@article {143,
	title = {Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease.},
	journal = {Cell},
	volume = {184},
	year = {2021},
	month = {2021 05 13},
	pages = {2633-2648.e19},
	abstract = {<p>Long non-coding RNA (lncRNA) genes have well-established and important impacts on molecular and cellular functions. However, among the thousands of lncRNA genes, it is still a major challenge to identify the subset with disease or trait relevance. To systematically characterize these lncRNA genes, we used Genotype Tissue Expression (GTEx) project v8 genetic and multi-tissue transcriptomic data to profile the expression, genetic regulation, cellular contexts, and trait associations of 14,100 lncRNA genes across 49 tissues for 101 distinct complex genetic traits. Using these approaches, we identified 1,432 lncRNA gene-trait associations, 800 of which were not explained by stronger effects of neighboring protein-coding genes. This included associations between lncRNA quantitative trait loci and inflammatory bowel disease, type 1 and type 2 diabetes, and coronary artery disease, as well as rare variant associations to body mass index.</p>},
	keywords = {Coronary Artery Disease, Diabetes Mellitus, Type 1, Diabetes Mellitus, Type 2, Disease, Gene Expression Profiling, Genetic Variation, Humans, Inflammatory Bowel Diseases, Multifactorial Inheritance, Organ Specificity, Population, Quantitative Trait Loci, RNA, Long Noncoding, Transcriptome},
	issn = {1097-4172},
	doi = {10.1016/j.cell.2021.03.050},
	author = {de Goede, Olivia M and Nachun, Daniel C and Ferraro, Nicole M and Gloudemans, Michael J and Rao, Abhiram S and Smail, Craig and Eulalio, Tiffany Y and Aguet, Francois and Ng, Bernard and Xu, Jishu and Barbeira, Alvaro N and Castel, Stephane E and Kim-Hellmuth, Sarah and Park, YoSon and Scott, Alexandra J and Strober, Benjamin J and Brown, Christopher D and Wen, Xiaoquan and Hall, Ira M and Battle, Alexis and Lappalainen, Tuuli and Im, Hae Kyung and Ardlie, Kristin G and Mostafavi, Sara and Quertermous, Thomas and Kirkegaard, Karla and Montgomery, Stephen B}
}
@article {57,
	title = {Opportunities and challenges for transcriptome-wide association studies.},
	journal = {Nat Genet},
	volume = {51},
	year = {2019},
	month = {2019 04},
	pages = {592-599},
	abstract = {<p>Transcriptome-wide association studies (TWAS) integrate genome-wide association studies (GWAS) and gene expression datasets to identify gene-trait associations. In this Perspective, we explore properties of TWAS as a potential approach to prioritize causal genes at GWAS loci, by using simulations and case studies of literature-curated candidate causal genes for schizophrenia, low-density-lipoprotein cholesterol and Crohn{\textquoteright}s disease. We explore risk loci where TWAS accurately prioritizes the likely causal gene as well as loci where TWAS prioritizes multiple genes, some likely to be non-causal, owing to sharing of expression quantitative trait loci (eQTL). TWAS is especially prone to spurious prioritization with expression data from non-trait-related tissues or cell types, owing to substantial cross-cell-type variation in expression levels and eQTL strengths. Nonetheless, TWAS prioritizes candidate causal genes more accurately than simple baselines. We suggest best practices for causal-gene prioritization with TWAS and discuss future opportunities for improvement. Our results showcase the strengths and limitations of using eQTL datasets to determine causal genes at GWAS loci.</p>},
	keywords = {Crohn Disease, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Humans, Lipoproteins, LDL, Quantitative Trait Loci, Schizophrenia, Transcriptome},
	issn = {1546-1718},
	doi = {10.1038/s41588-019-0385-z},
	author = {Wainberg, Michael and Sinnott-Armstrong, Nasa and Mancuso, Nicholas and Barbeira, Alvaro N and Knowles, David A and Golan, David and Ermel, Raili and Ruusalepp, Arno and Quertermous, Thomas and Hao, Ke and Bj{\"o}rkegren, Johan L M and Im, Hae Kyung and Pasaniuc, Bogdan and Rivas, Manuel A and Kundaje, Anshul}
}
