The Genotype-Tissue Expression (GTEx) project
Open accessAbstract
Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
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Of the 20 introgressed variants overlapping this window, 17 are splicing quantitative trait loci (sQTL, increasing intron excision, tag variant rs17544225: P = 3 × 10−9 [Bonferroni critical value P = 1 × 10−3]) in the spleen.
“Of the 20 introgressed variants overlapping this window, 17 are splicing quantitative trait loci (sQTL, increasing intron excision, tag variant rs17544225: P = 3 × 10−9 [Bonferroni critical value P = 1 × 10−3], Fig. 4E) in the spleen72.”
From Quantifying the contribution of Neanderthal introgression to the heritability of complex traits (2021) · cites this paper as [72]
The Statistical analysis and methods development section (page unavailable) identifies GTEx as a project intended to analyze splicing quantitative trait loci, so the citation supports the identity of the data resource. Our copy does not report the 17-of-20 count, rs17544225, the stated P value, increased intron excision, or a spleen-specific result. (LLM, conf=0.84)
Experimental — accuracy not yet measuredOnly 9 of the 953 genes with neuro-related IMPC phenotypes lack confirmed expression in any of the 34 neuro-related tissues tracked by IDG KMC.
“Because only 9 of the 953 genes lack confirmed expression in any of the 34 neuro-related tissues tracked by IDG KMC (for example, GTEx40,41, HPA42 and HPM43), these data suggest that the remaining 80% of this set have the potential to be associated with human neurobehavioural phenotypes, paving the way for new research avenues in this direction (see Supplementary Table S8).”
From Unexplored therapeutic opportunities in the human genome (2018) · cites this paper as [40]
Colocalization analyses using coloc and SMR/HEIDI support the hypothesis that the same causal SNP(s) influence SPI1 expression and AD risk.
“Colocalization analyses using coloc32 and SMR/HEIDI23 support the hypothesis that the same causal SNP(s) influence SPI1 expression and AD risk.”
From A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease (2017) · cites this paper as [23]
The Abstract discusses eQTLs generally, and the Statistical analysis and methods development section describes planned GTEx analyses. Neither reports coloc or SMR/HEIDI colocalization results, SPI1 expression, or Alzheimer’s disease risk. Searches for those terms and for shared causal SNPs found no passage addressing the claim. (LLM, conf=0.75)
Experimental — accuracy not yet measuredPolymorphisms in UQCC1 have been linked to human height and osteoarthritis.
“Polymorphisms in this gene have been linked to human height [42] and osteoarthritis [43], and rs2378353 has been found to have a significant impact on the splicing of UQCC1 in muscle-skeletal tissue, as well as its expression in multiple tissues including fibroblasts, muscle-skeletal tissue, and skin [44].”
From Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci (2023) · cites this paper as [44]
In the citing sentence, the height and osteoarthritis links are assigned to references [42] and [43], not to this GTEx paper [44]. A search of our copy for UQCC1, height, and osteoarthritis found no passage addressing those links; the Abstract discusses genetic variation and gene expression only in general terms. (LLM, conf=0.78)
Experimental — accuracy not yet measuredrs2378353 has a significant impact on the splicing of UQCC1 in muscle-skeletal tissue and its expression in multiple tissues including fibroblasts, muscle-skeletal tissue, and skin.
“Polymorphisms in this gene have been linked to human height [42] and osteoarthritis [43], and rs2378353 has been found to have a significant impact on the splicing of UQCC1 in muscle-skeletal tissue, as well as its expression in multiple tissues including fibroblasts, muscle-skeletal tissue, and skin [44].”
From Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci (2023) · cites this paper as [44]
The Abstract discusses genetic effects on expression and splicing generally, and the Design of the GTEx Project section describes collecting muscle, skin, and fibroblast samples. Searches for rs2378353 and UQCC1 found no passage reporting the claimed significant effects in those tissues. (LLM, conf=0.76)
Experimental — accuracy not yet measured
Large datasets of eQTLs are now available for a number of tissues in humans and animal models.
“Large datasets of eQTLs are now available for a number of tissues in humans and animal models [17, 22, 25, 26].”
From Multi-omics approaches to disease (2017) · cites this paper as [25]
The GTEx project integrated genetic variation with gene expression in the brain.
“the integration of genetic variation with gene expression in the brain by the Genotype-Tissue Expression (GTEx) project15”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [15]
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- Authors
- Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N., Foster, B., Moser, M., Karasik, E., Gillard, B., Ramsey, K., Sullivan, S., Bridge, J., Magazine, H., Syron, J., Fleming, J., Siminoff, L., Traino, H., Mosavel, M., Barker, L., Jewell, S., Rohrer, D., Maxim, D., Filkins, D., Harbach, P., Cortadillo, E., Berghuis, B., Turner, L., Hudson, E., Feenstra, K., Sobin, L., Robb, J., Branton, P., Korzeniewski, G., Shive, C., Tabor, D., Qi, L., Groch, K., Nampally, S., Buia, S., Zimmerman, A., Smith, A., Burges, R., Robinson, K., Valentino, K., Bradbury, D., Cosentino, M., Diaz-Mayoral, N., Kennedy, M., Engel, T., Williams, P., Erickson, K., Ardlie, K., Winckler, W., Getz, G., DeLuca, D., MacArthur, D., Kellis, M., Thomson, A., Young, T., Gelfand, E., Donovan, M., Meng, Y., Grant, G., Mash, D., Marcus, Y., Basile, M., Liu, J., Zhu, J., Tu, Z., Cox, N. J., Nicolae, D. L., Gamazon, E. R., Im, H. K., Konkashbaev, A., Pritchard, J., Stevens, M., Flutre, T., Wen, X., Dermitzakis, E. T., Lappalainen, T., Guigo, R., Monlong, J., Sammeth, M., Koller, D., Battle, A., Mostafavi, S., McCarthy, M., Rivas, M., Maller, J., Rusyn, I., Nobel, A., Wright, F., Shabalin, A., Feolo, M., Sharopova, N., Sturcke, A., Paschal, J., Anderson, J. M., Wilder, E. L., Derr, L. K., Green, E. D., Struewing, J. P., Temple, G., Volpi, S., Boyer, J. T., Thomson, E. J., Guyer, M. S., Ng, C., Abdallah, A., Colantuoni, D., Insel, T. R., Koester, S. E., Little, A. R., Bender, P. K., Lehner, T., Yao, Y., Compton, C. C., Vaught, J. B., Sawyer, S., Lockhart, N. C., Demchok, J., & Moore, H. F.
- Affiliations
- National Disease Research Interchange (US)
- Lifenet Health (US)
- Drexel University (US)
- Jefferson Einstein Philadelphia Hospital (US)
- Roswell Park Comprehensive Cancer Center (US)
- Virginia Commonwealth University (US)
- Van Andel Institute (US)
- Science Applications International Corporation (United States) (US)
- Broad Institute (US)
- University of Miami (US)
- Harvard University (US)
- Icahn School of Medicine at Mount Sinai (US)
- University of Chicago (US)
- Howard Hughes Medical Institute (US)
- University of Geneva (CH)
- Centre for Genomic Regulation (ES)
- Stanford University (US)
- University of Oxford (GB)
- University of North Carolina at Chapel Hill (US)
- National Institutes of Health (US)
- National Human Genome Research Institute (US)
- National Institute of Mental Health (US)
- National Cancer Institute (US)
- Corresponding author
- Winckler, Wendy
- Getz, Gad
- Struewing, Jeffery P
- ORCID
- Hasz, Richard
- Foster, Barbara
- Gillard, Bryan
- Siminoff, Laura
- Mosavel, Maghboeba
- Jewell, Scott
- Tabor, David
- Diaz-Mayoral, Norma
- Kennedy, Mary
- Ardlie, Kristin
- Winckler, Wendy
- Getz, Gad
- DeLuca, David
- MacArthur, Daniel
- Kellis, Manolis
- Thomson, Alexander
- Young, Taylor
- Meng, Yan
- Mash, Deborah
- Liu, Jun
- Zhu, Jun
- Tu, Zhidong
- Cox, Nancy J
- Nicolae, Dan L
- Gamazon, Eric R
- Im, Hae Kyung
- Konkashbaev, Anuar
- Pritchard, Jonathan
- Wen, Xiaoquan
- Dermitzakis, Emmanouil T
- Lappalainen, Tuuli
- Monlong, Jean
- Sammeth, Michael
- Koller, Daphne
- Battle, Alexis
- Mostafavi, Sara
- McCarthy, Mark
- Maller, Julian
- Rusyn, Ivan
- Nobel, Andrew
- Wright, Fred
- Shabalin, Andrey
- Anderson, James M
- Wilder, Elizabeth L
- Green, Eric D
- Struewing, Jeffery P
- Volpi, Simona
- Insel, Thomas R
- Little, A Roger
- Bender, Patrick K
- Lehner, Thomas
- Yao, Yin
- Compton, Carolyn C
- Sawyer, Sherilyn
- Venue
- Nature Genetics
- Published
- 2013-05-29
- Volume
- 45
- Issue
- 6
- Pages
- 580-585
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4010069
- OpenAlex
- W1585895556
- Semantic Scholar
- d868486f256994e1a6a7c94780af714f2974ecc7
- Cited by
- 263
- References
- 18
- Citations by year
- 2026: 1 · 2025: 27 · 2024: 39 · 2023: 39 · 2022: 49 · 2021: 37 · 2020: 26 · 2019: 20 · 2018: 9 · 2017: 10 · 2016: 2 · 2015: 2 · 2014: 2
- FWCI
- 1.32
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Genetics (publishedVersion, cc-by-nc-sa)
- HAL (submittedVersion, other-oa)
- HAL (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- Wellcome Trust (090532)
- National Institutes of Health (Z99 HG999999, HHSN261200800001C)
- National Heart, Lung, and Blood Institute (HHSN268201000029C)
- National Institute of Mental Health (R01MH090937, R01MH101819, R01 MH090948, R01-MH090941, R01MH090936, R01MH090951)
- National Institute on Drug Abuse (R01 DA033684, R01DA006227‐17, R01 DA006227)
- National Cancer Institute (HHSN261200800001E))
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- gene expression, genetic variation, regulatory polymorphisms, tissue-specific gene expression, human tissue banks, disease susceptibility, GWAS loci, expression quantitative trait loci
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