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2. Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits

Author

Brown, Andrew A., Fernandez-Tajes, Juan J., Hong, Mun-gwan, Brorsson, Caroline A., Koivula, Robert W., Davtian, David, Dupuis, Théo, Sartori, Ambra, Michalettou, Theodora-Dafni, Forgie, Ian M., Adam, Jonathan, Allin, Kristine H., Caiazzo, Robert, Cederberg, Henna, De Masi, Federico, Elders, Petra J. M., Giordano, Giuseppe N., Haid, Mark, Hansen, Torben, Hansen, Tue H., Hattersley, Andrew T., Heggie, Alison J., Howald, Cédric, Jones, Angus G., Kokkola, Tarja, Laakso, Markku, Mahajan, Anubha, Mari, Andrea, McDonald, Timothy J., McEvoy, Donna, Mourby, Miranda, Musholt, Petra B., Nilsson, Birgitte, Pattou, Francois, Penet, Deborah, Raverdy, Violeta, Ridderstråle, Martin, Romano, Luciana, Rutters, Femke, Sharma, Sapna, Teare, Harriet, ‘t Hart, Leen, Tsirigos, Konstantinos D., Vangipurapu, Jagadish, Vestergaard, Henrik, Brunak, Søren, Franks, Paul W., Frost, Gary, Grallert, Harald, Jablonka, Bernd, McCarthy, Mark I., Pavo, Imre, Pedersen, Oluf, Ruetten, Hartmut, Walker, Mark, Adamski, Jerzy, Schwenk, Jochen M., Pearson, Ewan R., Dermitzakis, Emmanouil T., and Viñuela, Ana

Published
2023
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3. Proteomic analysis of 92 circulating proteins and their effects in cardiometabolic diseases

Author

Carland, Corinne, Png, Grace, Malarstig, Anders, Kho, Pik Fang, Gustafsson, Stefan, Michaelsson, Karl, Lind, Lars, Tsafantakis, Emmanouil, Karaleftheri, Maria, Dedoussis, George, Ramisch, Anna, Macdonald-Dunlop, Erin, Klaric, Lucija, Joshi, Peter K., Chen, Yan, Björck, Hanna M., Eriksson, Per, Carrasco-Zanini, Julia, Wheeler, Eleanor, Suhre, Karsten, Gilly, Arthur, Zeggini, Eleftheria, Viñuela, Ana, Dermitzakis, Emmanouil T., Wilson, James F., Langenberg, Claudia, Thareja, Gaurav, Halama, Anna, Schmidt, Frank, Zanetti, Daniela, and Assimes, Themistocles

Published
2023
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4. Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population

Author

Rouskas, Konstantinos, Katsareli, Efthymia A., Amerikanou, Charalampia, Dimopoulos, Alexandros C., Glentis, Stavros, Kalantzi, Alexandra, Skoulakis, Anargyros, Panousis, Nikolaos, Ongen, Halit, Bielser, Deborah, Planchon, Alexandra, Romano, Luciana, Harokopos, Vaggelis, Reczko, Martin, Moulos, Panagiotis, Griniatsos, Ioannis, Diamantis, Theodoros, Dermitzakis, Emmanouil T., Ragoussis, Jiannis, Dedoussis, George, and Dimas, Antigone S.

Published
2023
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6. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency

Author

Forny, Patrick, Bonilla, Ximena, Lamparter, David, Shao, Wenguang, Plessl, Tanja, Frei, Caroline, Bingisser, Anna, Goetze, Sandra, van Drogen, Audrey, Harshman, Keith, Pedrioli, Patrick G. A., Howald, Cedric, Poms, Martin, Traversi, Florian, Bürer, Céline, Cherkaoui, Sarah, Morscher, Raphael J., Simmons, Luke, Forny, Merima, Xenarios, Ioannis, Aebersold, Ruedi, Zamboni, Nicola, Rätsch, Gunnar, Dermitzakis, Emmanouil T., Wollscheid, Bernd, Baumgartner, Matthias R., and Froese, D. Sean

Published
2023
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10. Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Author

Mishra, Neha, Aden, Konrad, Blase, Johanna I., Baran, Nathan, Bordoni, Dora, Tran, Florian, Conrad, Claudio, Avalos, Diana, Jaeckel, Charlot, Scherer, Michael, Sørensen, Signe B., Overgaard, Silja H., Schulte, Berenice, Nikolaus, Susanna, Rey, Guillaume, Gasparoni, Gilles, Lyons, Paul A., Schultze, Joachim L., Walter, Jörn, Andersen, Vibeke, Dermitzakis, Emmanouil T., Schreiber, Stefan, and Rosenstiel, Philip

Published
2022
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11. Multi‐omics correlates of insulin resistance and circadian parameters mapped directly from human serum.

Author

Du, Ngoc‐Hien, Sinturel, Flore, Nowak, Nora, Gosselin, Pauline, Saini, Camille, Guessous, Idris, Jornayvaz, François R., Philippe, Jacques, Rey, Guillaume, Dermitzakis, Emmanouil T., Zenobi, Renato, Dibner, Charna, and Brown, Steven A.

Subjects
BRANCHED chain amino acids, TYPE 2 diabetes, METABOLIC disorders, INSULIN sensitivity, INSULIN resistance
Abstract

While it is generally known that metabolic disorders and circadian dysfunction are intertwined, how the two systems affect each other is not well understood, nor are the genetic factors that might exacerbate this pathological interaction. Blood chemistry is profoundly changed in metabolic disorders, and we have previously shown that serum factors change cellular clock properties. To investigate if circulating factors altered in metabolic disorders have circadian modifying effects, and whether these effects are of genetic origin, we measured circadian rhythms in U2OS cell in the presence of serum collected from diabetic, obese or control subjects. We observed that circadian period lengthening in U2OS cells was associated with serum chemistry that is characteristic of insulin resistance. Characterizing the genetic variants that altered circadian period length by genome‐wide association analysis, we found that one of the top variants mapped to the E3 ubiquitin ligase MARCH1 involved in insulin sensitivity. Confirming our data, the serum circadian modifying variants were also enriched in type 2 diabetes and chronotype variants identified in the UK Biobank cohort. Finally, to identify serum factors that might be involved in period lengthening, we performed detailed metabolomics and found that the circadian modifying variants are particularly associated with branched chain amino acids, whose levels are known to correlate with diabetes and insulin resistance. Overall, our multi‐omics data showed comprehensively that systemic factors serve as a path through which metabolic disorders influence circadian system, and these can be examined in human populations directly by simple cellular assays in common cultured cells. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland

Author

Chen, Chaoran, Nadeau, Sarah Ann, Topolsky, Ivan, Manceau, Marc, Huisman, Jana S., Jablonski, Kim Philipp, Fuhrmann, Lara, Dreifuss, David, Jahn, Katharina, Beckmann, Christiane, Redondo, Maurice, Noppen, Christoph, Risch, Lorenz, Risch, Martin, Wohlwend, Nadia, Kas, Sinem, Bodmer, Thomas, Roloff, Tim, Stange, Madlen, Egli, Adrian, Eckerle, Isabella, Kaiser, Laurent, Denes, Rebecca, Feldkamp, Mirjam, Nissen, Ina, Santacroce, Natascha, Burcklen, Elodie, Aquino, Catharine, de Gouvea, Andreia Cabral, Moccia, Maria Domenica, Grüter, Simon, Sykes, Timothy, Opitz, Lennart, White, Griffin, Neff, Laura, Popovic, Doris, Patrignani, Andrea, Tracy, Jay, Schlapbach, Ralph, Dermitzakis, Emmanouil T., Harshman, Keith, Xenarios, Ioannis, Pegeot, Henri, Cerutti, Lorenzo, Penet, Deborah, Blin, Anthony, Elies, Melyssa, Althaus, Christian L., Beisel, Christian, Beerenwinkel, Niko, Ackermann, Martin, and Stadler, Tanja

Published
2021
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13. Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

Author

Yang, Fan, Wang, Jiebiao, Consortium, The GTEx, Pierce, Brandon L, Chen, Lin S, 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, Abell, Nathan S, Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K, Brown, Andrew, Brown, Christopher D, Castel, Stephane E, Chiang, Colby, Conrad, Donald F, Cox, Nancy J, 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 DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Jo, Brian, Kang, Eun Yong, Kim, Yungil, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, 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, Nicolae, Dan L, 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, and Wang, Gao

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 2.1 Biological and endogenous factors, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, Generic health relevance, Good Health and Well Being, Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Gene Regulatory Networks, Genetic Predisposition to Disease, Genome-Wide Association Study, Genomics, Humans, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Selection, Genetic, Tissue Distribution, GTEx Consortium, Medical and Health Sciences, Bioinformatics
Abstract

The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their biological mechanisms. One common trans-eQTLs mechanism is "mediation" by a local (cis) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are "cis-mediators" of trans-eQTLs, including those "cis-hubs" involved in regulation of many trans-genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans-eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis-mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis-hubs and trans-eQTL regulation across tissue types.

Published
2017

14. Co-expression networks reveal the tissue-specific regulation of transcription and splicing

Author

Saha, Ashis, Kim, Yungil, Gewirtz, Ariel DH, Jo, Brian, Gao, Chuan, McDowell, Ian C, Consortium, The GTEx, Engelhardt, Barbara E, Battle, Alexis, 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, Abell, Nathan S, Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Bogu, Gireesh K, Brown, Andrew, Brown, Christopher D, Castel, Stephane E, Chen, Lin S, Chiang, Colby, Conrad, Donald F, Cox, Nancy J, Damani, Farhan N, Davis, Joe R, Delaneau, Olivier, Dermitzakis, Emmanouil T, Eskin, Eleazar, Ferreira, Pedro G, Frésard, Laure, Gamazon, Eric R, Garrido-Martín, Diego, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Im, Hae Kyung, Kang, Eun Yong, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Li, Xin, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I, Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B, Muñoz-Aguirre, Manuel, Ndungu, Anne W, Nicolae, Dan L, 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, Sammeth, Michael, Scott, Alexandra J, Shabalin, Andrey A, Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E, Strober, Benjamin J, and Sul, Jae Hoon

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Generic health relevance, Bayes Theorem, Databases, Genetic, Gene Expression Profiling, Gene Expression Regulation, Gene Regulatory Networks, Genotyping Techniques, Humans, Organ Specificity, Polymorphism, Single Nucleotide, RNA Splicing, Sequence Analysis, RNA, GTEx Consortium, Medical and Health Sciences, Bioinformatics
Abstract

Gene co-expression networks capture biologically important patterns in gene expression data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of genetic variants. Most network analyses to date have been limited to assessing correlation between total gene expression levels in a single tissue or small sets of tissues. Here, we built networks that additionally capture the regulation of relative isoform abundance and splicing, along with tissue-specific connections unique to each of a diverse set of tissues. We used the Genotype-Tissue Expression (GTEx) project v6 RNA sequencing data across 50 tissues and 449 individuals. First, we developed a framework called Transcriptome-Wide Networks (TWNs) for combining total expression and relative isoform levels into a single sparse network, capturing the interplay between the regulation of splicing and transcription. We built TWNs for 16 tissues and found that hubs in these networks were strongly enriched for splicing and RNA binding genes, demonstrating their utility in unraveling regulation of splicing in the human transcriptome. Next, we used a Bayesian biclustering model that identifies network edges unique to a single tissue to reconstruct Tissue-Specific Networks (TSNs) for 26 distinct tissues and 10 groups of related tissues. Finally, we found genetic variants associated with pairs of adjacent nodes in our networks, supporting the estimated network structures and identifying 20 genetic variants with distant regulatory impact on transcription and splicing. Our networks provide an improved understanding of the complex relationships of the human transcriptome across tissues.

Published
2017

15. Dynamic landscape and regulation of RNA editing in mammals

Author

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, 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, Cox, Nancy J, 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 DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, 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, Nicolae, Dan L, 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, and Zappala, Zachary

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Adenosine Deaminase, Animals, Female, Genotype, HEK293 Cells, Humans, Male, Mice, Muscles, Nuclear Proteins, Organ Specificity, Primates, Proteolysis, RNA Editing, RNA-Binding Proteins, Spatio-Temporal Analysis, Species Specificity, Transcriptome, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, General Science & Technology
Abstract

Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing.

Published
2017

16. Landscape of X chromosome inactivation across human tissues

Author

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, 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, Cox, Nancy J, 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 DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, 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, Nicolae, Dan L, 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, and Zappala, Zachary

Subjects
Genetics, Clinical Research, Human Genome, Generic health relevance, Good Health and Well Being, Chromosomes, Human, X, Female, Genes, X-Linked, Genome, Human, Genomics, Humans, Male, Organ Specificity, Phenotype, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptome, X Chromosome Inactivation, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, General Science & Technology
Abstract

X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to one-third of X-chromosomal genes are expressed from both the active and inactive X chromosomes (Xa and Xi, respectively) in female cells, with the degree of 'escape' from inactivation varying between genes and individuals. The extent to which XCI is shared between cells and tissues remains poorly characterized, as does the degree to which incomplete XCI manifests as detectable sex differences in gene expression and phenotypic traits. Here we describe a systematic survey of XCI, integrating over 5,500 transcriptomes from 449 individuals spanning 29 tissues from GTEx (v6p release) and 940 single-cell transcriptomes, combined with genomic sequence data. We show that XCI at 683 X-chromosomal genes is generally uniform across human tissues, but identify examples of heterogeneity between tissues, individuals and cells. We show that incomplete XCI affects at least 23% of X-chromosomal genes, identify seven genes that escape XCI with support from multiple lines of evidence and demonstrate that escape from XCI results in sex biases in gene expression, establishing incomplete XCI as a mechanism that is likely to introduce phenotypic diversity. Overall, this updated catalogue of XCI across human tissues helps to increase our understanding of the extent and impact of the incompleteness in the maintenance of XCI.

Published
2017

17. The impact of rare variation on gene expression across tissues

Author

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, 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, Cox, Nancy J, 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 DH, Gliner, Genna, Gloudemans, Michael J, Guigo, Roderic, Hall, Ira M, Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, 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, Nicolae, Dan L, 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, and Zappala, Zachary

Subjects
Bayes Theorem, Female, Gene Expression Profiling, Genetic Variation, Genome, Human, Genomics, Genotype, Humans, Male, Models, Genetic, Organ Specificity, Sequence Analysis, RNA, GTEx Consortium, Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group, Statistical Methods groups—Analysis Working Group, Enhancing GTEx (eGTEx) groups, NIH Common Fund, NIH/NCI, NIH/NHGRI, NIH/NIMH, NIH/NIDA, Biospecimen Collection Source Site—NDRI, Biospecimen Collection Source Site—RPCI, Biospecimen Core Resource—VARI, Brain Bank Repository—University of Miami Brain Endowment Bank, Leidos Biomedical—Project Management, ELSI Study, Genome Browser Data Integration &Visualization—EBI, Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, General Science & Technology
Abstract

Rare genetic variants are abundant in humans and are expected to contribute to individual disease risk. While genetic association studies have successfully identified common genetic variants associated with susceptibility, these studies are not practical for identifying rare variants. Efforts to distinguish pathogenic variants from benign rare variants have leveraged the genetic code to identify deleterious protein-coding alleles, but no analogous code exists for non-coding variants. Therefore, ascertaining which rare variants have phenotypic effects remains a major challenge. Rare non-coding variants have been associated with extreme gene expression in studies using single tissues, but their effects across tissues are unknown. Here we identify gene expression outliers, or individuals showing extreme expression levels for a particular gene, across 44 human tissues by using combined analyses of whole genomes and multi-tissue RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project v6p release. We find that 58% of underexpression and 28% of overexpression outliers have nearby conserved rare variants compared to 8% of non-outliers. Additionally, we developed RIVER (RNA-informed variant effect on regulation), a Bayesian statistical model that incorporates expression data to predict a regulatory effect for rare variants with higher accuracy than models using genomic annotations alone. Overall, we demonstrate that rare variants contribute to large gene expression changes across tissues and provide an integrative method for interpretation of rare variants in individual genomes.

Published
2017

19. Fast and efficient QTL mapper for thousands of molecular phenotypes

Author

Ongen, Halit, Buil, Alfonso, Brown, Andrew Anand, Dermitzakis, Emmanouil T, and Delaneau, Olivier

Subjects
Human Genome, Genetics, Genomics, Phenotype, Quantitative Trait Loci, Software, Statistical Distributions, Clinical Research, Prostate Cancer, Prevention, Cancer, Aging, Urologic Diseases, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Male, Middle Aged, Molecular Sequence Annotation, Neoplasm Invasiveness, Odds Ratio, Prostatic Neoplasms, Racial Groups, Risk Factors, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction.

Published
2016

20. Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors.

Author

van de Bunt, Martijn, Manning Fox, Jocelyn E, Dai, Xiaoqing, Barrett, Amy, Grey, Caleb, Li, Lei, Bennett, Amanda J, Johnson, Paul R, Rajotte, Raymond V, Gaulton, Kyle J, Dermitzakis, Emmanouil T, MacDonald, Patrick E, McCarthy, Mark I, and Gloyn, Anna L

Subjects
Humans, Diabetes Mellitus, Type 2, Genetic Predisposition to Disease, Insulin, Glucose, Transcription Factors, Signal Transduction, Gene Expression Regulation, Quantitative Trait Loci, Exons, Insulin-Secreting Cells, Genome-Wide Association Study, Insulin Secretion, Diabetes Mellitus, Type 2, Developmental Biology, Genetics
Abstract

The intersection of genome-wide association analyses with physiological and functional data indicates that variants regulating islet gene transcription influence type 2 diabetes (T2D) predisposition and glucose homeostasis. However, the specific genes through which these regulatory variants act remain poorly characterized. We generated expression quantitative trait locus (eQTL) data in 118 human islet samples using RNA-sequencing and high-density genotyping. We identified fourteen loci at which cis-exon-eQTL signals overlapped active islet chromatin signatures and were coincident with established T2D and/or glycemic trait associations. ‎At some, these data provide an experimental link between GWAS signals and biological candidates, such as DGKB and ADCY5. At others, the cis-signals implicate genes with no prior connection to islet biology, including WARS and ZMIZ1. At the ZMIZ1 locus, we show that perturbation of ZMIZ1 expression in human islets and beta-cells influences exocytosis and insulin secretion, highlighting a novel role for ZMIZ1 in the maintenance of glucose homeostasis. Together, these findings provide a significant advance in the mechanistic insights of T2D and glycemic trait association loci.

Published
2015

21. Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability

Author

Lagou, Vasiliki, Mägi, Reedik, Hottenga, Jouke- Jan, Grallert, Harald, Perry, John R. B., Bouatia-Naji, Nabila, Marullo, Letizia, Rybin, Denis, Jansen, Rick, Min, Josine L., Dimas, Antigone S., Ulrich, Anna, Zudina, Liudmila, Gådin, Jesper R., Jiang, Longda, Faggian, Alessia, Bonnefond, Amélie, Fadista, Joao, Stathopoulou, Maria G., Isaacs, Aaron, Willems, Sara M., Navarro, Pau, Tanaka, Toshiko, Jackson, Anne U., Montasser, May E., O’Connell, Jeff R., Bielak, Lawrence F., Webster, Rebecca J., Saxena, Richa, Stafford, Jeanette M., Pourcain, Beate St, Timpson, Nicholas J., Salo, Perttu, Shin, So-Youn, Amin, Najaf, Smith, Albert V., Li, Guo, Verweij, Niek, Goel, Anuj, Ford, Ian, Johnson, Paul C. D., Johnson, Toby, Kapur, Karen, Thorleifsson, Gudmar, Strawbridge, Rona J., Rasmussen-Torvik, Laura J., Esko, Tõnu, Mihailov, Evelin, Fall, Tove, Fraser, Ross M., Mahajan, Anubha, Kanoni, Stavroula, Giedraitis, Vilmantas, Kleber, Marcus E., Silbernagel, Günther, Meyer, Julia, Müller-Nurasyid, Martina, Ganna, Andrea, Sarin, Antti-Pekka, Yengo, Loic, Shungin, Dmitry, Luan, Jian’an, Horikoshi, Momoko, An, Ping, Sanna, Serena, Boettcher, Yvonne, Rayner, N. William, Nolte, Ilja M., Zemunik, Tatijana, Iperen, Erik van, Kovacs, Peter, Hastie, Nicholas D., Wild, Sarah H., McLachlan, Stela, Campbell, Susan, Polasek, Ozren, Carlson, Olga, Egan, Josephine, Kiess, Wieland, Willemsen, Gonneke, Kuusisto, Johanna, Laakso, Markku, Dimitriou, Maria, Hicks, Andrew A., Rauramaa, Rainer, Bandinelli, Stefania, Thorand, Barbara, Liu, Yongmei, Miljkovic, Iva, Lind, Lars, Doney, Alex, Perola, Markus, Hingorani, Aroon, Kivimaki, Mika, Kumari, Meena, Bennett, Amanda J., Groves, Christopher J., Herder, Christian, Koistinen, Heikki A., Kinnunen, Leena, Faire, Ulf de, Bakker, Stephan J. L., Uusitupa, Matti, Palmer, Colin N. A., Jukema, J. Wouter, Sattar, Naveed, Pouta, Anneli, Snieder, Harold, Boerwinkle, Eric, Pankow, James S., Magnusson, Patrik K., Krus, Ulrika, Scapoli, Chiara, de Geus, Eco J. C. N., Blüher, Matthias, Wolffenbuttel, Bruce H. R., Province, Michael A., Abecasis, Goncalo R., Meigs, James B., Hovingh, G. Kees, Lindström, Jaana, Wilson, James F., Wright, Alan F., Dedoussis, George V., Bornstein, Stefan R., Schwarz, Peter E. H., Tönjes, Anke, Winkelmann, Bernhard R., Boehm, Bernhard O., März, Winfried, Metspalu, Andres, Price, Jackie F., Deloukas, Panos, Körner, Antje, Lakka, Timo A., Keinanen-Kiukaanniemi, Sirkka M., Saaristo, Timo E., Bergman, Richard N., Tuomilehto, Jaakko, Wareham, Nicholas J., Langenberg, Claudia, Männistö, Satu, Franks, Paul W., Hayward, Caroline, Vitart, Veronique, Kaprio, Jaakko, Visvikis-Siest, Sophie, Balkau, Beverley, Altshuler, David, Rudan, Igor, Stumvoll, Michael, Campbell, Harry, van Duijn, Cornelia M., Gieger, Christian, Illig, Thomas, Ferrucci, Luigi, Pedersen, Nancy L., Pramstaller, Peter P., Boehnke, Michael, Frayling, Timothy M., Shuldiner, Alan R., Peyser, Patricia A., Kardia, Sharon L. R., Palmer, Lyle J., Penninx, Brenda W., Meneton, Pierre, Harris, Tamara B., Navis, Gerjan, Harst, Pim van der, Smith, George Davey, Forouhi, Nita G., Loos, Ruth J. F., Salomaa, Veikko, Soranzo, Nicole, Boomsma, Dorret I., Groop, Leif, Tuomi, Tiinamaija, Hofman, Albert, Munroe, Patricia B., Gudnason, Vilmundur, Siscovick, David S., Watkins, Hugh, Lecoeur, Cecile, Vollenweider, Peter, Franco-Cereceda, Anders, Eriksson, Per, Jarvelin, Marjo-Riitta, Stefansson, Kari, Hamsten, Anders, Nicholson, George, Karpe, Fredrik, Dermitzakis, Emmanouil T., Lindgren, Cecilia M., McCarthy, Mark I., Froguel, Philippe, Kaakinen, Marika A., Lyssenko, Valeriya, Watanabe, Richard M., Ingelsson, Erik, Florez, Jose C., Dupuis, Josée, Barroso, Inês, Morris, Andrew P., and Prokopenko, Inga

Published
2021
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25. A brief history of human disease genetics

Author

Claussnitzer, Melina, Cho, Judy H., Collins, Rory, Cox, Nancy J., Dermitzakis, Emmanouil T., Hurles, Matthew E., and Kathiresan, Sekar

Subjects
Genomics -- Forecasts and trends, Diseases -- Genetic aspects -- History -- United States, Human genetics -- History -- Technology application, Market trend/market analysis, Technology application, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

A primary goal of human genetics is to identify DNA sequence variants that influence biomedical traits, particularly those related to the onset and progression of human disease. Over the past 25 years, progress in realizing this objective has been transformed by advances in technology, foundational genomic resources and analytical tools, and by access to vast amounts of genotype and phenotype data. Genetic discoveries have substantially improved our understanding of the mechanisms responsible for many rare and common diseases and driven development of novel preventative and therapeutic strategies. Medical innovation will increasingly focus on delivering care tailored to individual patterns of genetic predisposition. This Review describes progress in the study of human genetics, in which rapid advances in technology, foundational genomic resources and analytical tools have contributed to the understanding of the mechanisms responsible for many rare and common diseases and to preventative and therapeutic strategies for many of these conditions., Author(s): Melina Claussnitzer [sup.1] [sup.2] [sup.3] , Judy H. Cho [sup.4] [sup.5] [sup.6] , Rory Collins [sup.7] [sup.8] , Nancy J. Cox [sup.9] , Emmanouil T. Dermitzakis [sup.10] [sup.11] , [...]

Published
2020
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26. Discovery of biomarkers for glycaemic deterioration before and after the onset of type 2 diabetes: descriptive characteristics of the epidemiological studies within the IMI DIRECT Consortium

Author

Koivula, Robert W., Forgie, Ian M., Kurbasic, Azra, Viñuela, Ana, Heggie, Alison, Giordano, Giuseppe N., Hansen, Tue H., Hudson, Michelle, Koopman, Anitra D. M., Rutters, Femke, Siloaho, Maritta, Allin, Kristine H., Brage, Søren, Brorsson, Caroline A., Dawed, Adem Y., De Masi, Federico, Groves, Christopher J., Kokkola, Tarja, Mahajan, Anubha, Perry, Mandy H., Rauh, Simone P., Ridderstråle, Martin, Teare, Harriet J. A., Thomas, E. Louise, Tura, Andrea, Vestergaard, Henrik, White, Tom, Adamski, Jerzy, Bell, Jimmy D., Beulens, Joline W., Brunak, Søren, Dermitzakis, Emmanouil T., Froguel, Philippe, Frost, Gary, Gupta, Ramneek, Hansen, Torben, Hattersley, Andrew, Jablonka, Bernd, Kaye, Jane, Laakso, Markku, McDonald, Timothy J., Pedersen, Oluf, Schwenk, Jochen M., Pavo, Imre, Mari, Andrea, McCarthy, Mark I., Ruetten, Hartmut, Walker, Mark, Pearson, Ewan, Franks, Paul W., and for the IMI DIRECT Consortium

Published
2019
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27. Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

Author

Strawbridge, Rona J, Dupuis, Josée, Prokopenko, Inga, Barker, Adam, Ahlqvist, Emma, Rybin, Denis, Petrie, John R, Travers, Mary E, Bouatia-Naji, Nabila, Dimas, Antigone S, Nica, Alexandra, Wheeler, Eleanor, Chen, Han, Voight, Benjamin F, Taneera, Jalal, Kanoni, Stavroula, Peden, John F, Turrini, Fabiola, Gustafsson, Stefan, Zabena, Carina, Almgren, Peter, Barker, David JP, Barnes, Daniel, Dennison, Elaine M, Eriksson, Johan G, Eriksson, Per, Eury, Elodie, Folkersen, Lasse, Fox, Caroline S, Frayling, Timothy M, Goel, Anuj, Gu, Harvest F, Horikoshi, Momoko, Isomaa, Bo, Jackson, Anne U, Jameson, Karen A, Kajantie, Eero, Kerr-Conte, Julie, Kuulasmaa, Teemu, Kuusisto, Johanna, Loos, Ruth JF, Luan, Jian'an, Makrilakis, Konstantinos, Manning, Alisa K, Martínez-Larrad, María Teresa, Narisu, Narisu, Nastase Mannila, Maria, Ohrvik, John, Osmond, Clive, Pascoe, Laura, Payne, Felicity, Sayer, Avan A, Sennblad, Bengt, Silveira, Angela, Stancáková, Alena, Stirrups, Kathy, Swift, Amy J, Syvänen, Ann-Christine, Tuomi, Tiinamaija, van 't Hooft, Ferdinand M, Walker, Mark, Weedon, Michael N, Xie, Weijia, Zethelius, Björn, DIAGRAM Consortium, GIANT Consortium, MuTHER Consortium, CARDIoGRAM Consortium, C4D Consortium, Ongen, Halit, Mälarstig, Anders, Hopewell, Jemma C, Saleheen, Danish, Chambers, John, Parish, Sarah, Danesh, John, Kooner, Jaspal, Ostenson, Claes-Göran, Lind, Lars, Cooper, Cyrus C, Serrano-Ríos, Manuel, Ferrannini, Ele, Forsen, Tom J, Clarke, Robert, Franzosi, Maria Grazia, Seedorf, Udo, Watkins, Hugh, Froguel, Philippe, Johnson, Paul, Deloukas, Panos, Collins, Francis S, Laakso, Markku, Dermitzakis, Emmanouil T, Boehnke, Michael, McCarthy, Mark I, Wareham, Nicholas J, Groop, Leif, Pattou, François, Gloyn, Anna L, and Dedoussis, George V

Subjects
DIAGRAM Consortium, GIANT Consortium, MuTHER Consortium, CARDIoGRAM Consortium, C4D Consortium, Humans, Diabetes Mellitus, Type 2, Insulin, Proinsulin, Fasting, Genotype, Polymorphism, Single Nucleotide, Genome, Human, Adult, Female, Male, Genetic Variation, Diabetes Mellitus, Type 2, Polymorphism, Single Nucleotide, Genome, Human, Endocrinology & Metabolism, Medical and Health Sciences
Abstract

ObjectiveProinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology.Research design and methodsWe have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates.ResultsNine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets.ConclusionsWe have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis.

Published
2011

28. Evaluation of Candidate Stromal Epithelial Cross-Talk Genes Identifies Association between Risk of Serous Ovarian Cancer and TERT, a Cancer Susceptibility �Hot-Spot�

Author

Johnatty, Sharon E, Beesley, Jonathan, Chen, Xiaoqing, Macgregor, Stuart, Duffy, David L, Spurdle, Amanda B, deFazio, Anna, Gava, Natalie, Webb, Penelope M, Rossing, Mary Anne, Doherty, Jennifer Anne, Goodman, Marc T, Lurie, Galina, Thompson, Pamela J, Wilkens, Lynne R, Ness, Roberta B, Moysich, Kirsten B, Chang-Claude, Jenny, Wang-Gohrke, Shan, Cramer, Daniel W, Terry, Kathryn L, Hankinson, Susan E, Tworoger, Shelley S, Garcia-Closas, Montserrat, Yang, Hannah, Lissowska, Jolanta, Chanock, Stephen J, Pharoah, Paul D, Song, Honglin, Whitemore, Alice S, Pearce, Celeste L, Stram, Daniel O, Wu, Anna H, Pike, Malcolm C, Gayther, Simon A, Ramus, Susan J, Menon, Usha, Gentry-Maharaj, Aleksandra, Anton-Culver, Hoda, Ziogas, Argyrios, Hogdall, Estrid, Kjaer, Susanne K, Hogdall, Claus, Berchuck, Andrew, Schildkraut, Joellen M, Iversen, Edwin S, Moorman, Patricia G, Phelan, Catherine M, Sellers, Thomas A, Cunningham, Julie M, Vierkant, Robert A, Rider, David N, Goode, Ellen L, Haviv, Izhak, Chenevix-Trench, Georgia, Dermitzakis, Emmanouil T, and Ovarian Cancer Association Consortium", .

Subjects
genome-wide association, single-nucleotide polymorphisms, incessant ovulation, colorectal-cancer, expression, consortium, variants, prostate, locus, myc
Abstract

We hypothesized that variants in genes expressed as a consequence of interactions between ovarian cancer cells and the host micro-environment could contribute to cancer susceptibility. We therefore used a two-stage approach to evaluate common single nucleotide polymorphisms (SNPs) in 173 genes involved in stromal epithelial interactions in the Ovarian Cancer Association Consortium (OCAC). In the discovery stage, cases with epithelial ovarian cancer (n = 675) and controls (n = 1,162) were genotyped at 1,536 SNPs using an Illumina GoldenGate assay. Based on Positive Predictive Value estimates, three SNPs-PODXL rs1013368, ITGA6 rs13027811, and MMP3 rs522616-were selected for replication using TaqMan genotyping in up to 3,059 serous invasive cases and 8,905 controls from 16 OCAC case-control studies. An additional 18 SNPs with P(per-allele)= 0.5). However genotypes at TERT rs7726159 were associated with ovarian cancer risk in the smaller, five-study replication study (P(per-allele)=0.03). Combined analysis of the discovery and replication sets for this TERT SNP showed an increased risk of serous ovarian cancer among non-Hispanic whites [adj. OR(per-allele) 1.14 (1.04-1.24) p = 0.003]. Our study adds to the growing evidence that, like the 8q24 locus, the telomerase reverse transcriptase locus at 5p15.33, is a general cancer susceptibility locus.

Published
2010

31. Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

Author

Viñuela, Ana, Varshney, Arushi, van de Bunt, Martijn, Prasad, Rashmi B., Asplund, Olof, Bennett, Amanda, Boehnke, Michael, Brown, Andrew A., Erdos, Michael R., Fadista, João, Hansson, Ola, Hatem, Gad, Howald, Cédric, Iyengar, Apoorva K., Johnson, Paul, Krus, Ulrika, MacDonald, Patrick E., Mahajan, Anubha, Manning Fox, Jocelyn E., Narisu, Narisu, Nylander, Vibe, Orchard, Peter, Oskolkov, Nikolay, Panousis, Nikolaos I., Payne, Anthony, Stitzel, Michael L., Vadlamudi, Swarooparani, Welch, Ryan, Collins, Francis S., Mohlke, Karen L., Gloyn, Anna L., Scott, Laura J., Dermitzakis, Emmanouil T., Groop, Leif, Parker, Stephen C. J., and McCarthy, Mark I.

Published
2020
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32. Publisher Correction: MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer

Author

Mattesen, Trine B., Rasmussen, Mads H., Sandoval, Juan, Ongen, Halit, Árnadóttir, Sigrid S., Gladov, Josephine, Martinez-Cardus, Anna, de Moura, Manuel Castro, Madsen, Anders H., Laurberg, Søren, Dermitzakis, Emmanouil T., Esteller, Manel, Andersen, Claus L., and Bramsen, Jesper B.

Published
2020
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35. Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

Author

Gamazon, Eric R., Segrè, Ayellet V., van de Bunt, Martijn, Wen, Xiaoquan, Xi, Hualin S., Hormozdiari, Farhad, Ongen, Halit, Konkashbaev, Anuar, Derks, Eske M., Aguet, François, Quan, Jie, GTEx Consortium, Nicolae, Dan L., Eskin, Eleazar, Kellis, Manolis, Getz, Gad, McCarthy, Mark I., Dermitzakis, Emmanouil T., Cox, Nancy J., and Ardlie, Kristin G.

Published
2018
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36. Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population

Author

Rouskas, Konstantinos, primary, Katsareli, Efthymia A, additional, Amerikanou, Charalampia, additional, Dimopoulos, Alexandros C, additional, Glentis, Stavros, additional, Kalantzi, Alexandra, additional, Skoulakis, Anargyros, additional, Panousis, Nikolaos, additional, Ongen, Halit, additional, Bielser, Deborah, additional, Planchon, Alexandra, additional, Romano, Luciana, additional, Harokopos, Vaggelis, additional, Reczko, Martin, additional, Moulos, Panagiotis, additional, Griniatsos, Ioannis, additional, Diamantis, Theodoros, additional, Dermitzakis, Emmanouil T, additional, Ragoussis, Jiannis, additional, Dedoussis, George, additional, and Dimas, Antigone S, additional

Published
2023
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37. Proteomic analysis of 92 circulating proteins and their effects in cardiometabolic diseases

Author

Carland, Corinne, primary, Png, Grace, additional, Malarstig, Anders, additional, Kho, Pik Fang, additional, Gustafsson, Stefan, additional, Michaelsson, Karl, additional, Lind, Lars, additional, Tsafantakis, Emmanouil, additional, Karaleftheri, Maria, additional, Dedoussis, George, additional, Ramisch, Anna, additional, Macdonald-Dunlop, Erin, additional, Klaric, Lucija, additional, Joshi, Peter K., additional, Chen, Yan, additional, Björck, Hanna M., additional, Eriksson, Per, additional, Carrasco-Zanini, Julia, additional, Wheeler, Eleanor, additional, Suhre, Karsten, additional, Gilly, Arthur, additional, Zeggini, Eleftheria, additional, Viñuela, Ana, additional, Dermitzakis, Emmanouil T., additional, Wilson, James F., additional, Langenberg, Claudia, additional, Thareja, Gaurav, additional, Halama, Anna, additional, Schmidt, Frank, additional, Consortium, SCALLOP, additional, Zanetti, Daniela, additional, and Assimes, Themistocles, additional

Published
2023
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38. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency

Author

Forny, Patrick; https://orcid.org/0000-0003-1877-2976, Bonilla, Ximena; https://orcid.org/0000-0002-4950-6825, Lamparter, David; https://orcid.org/0000-0002-9216-8825, Shao, Wenguang; https://orcid.org/0000-0003-0905-0728, Plessl, Tanja, Frei, Caroline; https://orcid.org/0000-0002-8879-6327, Bingisser, Anna, Goetze, Sandra; https://orcid.org/0000-0001-6880-8020, van Drogen, Audrey, Harshman, Keith, Pedrioli, Patrick G A, Howald, Cédric, Poms, Martin; https://orcid.org/0000-0002-4426-314X, Traversi, Florian, Bürer, Céline, Cherkaoui, Sarah; https://orcid.org/0000-0002-0636-4177, Morscher, Raphael J; https://orcid.org/0000-0003-3378-9266, Simmons, Luke, Forny, Merima, Xenarios, Ioannis; https://orcid.org/0000-0002-3413-6841, Aebersold, Ruedi; https://orcid.org/0000-0002-9576-3267, Zamboni, Nicola; https://orcid.org/0000-0003-1271-1021, Rätsch, Gunnar; https://orcid.org/0000-0001-5486-8532, Dermitzakis, Emmanouil T, Wollscheid, Bernd; https://orcid.org/0000-0002-3923-1610, Baumgartner, Matthias R; https://orcid.org/0000-0002-9270-0826, Froese, D Sean; https://orcid.org/0000-0003-1557-3517, Forny, Patrick; https://orcid.org/0000-0003-1877-2976, Bonilla, Ximena; https://orcid.org/0000-0002-4950-6825, Lamparter, David; https://orcid.org/0000-0002-9216-8825, Shao, Wenguang; https://orcid.org/0000-0003-0905-0728, Plessl, Tanja, Frei, Caroline; https://orcid.org/0000-0002-8879-6327, Bingisser, Anna, Goetze, Sandra; https://orcid.org/0000-0001-6880-8020, van Drogen, Audrey, Harshman, Keith, Pedrioli, Patrick G A, Howald, Cédric, Poms, Martin; https://orcid.org/0000-0002-4426-314X, Traversi, Florian, Bürer, Céline, Cherkaoui, Sarah; https://orcid.org/0000-0002-0636-4177, Morscher, Raphael J; https://orcid.org/0000-0003-3378-9266, Simmons, Luke, Forny, Merima, Xenarios, Ioannis; https://orcid.org/0000-0002-3413-6841, Aebersold, Ruedi; https://orcid.org/0000-0002-9576-3267, Zamboni, Nicola; https://orcid.org/0000-0003-1271-1021, Rätsch, Gunnar; https://orcid.org/0000-0001-5486-8532, Dermitzakis, Emmanouil T, Wollscheid, Bernd; https://orcid.org/0000-0002-3923-1610, Baumgartner, Matthias R; https://orcid.org/0000-0002-9270-0826, and Froese, D Sean; https://orcid.org/0000-0003-1557-3517

Abstract

Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic causes and a poorly understood pathogenesis, leading to the absence of effective causal treatments. Here we employ multi-layered omics profiling combined with biochemical and clinical features of individuals with MMA to reveal a molecular diagnosis for 177 out of 210 (84%) cases, the majority (148) of whom display pathogenic variants in methylmalonyl-CoA mutase (MMUT). Stratification of these data layers by disease severity shows dysregulation of the tricarboxylic acid cycle and its replenishment (anaplerosis) by glutamine. The relevance of these disturbances is evidenced by multi-organ metabolomics of a hemizygous Mmut mouse model as well as through identification of physical interactions between MMUT and glutamine anaplerotic enzymes. Using stable-isotope tracing, we find that treatment with dimethyl-oxoglutarate restores deficient tricarboxylic acid cycling. Our work highlights glutamine anaplerosis as a potential therapeutic intervention point in MMA.

Published
2023

40. Multiallelic Copy Number Variation in ORM1 is Associated with Plasma Cell-Free DNA Levels as an Intermediate Phenotype for Venous Thromboembolism

Author

Martin-Fernandez, Laura, additional, Garcia-Martínez, Iris, additional, Lopez, Sonia, additional, Martinez-Perez, Angel, additional, Vilalta, Noelia, additional, Plaza, Melania, additional, Moret, Carla, additional, Viñuela, Ana, additional, Brown, Andrew A., additional, Panousis, Nikolaos I., additional, Buil, Alfonso, additional, Dermitzakis, Emmanouil T., additional, Corrales, Irene, additional, Souto, Juan Carlos, additional, Vidal, Francisco, additional, and Soria, Jose Manuel, additional

Published
2023
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41. The impact of rare variation on gene expression across tissues

Author

Li, Xin, Kim, Yungil, Tsang, Emily K., Davis, Joe R., Damani, Farhan N., Chiang, Colby, Hess, Gaelen T., Zappala, Zachary, Strober, Benjamin J., Scott, Alexandra J., Li, Amy, Ganna, Andrea, Bassik, Michael C., Merker, Jason D., Aguet, Franois, 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., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, 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., Conrad, Donald F., Cox, Nancy J., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D.H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, Kim-Hellmuth, Sarah, Lappalainen, Tuuli, Li, Gen, Liu, Boxiang, Mangul, Serghei, McCarthy, Mark I., McDowell, Ian C., Mohammadi, Pejman, Monlong, Jean, Montgomery, Stephen B., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., 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, Shabalin, Andrey A., Sodaei, Reza, Stephens, Matthew, Stranger, Barbara E., Sul, Jae Hoon, Urbut, Sarah, van de Bunt, Martijn, Wang, Gao, Wen, Xiaoquan, Wright, Fred A., Xi, Hualin S., Yeger-Lotem, Esti, Zaugg, Judith B., Zhou, Yi-Hui, Akey, Joshua M., Bates, Daniel, Chan, Joanne, 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, Billy Li, Jin, Li, Qin, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, 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, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., 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., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, and Zhu, Jingchun

Subjects
Disease susceptibility -- Genetic aspects, Genetic variation -- Observations, Gene expression -- Observations, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Xin Li [1]; Yungil Kim [2]; Emily K. Tsang [1, 3]; Joe R. Davis [1, 4]; Farhan N. Damani [2]; Colby Chiang [5]; Gaelen T. Hess [4]; Zachary Zappala [...]

Published
2017
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42. Dynamic landscape and regulation of RNA editing in mammals

Author

Tan, Meng How, Li, Qin, Shanmugam, Raghuvaran, Piskol, Robert, Kohler, Jennefer, Young, Amy N., Liu, Kaiwen Ivy, Zhang, Rui, Ramaswami, Gokul, Ariyoshi, Kentaro, Gupte, Ankita, Keegan, Liam P., George, Cyril X., Ramu, Avinash, Huang, Ni, Pollina, Elizabeth A., Leeman, Dena S., Rustighi, Alessandra, Goh, Y. P. Sharon, Aguet, Franois, 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., Segr, Ayellet V., Trowbridge, Casandra A., Tukiainen, Taru, 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., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, 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., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., 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, Akey, Joshua M., Bates, Daniel, Chan, Joanne, 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, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, 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, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., 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., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Chawla, Ajay, Del Sal, Giannino, Peltz, Gary, Brunet, Anne, Samuel, Charles E., OConnell, Mary A., Walkley, Carl R., and Nishikura, Kazuko

Subjects
Genetic research, Mammals -- Genetic aspects, RNA processing -- Research, Genetic regulation, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Meng How Tan (corresponding author) [1, 2, 3]; Qin Li [1]; Raghuvaran Shanmugam [2, 3]; Robert Piskol [1]; Jennefer Kohler [1]; Amy N. Young [1]; Kaiwen Ivy Liu [3]; [...]

Published
2017
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43. Landscape of X chromosome inactivation across human tissues

Author

Tukiainen, Taru, Villani, Alexandra-Chlo, Yen, Angela, Rivas, Manuel A., Marshall, Jamie L., Satija, Rahul, Aguirre, Matt, Gauthier, Laura, Fleharty, Mark, Kirby, Andrew, Cummings, Beryl B., Castel, Stephane E., Karczewski, Konrad J., Aguet, Franois, Byrnes, Andrea, Ardlie, Kristin G., Gelfand, Ellen T., Getz, Gad, Hadley, Kane, Handsaker, Robert E., Huang, Katherine H., Kashin, Seva, Lek, Monkol, Li, Xiao, MacArthur, Daniel G., Nedzel, Jared L., Nguyen, Duyen T., Noble, Michael S., Segr, Ayellet V., Trowbridge, Casandra A., Abell, Nathan S., Balliu, Brunilda, Barshir, Ruth, Basha, Omer, Battle, Alexis, Bogu, Gireesh K., Brown, Andrew, Brown, Christopher D., Chen, Lin S., Chiang, Colby, Conrad, Donald F., Cox, Nancy J., Damani, Farhan N., Davis, Joe R., Delaneau, Olivier, Dermitzakis, Emmanouil T., Engelhardt, Barbara E., Eskin, Eleazar, Ferreira, Pedro G., Frsard, Laure, Gamazon, Eric R., Garrido-Martn, Diego, Gewirtz, Ariel D. H., Gliner, Genna, Gloudemans, Michael J., Guigo, Roderic, Hall, Ira M., Han, Buhm, He, Yuan, Hormozdiari, Farhad, Howald, Cedric, Kyung Im, Hae, Jo, Brian, Yong Kang, Eun, 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., Muoz-Aguirre, Manuel, Ndungu, Anne W., Nicolae, Dan L., 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, Akey, Joshua M., Bates, Daniel, Chan, Joanne, 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, Lin, Jessica, Lin, Shin, Linder, Sandra, Linke, Caroline, Liu, Yaping, Maurano, Matthew T., Molinie, Benoit, Nelson, Jemma, Neri, Fidencio J., Park, Yongjin, Pierce, Brandon L., Rinaldi, Nicola J., Rizzardi, Lindsay F., Sandstrom, Richard, Skol, Andrew, Smith, Kevin S., Snyder, Michael P., Stamatoyannopoulos, John, Tang, Hua, Wang, Li, Wang, Meng, Van Wittenberghe, Nicholas, Wu, Fan, Zhang, Rui, Nierras, Concepcion R., Branton, Philip A., Carithers, Latarsha J., Guan, Ping, Moore, Helen M., Rao, Abhi, Vaught, Jimmie B., Gould, Sarah E., Lockart, Nicole C., Martin, Casey, Struewing, Jeffery P., Volpi, Simona, Addington, Anjene M., Koester, Susan E., Little, A. Roger, 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, Bridge, Jason, Foster, Barbara A., Gillard, Bryan M., Karasik, Ellen, Kumar, Rachna, Miklos, Mark, Moser, Michael T., Jewell, Scott D., Montroy, Robert G., Rohrer, Daniel C., Valley, Dana R., Davis, David A., Mash, Deborah C., 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., Barker, Laura K., Mosavel, Maghboeba, Siminoff, Laura A., Traino, Heather M., Flicek, Paul, Juettemann, Thomas, Ruffier, Magali, Sheppard, Dan, Taylor, Kieron, Trevanion, Stephen J., Zerbino, Daniel R., Craft, Brian, Goldman, Mary, Haeussler, Maximilian, Kent, W. James, Lee, Christopher M., Paten, Benedict, Rosenbloom, Kate R., Vivian, John, Zhu, Jingchun, Regev, Aviv, and Hacohen, Nir

Subjects
Chromosomes -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Taru Tukiainen (corresponding author) [1, 2]; Alexandra-Chlo Villani [2, 3]; Angela Yen [2, 4]; Manuel A. Rivas [1, 2, 5]; Jamie L. Marshall [1, 2]; Rahul Satija [2, 6, [...]

Published
2017
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45. The human transcriptome across tissues and individuals

Author

The GTEx Consortium, Melé, Marta, Ferreira, Pedro G., Reverter, Ferran, DeLuca, David S., Monlong, Jean, Sammeth, Michael, Young, Taylor R., Goldmann, Jakob M, Pervouchine, Dmitri D., Sullivan, Timothy J., Johnson, Rory, Segrè, Ayellet V., Djebali, Sarah, Niarchou, Anastasia, Wright, Fred A., Lappalainen, Tuuli, Calvo, Miquel, Getz, Gad, Dermitzakis, Emmanouil T., Ardlie, Kristin G., and Guigó, Roderic

Published
2015

46. Effect of predicted protein-truncating genetic variants on the human transcriptome

Author

The GTEx Consortium, The Geuvadis Consortium, Rivas, Manuel A., Pirinen, Matti, Conrad, Donald F., Lek, Monkol, Tsang, Emily K., Karczewski, Konrad J., Maller, Julian B., Kukurba, Kimberly R., DeLuca, David S., Fromer, Menachem, Ferreira, Pedro G., Smith, Kevin S., Zhang, Rui, Zhao, Fengmei, Banks, Eric, Poplin, Ryan, Ruderfer, Douglas M., Purcell, Shaun M., Tukiainen, Taru, Minikel, Eric V., Stenson, Peter D., Cooper, David N., Huang, Katharine H., Sullivan, Timothy J., Nedzel, Jared, Bustamante, Carlos D., Li, Jin Billy, Daly, Mark J., Guigo, Roderic, Donnelly, Peter, Ardlie, Kristin, Sammeth, Michael, Dermitzakis, Emmanouil T., McCarthy, Mark I., Montgomery, Stephen B., Lappalainen, Tuuli, and MacArthur, Daniel G.

Published
2015

49. Comprehensive evaluation of coding region point mutations in microsatellite‐unstable colorectal cancer

Author

Kondelin, Johanna, Salokas, Kari, Saarinen, Lilli, Ovaska, Kristian, Rauanheimo, Heli, Plaketti, Roosa‐Maria, Hamberg, Jiri, Liu, Xiaonan, Yadav, Leena, Gylfe, Alexandra E, Cajuso, Tatiana, Hänninen, Ulrika A, Palin, Kimmo, Ristolainen, Heikki, Katainen, Riku, Kaasinen, Eevi, Tanskanen, Tomas, Aavikko, Mervi, Taipale, Minna, Taipale, Jussi, Renkonen‐Sinisalo, Laura, Lepistö, Anna, Koskensalo, Selja, Böhm, Jan, Mecklin, Jukka‐Pekka, Ongen, Halit, Dermitzakis, Emmanouil T, Kilpivaara, Outi, Vahteristo, Pia, Turunen, Mikko, Hautaniemi, Sampsa, Tuupanen, Sari, Karhu, Auli, Välimäki, Niko, Varjosalo, Markku, Pitkänen, Esa, and Aaltonen, Lauri A

Published
2018
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