: 9
Issue: 1
Pages: 1825-1825
ISSN: 2041-1723 (ISSN-L)
DOI: 10.1038/s41467-018-03621-1
PMC: PMC5940825
OpenAlex: W2952346218
Cited by: 69
References: 50
Citations by year: 2026: 16 · 2025: 3 · 2024: 4 · 2023: 2 · 2022: 1 · 2021: 6 · 2020: 2 · 2019: 10 · 2018: 16
FWCI: 5.20
Type: journal article
Language: en
Open access: gold
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Licence: cc-by
creativecommons.org/licenses/by/4.0 (tdm)
creativecommons.org/licenses/by/4.0 (vor)
Locations: Nature Communications (publishedVersion, cc-by)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Repositori digital de la UPF (Universitat Pompeu Fabra) (publishedVersion, cc-by)
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Funders: University of Miami
University of Pennsylvania
Harvard University
Loyola University Chicago
Georgia Clinical and Translational Science Alliance (UL1 TR000430)
Université de Genève
National Institutes of Health (UL1TR000430, 5p50mh094267-05)
Medical Research Council (MR/N01104X/1)
National Heart, Lung, and Blood Institute
National Institute of Mental Health (R01MH101814, T32MH020065, R01MH101822, R01MH090937, R01MH107666, R01MH101810, R01MH101782, R01MH101819, R01MH101820, R01MH090948, R01MH101825, R01MH090941, R01MH090936, R01MH090951)
National Institute on Drug Abuse (R01DA033684, R01DA006227, P50DA037844)
National Human Genome Research Institute (R15HG009569)
NIH Office of the Director
National Cancer Institute
National Institute of Diabetes and Digestive and Kidney Diseases (F31DK101202, P30DK020595)
National Institute of Neurological Disorders and Stroke
Common Fund
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
Keywords: tissue-specific gene expression, expression quantitative trait loci, PrediXcan, GWAS summary statistics, GTEx, gene mapping, phenotypic association, colocalization
MeSH terms: Chromosome Mapping, Computer Simulation, Humans, Models, Genetic, Organ Specificity, Phenotype, Genetic Variation, Meta-Analysis as Topic, Gene Expression, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study

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Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

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