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2. Circulating proteins to predict COVID-19 severity

Author

Su, Chen-Yang, Zhou, Sirui, Gonzalez-Kozlova, Edgar, Butler-Laporte, Guillaume, Brunet-Ratnasingham, Elsa, Nakanishi, Tomoko, Jeon, Wonseok, Morrison, David R, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A, Schadt, Eric, Nie, Kai, Simons, Nicole W, Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Mount Sinai COVID-19 Biobank Team, Greenwood, Celia MT, Paterson, Clare, Hinterberg, Michael A, Langenberg, Claudia, Forgetta, Vincenzo, Pineau, Joelle, Mooser, Vincent, Marron, Thomas, Beckmann, Noam D, Kim-Schulze, Seunghee, Charney, Alexander W, Gnjatic, Sacha, Kaufmann, Daniel E, Merad, Miriam, Richards, J Brent, and Apollo - University of Cambridge Repository

Subjects
Risk Factors, Disease Progression, Humans, COVID-19, Proteins, Retrospective Studies
Abstract

Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict COVID-19 severity in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different COVID-19 severity were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of COVID-19 severity. Further research is needed to understand how to incorporate protein measurement into clinical care.

Published
2023

3. A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients

Author

Peters, Lauren A., primary, Friedman, Joshua R., additional, Stojmirovic, Aleksandar, additional, Hagen, Jacob, additional, Houten, Sander, additional, Dodatko, Tetyana, additional, Amaro, Mariana P., additional, Restrepo, Paula, additional, Chai, Zhi, additional, Rodrigo Mora, J., additional, Raymond, Holly A., additional, Curran, Mark, additional, Dobrin, Radu, additional, Das, Anuk, additional, Xiong, Huabao, additional, Schadt, Eric E., additional, Argmann, Carmen, additional, and Losic, Bojan, additional

Published
2023
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5. The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals

Author

Butler-Laporte, Guillaume, Gonzalez-Kozlova, Edgar, Su, Chen-Yang, Zhou, Sirui, Nakanishi, Tomoko, Brunet-Ratnasingham, Elsa, Morrison, David, Laurent, Laetitia, Afilalo, Jonathan, Afilalo, Marc, Henry, Danielle, Chen, Yiheng, Carrasco-Zanini, Julia, Farjoun, Yossi, Pietzner, Maik, Kimchi, Nofar, Afrasiabi, Zaman, Rezk, Nardin, Bouab, Meriem, Petitjean, Louis, Guzman, Charlotte, Xue, Xiaoqing, Tselios, Chris, Vulesevic, Branka, Adeleye, Olumide, Abdullah, Tala, Almamlouk, Noor, Moussa, Yara, DeLuca, Chantal, Duggan, Naomi, Schurr, Erwin, Brassard, Nathalie, Durand, Madeleine, Del Valle, Diane Marie, Thompson, Ryan, Cedillo, Mario A, Schadt, Eric, Nie, Kai, Simons, Nicole W, Mouskas, Konstantinos, Zaki, Nicolas, Patel, Manishkumar, Xie, Hui, Harris, Jocelyn, Marvin, Robert, Cheng, Esther, Tuballes, Kevin, Argueta, Kimberly, Scott, Ieisha, Mount Sinai COVID-19 Biobank Team, Greenwood, Celia MT, Paterson, Clare, Hinterberg, Michael, Langenberg, Claudia, Forgetta, Vincenzo, Mooser, Vincent, Marron, Thomas, Beckmann, Noam, Kenigsberg, Ephraim, Charney, Alexander W, Kim-Schulze, Seunghee, Merad, Miriam, Kaufmann, Daniel E, Gnjatic, Sacha, Richards, J Brent, Richards, J Brent [0000-0002-3746-9086], and Apollo - University of Cambridge Repository

Subjects
Proteomics, Research, Immunity, COVID-19, SOMAscan
Abstract

Funder: Public health agency of Canada, Funder: Canadian institute for health research, Funder: Génome Québec; doi: http://dx.doi.org/10.13039/100013062, Funder: Fonds de Recherche du Québec - Santé; doi: http://dx.doi.org/10.13039/501100000156, INTRODUCTION: Severe COVID-19 leads to important changes in circulating immune-related proteins. To date it has been difficult to understand their temporal relationship and identify cytokines that are drivers of severe COVID-19 outcomes and underlie differences in outcomes between sexes. Here, we measured 147 immune-related proteins during acute COVID-19 to investigate these questions. METHODS: We measured circulating protein abundances using the SOMAscan nucleic acid aptamer panel in two large independent hospital-based COVID-19 cohorts in Canada and the United States. We fit generalized additive models with cubic splines from the start of symptom onset to identify protein levels over the first 14 days of infection which were different between severe cases and controls, adjusting for age and sex. Severe cases were defined as individuals with COVID-19 requiring invasive or non-invasive mechanical respiratory support. RESULTS: 580 individuals were included in the analysis. Mean subject age was 64.3 (sd 18.1), and 47% were male. Of the 147 proteins, 69 showed a significant difference between cases and controls (p < 3.4 × 10-4). Three clusters were formed by 108 highly correlated proteins that replicated in both cohorts, making it difficult to determine which proteins have a true causal effect on severe COVID-19. Six proteins showed sex differences in levels over time, of which 3 were also associated with severe COVID-19: CCL26, IL1RL2, and IL3RA, providing insights to better understand the marked differences in outcomes by sex. CONCLUSIONS: Severe COVID-19 is associated with large changes in 69 immune-related proteins. Further, five proteins were associated with sex differences in outcomes. These results provide direct insights into immune-related proteins that are strongly influenced by severe COVID-19 infection.

Published
2022

6. Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions

Author

Sieberts, Solveig K., Perumal, Thanneer M., Carrasquillo, Minerva M., Allen, Mariet, Reddy, Joseph S., Hoffman, Gabriel E., Dang, Kristen K., Calley, John, Ebert, Philip J., Eddy, James, Wang, Xue, Greenwood, Anna K., Mostafavi, Sara, Akbarian, Schahram, Bendl, Jaroslav, Breen, Michael S., Brennand, Kristen, Brown, Leanne, Browne, Andrew, Buxbaum, Joseph D., Charney, Alexander, Chess, Andrew, Couto, Lizette, Crawford, Greg, Devillers, Olivia, Devlin, Bernie, Dobbyn, Amanda, Domenici, Enrico, Filosi, Michele, Flatow, Elie, Francoeur, Nancy, Fullard, John, Gil, Sergio Espeso, Girdhar, Kiran, Gulyás-Kovács, Attila, Gur, Raquel, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads Engel, Huckins, Laura, Jacobov, Rivky, Jiang, Yan, Johnson, Jessica S., Kassim, Bibi, Kim, Yungil, Klei, Lambertus, Kramer, Robin, Lauria, Mario, Lehner, Thomas, Lewis, David A., Lipska, Barbara K., Montgomery, Kelsey, Park, Royce, Rosenbluh, Chaggai, Roussos, Panagiotis, Ruderfer, Douglas M., Senthil, Geetha, Shah, Hardik R., Sloofman, Laura, Song, Lingyun, Stahl, Eli, Sullivan, Patrick, Visintainer, Roberto, Wang, Jiebiao, Wang, Ying-Chih, Wiseman, Jennifer, Xia, Eva, Zhang, Wen, Zharovsky, Elizabeth, Addis, Laura, Addo, Sadiya N., Airey, David Charles, Arnold, Matthias, Bennett, David A., Bi, Yingtao, Biber, Knut, Blach, Colette, Bradhsaw, Elizabeth, Brennan, Paul, Canet-Aviles, Rosa, Cao, Sherry, Cavalla, Anna, Chae, Yooree, Chen, William W., Cheng, Jie, Collier, David Andrew, Dage, Jeffrey L., Dammer, Eric B., Davis, Justin Wade, Davis, John, Drake, Derek, Duong, Duc, Eastwood, Brian J., Ehrlich, Michelle, Ellingson, Benjamin, Engelmann, Brett W., Esmaeelinieh, Sahar, Felsky, Daniel, Funk, Cory, Gaiteri, Chris, Gandy, Samuel, Gao, Fan, Gileadi, Opher, Golde, Todd, Grosskurth, Shaun E., Gupta, Rishi R., Gutteridge, Alex X., Hooli, Basavaraj, Humphryes-Kirilov, Neil, Iijima, Koichi, James, Corey, Jung, Paul M., Kaddurah-Daouk, Rima, Kastenmuller, Gabi, Klein, Hans-Ulrich, Kummer, Markus, Lacor, Pascale N., Lah, James, Laing, Emma, Levey, Allan, Li, Yupeng, Lipsky, Samantha, Liu, Yushi, Liu, Jimmy, Liu, Zhandong, Louie, Gregory, Lu, Tao, Ma, Yiyi, Matsuoka, Yasuji Y., Menon, Vilas, Miller, Bradley, Misko, Thomas P., Mollon, Jennifer E., Mukherjee, Sumit, Noggle, Scott, Pao, Ping-Chieh, Pearce, Tracy Young, Pearson, Neil, Penny, Michelle, Petyuk, Vladislav A., Price, Nathan, Quarless, Danjuma X., Ravikumar, Brinda, Ried, Janina S., Ruble, Cara Lee Ann, Runz, Heiko, Saykin, Andrew J., Schadt, Eric, Scherschel, James E., Seyfried, Nicholas, Shulman, Joshua M., Snyder, Phil, Soares, Holly, Srivastava, Gyan P., Stockmann, Henning, Taga, Mariko, Tasaki, Shinya, Tenenbaum, Jessie, Tsai, Li-Huei, Vasanthakumar, Aparna, Wachter, Astrid, Wang, Yaming, Wang, Hong, Wang, Minghui, Whelan, Christopher D., White, Charles, Woo, Kara H., Wren, Paul, Wu, Jessica W., Xi, Hualin S., Yankner, Bruce A., Younkin, Steven G., Yu, Lei, Zavodszky, Maria, Zhang, Wenling, Zhang, Guoqiang, Zhang, Bin, Zhu, Jun, Omberg, Larsson, Peters, Mette A., Logsdon, Benjamin A., De Jager, Philip L., Ertekin-Taner, Nilüfer, Mangravite, Lara M., Sieberts, Solveig K., Perumal, Thanneer M., Carrasquillo, Minerva M., Allen, Mariet, Reddy, Joseph S., Hoffman, Gabriel E., Dang, Kristen K., Calley, John, Ebert, Philip J., Eddy, James, Wang, Xue, Greenwood, Anna K., Mostafavi, Sara, Akbarian, Schahram, Bendl, Jaroslav, Breen, Michael S., Brennand, Kristen, Brown, Leanne, Browne, Andrew, Buxbaum, Joseph D., Charney, Alexander, Chess, Andrew, Couto, Lizette, Crawford, Greg, Devillers, Olivia, Devlin, Bernie, Dobbyn, Amanda, Domenici, Enrico, Filosi, Michele, Flatow, Elie, Francoeur, Nancy, Fullard, John, Gil, Sergio Espeso, Girdhar, Kiran, Gulyás-Kovács, Attila, Gur, Raquel, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads Engel, Huckins, Laura, Jacobov, Rivky, Jiang, Yan, Johnson, Jessica S., Kassim, Bibi, Kim, Yungil, Klei, Lambertus, Kramer, Robin, Lauria, Mario, Lehner, Thomas, Lewis, David A., Lipska, Barbara K., Montgomery, Kelsey, Park, Royce, Rosenbluh, Chaggai, Roussos, Panagiotis, Ruderfer, Douglas M., Senthil, Geetha, Shah, Hardik R., Sloofman, Laura, Song, Lingyun, Stahl, Eli, Sullivan, Patrick, Visintainer, Roberto, Wang, Jiebiao, Wang, Ying-Chih, Wiseman, Jennifer, Xia, Eva, Zhang, Wen, Zharovsky, Elizabeth, Addis, Laura, Addo, Sadiya N., Airey, David Charles, Arnold, Matthias, Bennett, David A., Bi, Yingtao, Biber, Knut, Blach, Colette, Bradhsaw, Elizabeth, Brennan, Paul, Canet-Aviles, Rosa, Cao, Sherry, Cavalla, Anna, Chae, Yooree, Chen, William W., Cheng, Jie, Collier, David Andrew, Dage, Jeffrey L., Dammer, Eric B., Davis, Justin Wade, Davis, John, Drake, Derek, Duong, Duc, Eastwood, Brian J., Ehrlich, Michelle, Ellingson, Benjamin, Engelmann, Brett W., Esmaeelinieh, Sahar, Felsky, Daniel, Funk, Cory, Gaiteri, Chris, Gandy, Samuel, Gao, Fan, Gileadi, Opher, Golde, Todd, Grosskurth, Shaun E., Gupta, Rishi R., Gutteridge, Alex X., Hooli, Basavaraj, Humphryes-Kirilov, Neil, Iijima, Koichi, James, Corey, Jung, Paul M., Kaddurah-Daouk, Rima, Kastenmuller, Gabi, Klein, Hans-Ulrich, Kummer, Markus, Lacor, Pascale N., Lah, James, Laing, Emma, Levey, Allan, Li, Yupeng, Lipsky, Samantha, Liu, Yushi, Liu, Jimmy, Liu, Zhandong, Louie, Gregory, Lu, Tao, Ma, Yiyi, Matsuoka, Yasuji Y., Menon, Vilas, Miller, Bradley, Misko, Thomas P., Mollon, Jennifer E., Mukherjee, Sumit, Noggle, Scott, Pao, Ping-Chieh, Pearce, Tracy Young, Pearson, Neil, Penny, Michelle, Petyuk, Vladislav A., Price, Nathan, Quarless, Danjuma X., Ravikumar, Brinda, Ried, Janina S., Ruble, Cara Lee Ann, Runz, Heiko, Saykin, Andrew J., Schadt, Eric, Scherschel, James E., Seyfried, Nicholas, Shulman, Joshua M., Snyder, Phil, Soares, Holly, Srivastava, Gyan P., Stockmann, Henning, Taga, Mariko, Tasaki, Shinya, Tenenbaum, Jessie, Tsai, Li-Huei, Vasanthakumar, Aparna, Wachter, Astrid, Wang, Yaming, Wang, Hong, Wang, Minghui, Whelan, Christopher D., White, Charles, Woo, Kara H., Wren, Paul, Wu, Jessica W., Xi, Hualin S., Yankner, Bruce A., Younkin, Steven G., Yu, Lei, Zavodszky, Maria, Zhang, Wenling, Zhang, Guoqiang, Zhang, Bin, Zhu, Jun, Omberg, Larsson, Peters, Mette A., Logsdon, Benjamin A., De Jager, Philip L., Ertekin-Taner, Nilüfer, and Mangravite, Lara M.

Abstract

© 2020, The Author(s). The availability of high-quality RNA-sequencing and genotyping data of post-mortem brain collections from consortia such as CommonMind Consortium (CMC) and the Accelerating Medicines Partnership for Alzheimer’s Disease (AMP-AD) Consortium enable the generation of a large-scale brain cis-eQTL meta-analysis. Here we generate cerebral cortical eQTL from 1433 samples available from four cohorts (identifying >4.1 million significant eQTL for >18,000 genes), as well as cerebellar eQTL from 261 samples (identifying 874,836 significant eQTL for >10,000 genes). We find substantially improved power in the meta-analysis over individual cohort analyses, particularly in comparison to the Genotype-Tissue Expression (GTEx) Project eQTL. Additionally, we observed differences in eQTL patterns between cerebral and cerebellar brain regions. We provide these brain eQTL as a resource for use by the research community. As a proof of principle for their utility, we apply a colocalization analysis to identify genes underlying the GWAS association peaks for schizophrenia and identify a potentially novel gene colocalization with lncRNA RP11-677M14.2 (posterior probability of colocalization 0.975).

Published
2022

7. Improving preeclampsia risk prediction by modeling pregnancy trajectories from routinely collected electronic medical record data

Author

Li, Shilong, primary, Wang, Zichen, additional, Vieira, Luciana A., additional, Zheutlin, Amanda B., additional, Ru, Boshu, additional, Schadt, Emilio, additional, Wang, Pei, additional, Copperman, Alan B., additional, Stone, Joanne L., additional, Gross, Susan J., additional, Kao, Yu-Han, additional, Lau, Yan Kwan, additional, Dolan, Siobhan M., additional, Schadt, Eric E., additional, and Li, Li, additional

Published
2022
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9. Integrative network analysis of early-stage lung adenocarcinoma identifies aurora kinase inhibition as interceptor of invasion and progression

Author

Yoo, Seungyeul, primary, Sinha, Abhilasha, additional, Yang, Dawei, additional, Altorki, Nasser K., additional, Tandon, Radhika, additional, Wang, Wenhui, additional, Chavez, Deebly, additional, Lee, Eunjee, additional, Patel, Ayushi S., additional, Sato, Takashi, additional, Kong, Ranran, additional, Ding, Bisen, additional, Schadt, Eric E., additional, Watanabe, Hideo, additional, Massion, Pierre P., additional, Borczuk, Alain C., additional, Zhu, Jun, additional, and Powell, Charles A., additional

Published
2022
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10. A mechanistic framework for cardiometabolic and coronary artery diseases

Author

Koplev, Simon, primary, Seldin, Marcus, additional, Sukhavasi, Katyayani, additional, Ermel, Raili, additional, Pang, Shichao, additional, Zeng, Lingyao, additional, Bankier, Sean, additional, Di Narzo, Antonio, additional, Cheng, Haoxiang, additional, Meda, Vamsidhar, additional, Ma, Angela, additional, Talukdar, Husain, additional, Cohain, Ariella, additional, Amadori, Letizia, additional, Argmann, Carmen, additional, Houten, Sander M., additional, Franzén, Oscar, additional, Mocci, Giuseppe, additional, Meelu, Omar A., additional, Ishikawa, Kiyotake, additional, Whatling, Carl, additional, Jain, Anamika, additional, Jain, Rajeev Kumar, additional, Gan, Li-Ming, additional, Giannarelli, Chiara, additional, Roussos, Panos, additional, Hao, Ke, additional, Schunkert, Heribert, additional, Michoel, Tom, additional, Ruusalepp, Arno, additional, Schadt, Eric E., additional, Kovacic, Jason C., additional, Lusis, Aldon J., additional, and Björkegren, Johan L. M., additional

Published
2022
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11. Impact of body mass index on the efficacy of aromatase inhibitors in patients with metastatic breast cancer

Author

Patel, Rima, primary, Li, Zhiqiang, additional, Zimmerman, Brittney S., additional, Fink, Marc Y., additional, Wells, Jason D., additional, Zhou, Xiang, additional, Ayers, Kristin, additional, Redfern, Arielle, additional, Newman, Scott, additional, Schadt, Eric, additional, Oh, William K., additional, Chen, Rong, additional, and Tiersten, Amy, additional

Published
2022
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12. Population-based estimates of breast cancer risk for carriers of pathogenic variants identified by gene-panel testing

Author

Southey, Melissa C., Dowty, James G., Riaz, Moeen, Steen, Jason A., Renault, Anne-Laure, Tucker, Katherine, Kirk, Judy, James, Paul, Winship, Ingrid, Pachter, Nicholas, Poplawski, Nicola, Grist, Scott, Park, Daniel J., Pope, Bernard J., Mahmood, Khalid, Hammet, Fleur, Mahmoodi, Maryam, Tsimiklis, Helen, Theys, Derrick, Rewse, Amanda, Willis, Amanda, Morrow, April, Speechly, Catherine, Harris, Rebecca, Sebra, Robert, Schadt, Eric, Lacaze, Paul, McNeil, John J., Giles, Graham G., Milne, Roger L., Hopper, John L., and Nguyen-Dumont, Tú

Subjects
Breast cancer, Genetic testing, Oncology, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, Pharmacology (medical), Radiology, Nuclear Medicine and imaging, RC254-282, Article
Abstract

Population-based estimates of breast cancer risk for carriers of pathogenic variants identified by gene-panel testing are urgently required. Most prior research has been based on women selected for high-risk features and more data is needed to make inference about breast cancer risk for women unselected for family history, an important consideration of population screening. We tested 1464 women diagnosed with breast cancer and 862 age-matched controls participating in the Australian Breast Cancer Family Study (ABCFS), and 6549 healthy, older Australian women enroled in the ASPirin in Reducing Events in the Elderly (ASPREE) study for rare germline variants using a 24-gene-panel. Odds ratios (ORs) were estimated using unconditional logistic regression adjusted for age and other potential confounders. We identified pathogenic variants in 11.1% of the ABCFS cases, 3.7% of the ABCFS controls and 2.2% of the ASPREE (control) participants. The estimated breast cancer OR [95% confidence interval] was 5.3 [2.1–16.2] for BRCA1, 4.0 [1.9–9.1] for BRCA2, 3.4 [1.4–8.4] for ATM and 4.3 [1.0–17.0] for PALB2. Our findings provide a population-based perspective to gene-panel testing for breast cancer predisposition and opportunities to improve predictors for identifying women who carry pathogenic variants in breast cancer predisposition genes.

Published
2021
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13. Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes

Author

Malik, Rainer, Chauhan, Ganesh, Anderson, Christopher D, Salomaa, Veikko, Sapkota, Bishwa R, Schmidt, Reinhold, Schmidt, Carsten O, Schminke, Ulf, Sharma, Pankaj, Slowik, Agnieszka, Sudlow, Cathie L M, Tanislav, Christian, Tatlisumak, Turgut, Chong, Michael, Taylor, Kent D, Thijs, Vincent N S, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Tiedt, Steffen, Trompet, Stella, Tzourio, Christophe, van Duijn, Cornelia M, Walters, Matthew, Wareham, Nicholas J, Adams, Hieab H H, Wassertheil-Smoller, Sylvia, Wilson, James G, Wiggins, Kerri L, Yang, Qiong, Yusuf, Salim, Consortium, AFGen, Epidemiology, Cohorts for Heart and Aging Research in Genomic, Pressure, International Genomics of Blood, Consortium, INVENT, STARNET, Ago, Tetsuro, Bis, Joshua C, Pastinen, Tomi, Ruusalepp, Arno, Schadt, Eric E, Koplev, Simon, Björkegren, Johan L M, Codoni, Veronica, Civelek, Mete, Smith, Nicholas L, Trégouët, David A, Almgren, Peter, Christophersen, Ingrid E, Roselli, Carolina, Lubitz, Steven A, Ellinor, Patrick T, Tai, E Shyong, Kooner, Jaspal S, Kato, Norihiro, He, Jiang, van der Harst, Pim, Elliott, Paul, Amouyel, Philippe, Chambers, John C, Takeuchi, Fumihiko, Johnson, Andrew D, Group, BioBank Japan Cooperative Hospital, Consortium, COMPASS, Consortium, EPIC-CVD, Consortium, EPIC-InterAct, Consortium, International Stroke Genetics, Consortium, METASTROKE, Consortium, Neurology Working Group of the CHARGE, Ay, Hakan, Network, NINDS Stroke Genetics, Study, UK Young Lacunar DNA, Consortium, MEGASTROKE, Sanghera, Dharambir K, Melander, Olle, Jern, Christina, Strbian, Daniel, Fernandez-Cadenas, Israel, Longstreth, W. T., Rolfs, Arndt, Bartz, Traci M, Hata, Jun, Woo, Daniel, Rosand, Jonathan, Pare, Guillaume, Hopewell, Jemma C, Saleheen, Danish, Stefansson, Kari, Worrall, Bradford B, Kittner, Steven J, Seshadri, Sudha, Benavente, Oscar R, Fornage, Myriam, Markus, Hugh S, Howson, Joanna M M, Kamatani, Yoichiro, Debette, Stephanie, Dichgans, Martin, Traylor, Matthew, Sargurupremraj, Muralidharan, Bevan, Steve, Okada, Yukinori, Mishra, Aniket, Rutten-Jacobs, Loes, Giese, Anne-Katrin, van der Laan, Sander W, Gretarsdottir, Solveig, Boncoraglio, Giorgio B, Brown, Robert D, Butterworth, Adam S, Carrera, Caty, Carty, Cara L, Chasman, Daniel I, Chen, Wei-Min, Cole, John W, Correa, Adolfo, Cotlarciuc, Ioana, Cruchaga, Carlos, Danesh, John, de Bakker, Paul I W, DeStefano, Anita L, Hoed, Marcel den, Duan, Qing, Engelter, Stefan T, Falcone, Guido J, Gottesman, Rebecca F, Grewal, Raji P, Gudnason, Vilmundur, Gustafsson, Stefan, Haessler, Jeffrey, Harris, Tamara B, Hassan, Ahamad, Havulinna, Aki S, Heckbert, Susan R, Holliday, Elizabeth G, Howard, George, Hsu, Fang-Chi, Hyacinth, Hyacinth I, Ikram, M Arfan, Ingelsson, Erik, Irvin, Marguerite R, Jian, Xueqiu, Jiménez-Conde, Jordi, Johnson, Julie A, Jukema, J Wouter, Kanai, Masahiro, Keene, Keith L, Kissela, Brett M, Kleindorfer, Dawn O, Kooperberg, Charles, Kubo, Michiaki, Lange, Leslie A, Langefeld, Carl D, Langenberg, Claudia, Launer, Lenore J, Lee, Jin-Moo, Lemmens, Robin, Leys, Didier, Lewis, Cathryn M, Lin, Wei-Yu, Lindgren, Arne G, Lorentzen, Erik, Magnusson, Patrik K, Maguire, Jane, Manichaikul, Ani, McArdle, Patrick F, Meschia, James F, Mitchell, Braxton D, Mosley, Thomas H, Nalls, Michael A, Ninomiya, Toshiharu, O'Donnell, Martin J, Psaty, Bruce M, Pulit, Sara L, Rannikmäe, Kristiina, Reiner, Alexander P, Rexrode, Kathryn M, Rice, Kenneth, Rich, Stephen S, Ridker, Paul M, Rost, Natalia S, Rothwell, Peter M, Rotter, Jerome I, Rundek, Tatjana, Sacco, Ralph L, Sakaue, Saori, Sale, Michele M, Amin, Najaf, Aparicio, Hugo S, Arnett, Donna K, Attia, John, Beiser, Alexa S, Berr, Claudine, Buring, Julie E, Bustamante, Mariana, Caso, Valeria, Cheng, Yu-Ching, Choi, Seung Hoan, Chowhan, Ayesha, Cullell, Natalia, Dartigues, Jean-François, Delavaran, Hossein, Delgado, Pilar, Dörr, Marcus, Engström, Gunnar, Ford, Ian, Gurpreet, Wander S, Hamsten, Anders, Heitsch, Laura, Hozawa, Atsushi, Ibanez, Laura, Ilinca, Andreea, Ingelsson, Martin, Iwasaki, Motoki, Jackson, Rebecca D, Jood, Katarina, den Hoed, Marcel, Jousilahti, Pekka, Kaffashian, Sara, Kalra, Lalit, Kamouchi, Masahiro, Kitazono, Takanari, Kjartansson, Olafur, Kloss, Manja, Koudstaal, Peter J, Krupinski, Jerzy, Labovitz, Daniel L, Laurie, Cathy C, Levi, Christopher R, Li, Linxin, Lind, Lars, Lindgren, Cecilia M, Lioutas, Vasileios, Liu, Yong Mei, Lopez, Oscar L, Makoto, Hirata, Martinez-Majander, Nicolas, Matsuda, Koichi, Minegishi, Naoko, Montaner, Joan, Morris, Andrew P, Muiño, Elena, Müller-Nurasyid, Martina, Norrving, Bo, Ogishima, Soichi, Parati, Eugenio A, Peddareddygari, Leema Reddy, Pedersen, Nancy L, Pera, Joanna, Perola, Markus, Pezzini, Alessandro, Pileggi, Silvana, Rabionet, Raquel, Riba-Llena, Iolanda, Ribasés, Marta, Romero, Jose R, Roquer, Jaume, Rudd, Anthony G, Sarin, Antti-Pekka, Sarju, Ralhan, Sarnowski, Chloe, Sasaki, Makoto, Satizabal, Claudia L, Satoh, Mamoru, Sattar, Naveed, Sawada, Norie, Sibolt, Gerli, Sigurdsson, Ásgeir, Smith, Albert, Sobue, Kenji, Soriano-Tárraga, Carolina, Stanne, Tara, Stine, O Colin, Stott, David J, Strauch, Konstantin, Takai, Takako, Tanaka, Hideo, Tanno, Kozo, Teumer, Alexander, Tomppo, Liisa, Torres-Aguila, Nuria P, Touze, Emmanuel, Tsugane, Shoichiro, Uitterlinden, Andre G, Valdimarsson, Einar M, van der Lee, Sven J, Völzke, Henry, Wakai, Kenji, Weir, David, Williams, Stephen R, Wolfe, Charles D A, Wong, Quenna, Xu, Huichun, Yamaji, Taiki, Bordeaux population health (BPH), Université de Bordeaux (UB)-Institut de Santé Publique, d'Épidémiologie et de Développement (ISPED)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pathology, Epidemiology, Radiology & Nuclear Medicine, Cardiovascular Centre (CVC), Universitat de Barcelona, Traylor, Matthew [0000-0001-6624-8621], Okada, Yukinori [0000-0002-0311-8472], Rutten-Jacobs, Loes [0000-0003-3223-885X], van der Laan, Sander W [0000-0001-6888-1404], Adams, Hieab HH [0000-0003-3687-2508], Almgren, Peter [0000-0002-0473-0241], Amouyel, Philippe [0000-0001-9088-234X], Correa, Adolfo [0000-0002-9501-600X], Cruchaga, Carlos [0000-0002-0276-2899], den Hoed, Marcel [0000-0001-8081-428X], Gustafsson, Stefan [0000-0001-5894-0351], Havulinna, Aki S [0000-0002-4787-8959], Ikram, M Arfan [0000-0003-0372-8585], Jukema, J Wouter [0000-0002-3246-8359], Kanai, Masahiro [0000-0001-5165-4408], Lewis, Cathryn M [0000-0002-8249-8476], Lin, Wei-Yu [0000-0002-9267-7988], Magnusson, Patrik K [0000-0002-7315-7899], Pulit, Sara L [0000-0002-2502-3669], Wiggins, Kerri L [0000-0003-2749-1279], Yang, Qiong [0000-0002-3658-1375], Schadt, Eric E [0000-0002-7892-8808], Koplev, Simon [0000-0002-8586-5614], Civelek, Mete [0000-0002-8141-0284], Trégouët, David A [0000-0001-9084-7800], Christophersen, Ingrid E [0000-0002-6141-4712], Roselli, Carolina [0000-0001-5267-6756], Ellinor, Patrick T [0000-0002-2067-0533], van der Harst, Pim [0000-0002-2713-686X], Elliott, Paul [0000-0002-7511-5684], Takeuchi, Fumihiko [0000-0003-3185-5661], Jern, Christina [0000-0002-7531-2354], Saleheen, Danish [0000-0001-6193-020X], Kamatani, Yoichiro [0000-0001-8748-5597], Dichgans, Martin [0000-0002-0654-387X], and Apollo - University of Cambridge Repository

Subjects
Male, 0301 basic medicine, COMPASS Consortium, Linkage disequilibrium, Candidate gene, UK Young Lacunar DNA Study, Genome-wide association study, SEPIA, Linkage Disequilibrium, Epigenesis, Genetic, classification [Stroke], International Stroke Genetics Consortium (ISGC), 0302 clinical medicine, INDEL Mutation, HEMORRHAGIC STROKE, Risk Factors, Pleiotropy, Databases, Genetic, Neurology Working Group of the CHARGE Consortium, WHITE-MATTER HYPERINTENSITIES, Gene Regulatory Networks, Stroke, Genetics & Heredity, Genetics, International Genomics of Blood Pressure (iGEN-BP) Consortium, physiopathology [Stroke], AFGen Consortium, 11 Medical And Health Sciences, Genomics, 3. Good health, [MEGASTROKE Consortium], ISCHEMIC-STROKE, VINTAGE, genetics [Stroke], CORONARY-ARTERY-DISEASE, Medical genetics, Female, EPIC-InterAct Consortium, MEGASTROKE Consortium, Life Sciences & Biomedicine, Gens, medicine.medical_specialty, SUSCEPTIBILITY LOCI, STARNET, INVENT Consortium, SMALL-VESSEL DISEASE, Biology, Polymorphism, Single Nucleotide, EPIC-CVD Consortium, Article, Chromosomes, HUMAN GENETIC-VARIATION, NINDS Stroke Genetics Network (SiGN), 03 medical and health sciences, ddc:570, Genetic variation, medicine, Humans, Genetic Predisposition to Disease, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, Science & Technology, Models, Genetic, COMPLEX TRAITS, Computational Biology, 06 Biological Sciences, medicine.disease, METASTROKE Consortium, Human genetics, Cromosomes, BioBank Japan Cooperative Hospital Group, Genòmica, 030104 developmental biology, Genes, Genetic Loci, ATRIAL-FIBRILLATION, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, SUDDEN CARDIAC DEATH, 030217 neurology & neurosurgery, Developmental Biology, Genome-Wide Association Study
Abstract

Stroke has multiple etiologies, but the underlying genes and pathways are largely unknown. We conducted a multiancestry genome-wide-association meta-analysis in 521,612 individuals (67,162 cases and 454,450 controls) and discovered 22 new stroke risk loci, bringing the total to 32. We further found shared genetic variation with related vascular traits, including blood pressure, cardiac traits, and venous thromboembolism, at individual loci (n = 18), and using genetic risk scores and linkage-disequilibrium-score regression. Several loci exhibited distinct association and pleiotropy patterns for etiological stroke sub-types. Eleven new susceptibility loci indicate mechanisms not previously implicated in stroke pathophysiology, with prioritization of risk variants and genes accomplished through bioinformatics analyses using extensive functional datasets. Stroke risk loci were significantly enriched in drug targets for antithrombotic therapy.

Published
2018
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14. Genetic variants associated with inherited cardiovascular disorders among 13,131 asymptomatic older adults of European descent

Author

Lacaze, Paul, primary, Sebra, Robert, additional, Riaz, Moeen, additional, Ingles, Jodie, additional, Tiller, Jane, additional, Thompson, Bryony A., additional, James, Paul A., additional, Fatkin, Diane, additional, Semsarian, Christopher, additional, Reid, Christopher M., additional, Tonkin, Andrew M., additional, Winship, Ingrid, additional, Schadt, Eric, additional, and McNeil, John J., additional

Published
2021
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16. A composite biomarker of neutrophil-lymphocyte ratio and hemoglobin level correlates with clinical response to PD-1 and PD-L1 inhibitors in advanced non-small cell lung cancers

Author

Ayers, Kristin L., primary, Ma, Meng, additional, Debussche, Gaspard, additional, Corrigan, David, additional, McCafferty, Jonathan, additional, Lee, Kyeryoung, additional, Newman, Scott, additional, Zhou, Xiang, additional, Hirsch, Fred R., additional, Mack, Philip C., additional, Liu, Jane J., additional, Schadt, Eric E., additional, Chen, Rong, additional, and Li, Shuyu D., additional

Published
2021
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17. An integrative multiomic network model links lipid metabolism to glucose regulation in coronary artery disease

Author

Cohain, Ariella T., primary, Barrington, William T., additional, Jordan, Daniel M., additional, Beckmann, Noam D., additional, Argmann, Carmen A., additional, Houten, Sander M., additional, Charney, Alexander W., additional, Ermel, Raili, additional, Sukhavasi, Katyayani, additional, Franzen, Oscar, additional, Koplev, Simon, additional, Whatling, Carl, additional, Belbin, Gillian M., additional, Yang, Jialiang, additional, Hao, Ke, additional, Kenny, Eimear E., additional, Tu, Zhidong, additional, Zhu, Jun, additional, Gan, Li-Ming, additional, Do, Ron, additional, Giannarelli, Chiara, additional, Kovacic, Jason C., additional, Ruusalepp, Arno, additional, Lusis, Aldons J., additional, Bjorkegren, Johan L. M., additional, and Schadt, Eric E., additional

Published
2021
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18. Aberrant methylation underlies insulin gene expression in human insulinoma

Author

Karakose, Esra, primary, Wang, Huan, additional, Inabnet, William, additional, Thakker, Rajesh V., additional, Libutti, Steven, additional, Fernandez-Ranvier, Gustavo, additional, Suh, Hyunsuk, additional, Stevenson, Mark, additional, Kinoshita, Yayoi, additional, Donovan, Michael, additional, Antipin, Yevgeniy, additional, Li, Yan, additional, Liu, Xiaoxiao, additional, Jin, Fulai, additional, Wang, Peng, additional, Uzilov, Andrew, additional, Argmann, Carmen, additional, Schadt, Eric E., additional, Stewart, Andrew F., additional, Scott, Donald K., additional, and Lambertini, Luca, additional

Published
2020
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19. An inflammatory cytokine signature predicts COVID-19 severity and survival

Author

Del Valle, Diane Marie, primary, Kim-Schulze, Seunghee, additional, Huang, Hsin-Hui, additional, Beckmann, Noam D., additional, Nirenberg, Sharon, additional, Wang, Bo, additional, Lavin, Yonit, additional, Swartz, Talia H., additional, Madduri, Deepu, additional, Stock, Aryeh, additional, Marron, Thomas U., additional, Xie, Hui, additional, Patel, Manishkumar, additional, Tuballes, Kevin, additional, Van Oekelen, Oliver, additional, Rahman, Adeeb, additional, Kovatch, Patricia, additional, Aberg, Judith A., additional, Schadt, Eric, additional, Jagannath, Sundar, additional, Mazumdar, Madhu, additional, Charney, Alexander W., additional, Firpo-Betancourt, Adolfo, additional, Mendu, Damodara Rao, additional, Jhang, Jeffrey, additional, Reich, David, additional, Sigel, Keith, additional, Cordon-Cardo, Carlos, additional, Feldmann, Marc, additional, Parekh, Samir, additional, Merad, Miriam, additional, and Gnjatic, Sacha, additional

Published
2020
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20. Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease

Author

Beckmann, Noam D., primary, Lin, Wei-Jye, additional, Wang, Minghui, additional, Cohain, Ariella T., additional, Charney, Alexander W., additional, Wang, Pei, additional, Ma, Weiping, additional, Wang, Ying-Chih, additional, Jiang, Cheng, additional, Audrain, Mickael, additional, Comella, Phillip H., additional, Fakira, Amanda K., additional, Hariharan, Siddharth P., additional, Belbin, Gillian M., additional, Girdhar, Kiran, additional, Levey, Allan I., additional, Seyfried, Nicholas T., additional, Dammer, Eric B., additional, Duong, Duc, additional, Lah, James J., additional, Haure-Mirande, Jean-Vianney, additional, Shackleton, Ben, additional, Fanutza, Tomas, additional, Blitzer, Robert, additional, Kenny, Eimear, additional, Zhu, Jun, additional, Haroutunian, Vahram, additional, Katsel, Pavel, additional, Gandy, Sam, additional, Tu, Zhidong, additional, Ehrlich, Michelle E., additional, Zhang, Bin, additional, Salton, Stephen R., additional, and Schadt, Eric E., additional

Published
2020
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21. Genomic analyses implicate noncoding de novo variants in congenital heart disease

Author

Richter, Felix, primary, Morton, Sarah U., additional, Kim, Seong Won, additional, Kitaygorodsky, Alexander, additional, Wasson, Lauren K., additional, Chen, Kathleen M., additional, Zhou, Jian, additional, Qi, Hongjian, additional, Patel, Nihir, additional, DePalma, Steven R., additional, Parfenov, Michael, additional, Homsy, Jason, additional, Gorham, Joshua M., additional, Manheimer, Kathryn B., additional, Velinder, Matthew, additional, Farrell, Andrew, additional, Marth, Gabor, additional, Schadt, Eric E., additional, Kaltman, Jonathan R., additional, Newburger, Jane W., additional, Giardini, Alessandro, additional, Goldmuntz, Elizabeth, additional, Brueckner, Martina, additional, Kim, Richard, additional, Porter, George A., additional, Bernstein, Daniel, additional, Chung, Wendy K., additional, Srivastava, Deepak, additional, Tristani-Firouzi, Martin, additional, Troyanskaya, Olga G., additional, Dickel, Diane E., additional, Shen, Yufeng, additional, Seidman, Jonathan G., additional, Seidman, Christine E., additional, and Gelb, Bruce D., additional

Published
2020
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22. Large-scale proteomic analysis of Alzheimer’s disease brain and cerebrospinal fluid reveals early changes in energy metabolism associated with microglia and astrocyte activation

Author

Johnson, Erik C. B., primary, Dammer, Eric B., additional, Duong, Duc M., additional, Ping, Lingyan, additional, Zhou, Maotian, additional, Yin, Luming, additional, Higginbotham, Lenora A., additional, Guajardo, Andrew, additional, White, Bartholomew, additional, Troncoso, Juan C., additional, Thambisetty, Madhav, additional, Montine, Thomas J., additional, Lee, Edward B., additional, Trojanowski, John Q., additional, Beach, Thomas G., additional, Reiman, Eric M., additional, Haroutunian, Vahram, additional, Wang, Minghui, additional, Schadt, Eric, additional, Zhang, Bin, additional, Dickson, Dennis W., additional, Ertekin-Taner, Nilüfer, additional, Golde, Todd E., additional, Petyuk, Vladislav A., additional, De Jager, Philip L., additional, Bennett, David A., additional, Wingo, Thomas S., additional, Rangaraju, Srikant, additional, Hajjar, Ihab, additional, Shulman, Joshua M., additional, Lah, James J., additional, Levey, Allan I., additional, and Seyfried, Nicholas T., additional

Published
2020
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24. Intratumoral heterogeneity and clonal evolution in liver cancer

Author

Losic, Bojan, primary, Craig, Amanda J., additional, Villacorta-Martin, Carlos, additional, Martins-Filho, Sebastiao N., additional, Akers, Nicholas, additional, Chen, Xintong, additional, Ahsen, Mehmet E., additional, von Felden, Johann, additional, Labgaa, Ismail, additional, DʹAvola, Delia, additional, Allette, Kimaada, additional, Lira, Sergio A., additional, Furtado, Glaucia C., additional, Garcia-Lezana, Teresa, additional, Restrepo, Paula, additional, Stueck, Ashley, additional, Ward, Stephen C., additional, Fiel, Maria I., additional, Hiotis, Spiros P., additional, Gunasekaran, Ganesh, additional, Sia, Daniela, additional, Schadt, Eric E., additional, Sebra, Robert, additional, Schwartz, Myron, additional, Llovet, Josep M., additional, Thung, Swan, additional, Stolovitzky, Gustavo, additional, and Villanueva, Augusto, additional

Published
2020
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25. VGF-derived peptide TLQP-21 modulates microglial function through C3aR1 signaling pathways and reduces neuropathology in 5xFAD mice

Author

El Gaamouch, Farida, primary, Audrain, Mickael, additional, Lin, Wei-Jye, additional, Beckmann, Noam, additional, Jiang, Cheng, additional, Hariharan, Siddharth, additional, Heeger, Peter S., additional, Schadt, Eric E., additional, Gandy, Sam, additional, Ehrlich, Michelle E., additional, and Salton, Stephen R., additional

Published
2020
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26. Sampling the host response to SARS-CoV-2 in hospitals under siege

Author

Charney, Alexander W., Simons, Nicole W., Mouskas, Konstantinos, Lepow, Lauren, Cheng, Esther, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Del Valle, Diane Marie, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Patel, Manishkumar, Xie, Hui, Yi, Nancy, Yu, Alex, Kang, Gurpawan, Mendoza, Anthony, Liharska, Lora E., Moya, Emily, Hartnett, Matthew, Hatem, Sandra, Wilkins, Lillian, Eaton, Melody, Jamal, Hajra, Tuballes, Kevin, Chen, Steven T., Tabachnikova, Alexandra, Chung, Jonathan, Harris, Jocelyn, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Argueta, Kimberly, Karekar, Neha, Lee, Brian, Kelly, Geoffrey, Geanon, Daniel, Handler, Diana, Leech, John, Stefanos, Hiyab, Dawson, Travis, Scott, Ieisha, Francoeur, Nancy, Johnson, Jessica S., Vaid, Akhil, Glicksberg, Benjamin S., Nadkarni, Girish N., Schadt, Eric E., Gelb, Bruce D., Rahman, Adeeb, Sebra, Robert, Martin, Glenn, Agashe, Charuta, Agrawal, Priyal, Akyatan, Alara, Alesso-Carra, Kasey, Alibo, Eziwoma, Alvarez, Kelvin, Amabile, Angelo, Ascolillo, Steven, Bailey, Rasheed, Begani, Priya, Correra, Paloma Bravo, Brown, Stacey-Ann, Buckup, Mark, Burka, Larissa, Cambron, Lena, Carrara, Gina, Chang, Serena, Chien, Jonathan, Chowdhury, Mashkura, Bozkus, Cansu Cimen, Comella, Phillip, Cosgrove, Dana, Cossarini, Francesca, Cotter, Liam, Dave, Arpit, Dayal, Bheesham, Dhainaut, Maxime, Dornfeld, Rebecca, Dul, Katie, Eber, Nissan, Elaiho, Cordelia, Fabris, Frank, Faith, Jeremiah, Falci, Dominique, Feng, Susie, Fennessy, Brian, Fernandes, Marie, Gangadharan, Sandeep, Grabowska, Joanna, Gyimesi, Gavin, Hamdani, Maha, Herbinet, Manon, Herrera, Elva, Hochman, Arielle, Hoffman, Gabriel E., Hook, Jaime, Horta, Laila, Humblin, Etienne, Karim, Subha, Kim, Jessica, Lebovitch, Dannielle, Lee, Grace, Lee, Gyu Ho, Lee, Jacky, Leventhal, Mike, Lindblad, Katherine, Livanos, Alexandra, Machado, Rosalie, Mahmood, Zafar, Mar, Kelcey, Maskey, Shrisha, Matthews, Paul, Meckel, Katherine, Mehandru, Saurabh, Mercedes, Cynthia, Meyer, Dara, Mollaoglu, Gurkan, Morris, Sarah, Nie, Kai, Nisenholtz, Marjorie, Ofori-Amanfo, George, Onel, Kenan, Ounadjela, Merouane, Patel, Vishwendra, Pruitt, Cassandra, Rathi, Shivani, Redes, Jamie, Reyes-Torres, Ivan, Rodrigues, Alcina, Rodriguez, Alfonso, Roudko, Vladimir, Ruiz, Evelyn, Scalzo, Pearl, Silva, Pedro, Schanoski, Alessandra Soares, Straw, Meghan, Tabachnikova, Sasha, Teague, Collin, Upadhyaya, Bhaskar, Van Der Heide, Verena, Vaninov, Natalie, Wacker, Daniel, Walsh, Hadley, Wilk, C. Matthias, Wilson, Jessica, Wilson, Karen M., Xue, Li, Yeboah, Naa-akomaah, Young, Sabina, Zaks, Nina, Zha, Renyuan, Marron, Thomas, Beckmann, Noam, Kim-Schulze, Seunghee, Gnjatic, Sacha, and Merad, Miriam

Subjects
Siege, 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), biology, business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Host response, Sampling (statistics), General Medicine, biology.organism_classification, Virology, General Biochemistry, Genetics and Molecular Biology, Pandemic, Medicine, business, Betacoronavirus
Published
2020
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27. Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

Author

Oliveira, Pedro H., primary, Ribis, John W., additional, Garrett, Elizabeth M., additional, Trzilova, Dominika, additional, Kim, Alex, additional, Sekulovic, Ognjen, additional, Mead, Edward A., additional, Pak, Theodore, additional, Zhu, Shijia, additional, Deikus, Gintaras, additional, Touchon, Marie, additional, Lewis-Sandari, Martha, additional, Beckford, Colleen, additional, Zeitouni, Nathalie E., additional, Altman, Deena R., additional, Webster, Elizabeth, additional, Oussenko, Irina, additional, Bunyavanich, Supinda, additional, Aggarwal, Aneel K., additional, Bashir, Ali, additional, Patel, Gopi, additional, Wallach, Frances, additional, Hamula, Camille, additional, Huprikar, Shirish, additional, Schadt, Eric E., additional, Sebra, Robert, additional, van Bakel, Harm, additional, Kasarskis, Andrew, additional, Tamayo, Rita, additional, Shen, Aimee, additional, and Fang, Gang, additional

Published
2019
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28. Correction to: Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits

Author

Glicksberg, Benjamin S., primary, Amadori, Letizia, additional, Akers, Nicholas K., additional, Sukhavasi, Katyayani, additional, Franzén, Oscar, additional, Li, Li, additional, Belbin, Gillian M., additional, Ayers, Kristin L., additional, Shameer, Khader, additional, Badgeley, Marcus A., additional, Johnson, Kipp W., additional, Readhead, Ben, additional, Darrow, Bruce J., additional, Kenny, Eimear E., additional, Betsholtz, Christer, additional, Ermel, Raili, additional, Skogsberg, Josefin, additional, Ruusalepp, Arno, additional, Schadt, Eric E., additional, Dudley, Joel T., additional, Ren, Hongxia, additional, Kovacic, Jason C., additional, Giannarelli, Chiara, additional, Li, Shuyu D., additional, Björkegren, Johan L. M., additional, and Chen, Rong, additional

Published
2019
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30. Discovering genetic interactions bridging pathways in genome-wide association studies

Author

Fang, Gang, primary, Wang, Wen, additional, Paunic, Vanja, additional, Heydari, Hamed, additional, Costanzo, Michael, additional, Liu, Xiaoye, additional, Liu, Xiaotong, additional, VanderSluis, Benjamin, additional, Oately, Benjamin, additional, Steinbach, Michael, additional, Van Ness, Brian, additional, Schadt, Eric E., additional, Pankratz, Nathan D., additional, Boone, Charles, additional, Kumar, Vipin, additional, and Myers, Chad L., additional

Published
2019
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31. Integrative transcriptome imputation reveals tissue-specific and shared biological mechanisms mediating susceptibility to complex traits

Author

Zhang, Wen, primary, Voloudakis, Georgios, additional, Rajagopal, Veera M., additional, Readhead, Ben, additional, Dudley, Joel T., additional, Schadt, Eric E., additional, Björkegren, Johan L. M., additional, Kim, Yungil, additional, Fullard, John F., additional, Hoffman, Gabriel E., additional, and Roussos, Panos, additional

Published
2019
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32. Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits

Author

Glicksberg, Benjamin S., primary, Amadori, Letizia, additional, Akers, Nicholas K., additional, Sukhavasi, Katyayani, additional, Franzén, Oscar, additional, Li, Li, additional, Belbin, Gillian M., additional, Akers, Kristin L., additional, Shameer, Khader, additional, Badgeley, Marcus A., additional, Johnson, Kipp W., additional, Readhead, Ben, additional, Darrow, Bruce J., additional, Kenny, Eimear E., additional, Betsholtz, Christer, additional, Ermel, Raili, additional, Skogsberg, Josefin, additional, Ruusalepp, Arno, additional, Schadt, Eric E., additional, Dudley, Joel T., additional, Ren, Hongxia, additional, Kovacic, Jason C., additional, Giannarelli, Chiara, additional, Li, Shuyu D., additional, Björkegren, Johan L. M., additional, and Chen, Rong, additional

Published
2019
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34. High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis

Author

Goyette, Philippe, Boucher, Gabrielle, Mallon, Dermot, Ellinghaus, Eva, Jostins, Luke, Huang, Hailiang, Ripke, Stephan, Gusareva, Elena S., Annese, Vito, Hauser, Stephen L., Oksenberg, Jorge R., Thomsen, Ingo, Leslie, Stephen, Daly, Mark J., Van Steen, Kristel, Duerr, Richard H., Barrett, Jeffrey C., Mcgovern, Dermot P. B., Schumm, L. Philip, Traherne, James A., Carrington, Mary N., Kosmoliaptsis, Vasilis, Karlsen, Tom H., Franke, Andre, Rioux, John D., Abraham, Clara, Achkar, Jean Paul, Ahmad, Tariq, Amininejad, Leila, Ananthakrishnan, Ashwin N., Andersen, Vibeke, Anderson, Carl A., Andrews, Jane M., Aumais, Guy, Baidoo, Leonard, Baldassano, Robert N., Balschun, Tobias, Bampton, Peter A., Barclay, Murray, Bayless, Theodore M., Bethge, Johannes, Bis, Joshua C., Bitton, Alain, Brand, Stephan, Brant, Steven R., Buning, Carsten, Chew, Angela, Cho, Judy H., Cleynen, Isabelle, Cohain, Ariella, Croft, Anthony, D'Amato, Mauro, Danese, Silvio, De Jong, Dirk, De Vos, Martine, Denapiene, Goda, Denson, Lee A., Devaney, Kathy L., Dewit, Olivier, D'Inca, Renata, Dubinsky, Marla, Edwards, Cathryn, Ellinghaus, David, Essers, Jonah, Ferguson, Lynnette R., Festen, Eleonora A., Fleshner, Philip, Florin, Tim, Franchimont, Denis, Fransen, Karin, Gearry, Richard, Georges, Michel, Gieger, Christian, Glas, Jurgen, Green, Todd, Griffiths, Anne M., Guthery, Stephen L., Hakonarson, Hakon, Halfvarson, Jonas, Hanigan, Katherine, Haritunians, Talin, Hart, Ailsa, Hawkey, Chris, Hayward, Nicholas K., Hedl, Matija, Henderson, Paul, Xinli, Hu, Hui, Ken Y., Imielinski, Marcin, Ippoliti, Andrew, Jonaitis, Laimas, Kennedy, Nicholas A., Khan, Mohammed Azam, Kiudelis, Gediminas, Kugathasan, Subra, Kupcinskas, Limas, Latiano, Anna, Laukens, Debby, Lawrance, Ian C., Lee, James C., Lees, Charlie W., Leja, Marcis, Van Limbergen, Johan, Lionetti, Paolo, Liu, Jimmy Z., Louis, Edouard, Mahy, Gillian, Mansfield, John, Massey, Dunecan, Mathew, Christopher G., Milgrom, Raquel, Mitrovic, Mitja, Montgomery, Grant, Mowat, Craig, Newman, Wwilliam, Aylwin, Ng, Siew C., Ng, Evelyn Ng, Sok Meng, Nikolaus, Susanna, Ning, Kaida, Nothen, Markus, Oikonomou, Ioannis, Palmieri, Orazio, Parkes, Miles, Phillips, Anne, Ponsioen, Cyriel Y., Potocnik, Uros, Prescott, Natalie J., Proctor, Deborah D., Radford Smith, Graham, Rahier, Jean Francois, Raychaudhur, Soumya, Regueiro, Miguel, Rieder, Florian, Roberts, Rebecca, Russell, Richard K., Sanderson, Jeremy D., Sans, Miquel, Satsangi, Jack, Schadt, Eric E., Schreiber, Stefan, Scott, Regan, Seielstad, Mark, Sharma, Yashoda, Silverberg, Mark S., Simms, Lisa A., Skieceviciene, Jurgita, Spain, Sarah L., Steinhart, A. Hillary, Stempak, Joanne M., Stronati, Laura, Sventoraityte, Jurgita, Targan, Stephan R., Taylor, Kirstin M., Ter Velde, Anje, Theatre, Emilie, Torkvist, Leif, Tremelling, Mark, Van Der Meulen, Andrea, Van Sommeren, Suzanne, Vasiliauskas, Eric, Vermeire, Severine, Verspaget, Hein W., Walters, Thomas, Wwang, Kai, Wwang, Ming Hsi, Wweersma, Rinse K., Wei, Zhi, Whiteman, David, Wijmenga, Cisca, Wilson, David C., Winkelmann, Juliane, Xavier, Ramnik J., Zeissig, Sebastian, Zhang, Bin, Zhang, Clarence K., Zhang, Hu, Zhang, Wwei, Zhao, Hongyu, Zhao, Zhen Z., Gastroenterology and Hepatology, Traherne, James [0000-0002-6003-8559], Kosmoliaptsis, Vasilis [0000-0001-7298-1387], and Apollo - University of Cambridge Repository

Subjects
Heterozygote, Genotype, Genotyping Techniques, Genetic Linkage, Ulcerative, Human leukocyte antigen, Biology, Major histocompatibility complex, Polymorphism, Single Nucleotide, Article, Primary sclerosing cholangitis, Major Histocompatibility Complex, Alleles, Chromosome Mapping, Colitis, Ulcerative, Crohn Disease, Genetic Predisposition to Disease, Genome-Wide Association Study, HLA-DRB1 Chains, Humans, Inflammatory Bowel Diseases, Phenotype, Genetics, medicine, HLA-DR, Polymorphism, Colitis, HLA-DRB1, Crohn's disease, Single Nucleotide, medicine.disease, Ulcerative colitis, digestive system diseases, Immunology, biology.protein
Abstract

Genome-wide association studies of the related chronic inflammatory bowel diseases (IBD) known as Crohn's disease and ulcerative colitis have shown strong evidence of association to the major histocompatibility complex (MHC). This region encodes a large number of immunological candidates, including the antigen-presenting classical human leukocyte antigen (HLA) molecules. Studies in IBD have indicated that multiple independent associations exist at HLA and non-HLA genes, but they have lacked the statistical power to define the architecture of association and causal alleles. To address this, we performed high-density SNP typing of the MHC in >32,000 individuals with IBD, implicating multiple HLA alleles, with a primary role for HLA-DRB1*01:03 in both Crohn's disease and ulcerative colitis. Noteworthy differences were observed between these diseases, including a predominant role for class II HLA variants and heterozygous advantage observed in ulcerative colitis, suggesting an important role of the adaptive immune response in the colonic environment in the pathogenesis of IBD.

Published
2015
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37. Correction: Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden

Author

Haure-Mirande, Jean-Vianney, primary, Wang, Minghui, additional, Audrain, Mickael, additional, Fanutza, Tomas, additional, Kim, Soong Ho, additional, Heja, Szilvia, additional, Readhead, Ben, additional, Dudley, Joel T., additional, Blitzer, Robert D., additional, Schadt, Eric E., additional, Zhang, Bin, additional, Gandy, Sam, additional, and Ehrlich, Michelle E., additional

Published
2018
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38. Author Correction: Expression-based drug screening of neural progenitor cells from individuals with schizophrenia

Author

Readhead, Benjamin, primary, Hartley, Brigham J., additional, Eastwood, Brian J., additional, Collier, David A., additional, Evans, David, additional, Farias, Richard, additional, He, Ching, additional, Hoffman, Gabriel, additional, Sklar, Pamela, additional, Dudley, Joel T., additional, Schadt, Eric E., additional, Savić, Radoslav, additional, and Brennand, Kristen J., additional

Published
2018
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39. Expression-based drug screening of neural progenitor cells from individuals with schizophrenia

Author

Readhead, Benjamin, primary, Hartley, Brigham J., additional, Eastwood, Brian J., additional, Collier, David A., additional, Evans, David, additional, Farias, Richard, additional, He, Ching, additional, Hoffman, Gabriel, additional, Sklar, Pamela, additional, Dudley, Joel T., additional, Schadt, Eric E., additional, Savić, Radoslav, additional, and Brennand, Kristen J., additional

Published
2018
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40. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

Author

Raj, Towfique, primary, Li, Yang I., additional, Wong, Garrett, additional, Humphrey, Jack, additional, Wang, Minghui, additional, Ramdhani, Satesh, additional, Wang, Ying-Chih, additional, Ng, Bernard, additional, Gupta, Ishaan, additional, Haroutunian, Vahram, additional, Schadt, Eric E., additional, Young-Pearse, Tracy, additional, Mostafavi, Sara, additional, Zhang, Bin, additional, Sklar, Pamela, additional, Bennett, David A., additional, and De Jager, Philip L., additional

Published
2018
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41. Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in cerebral Aβ amyloidosis mouse normalizes clinical phenotype and complement subnetwork molecular pathology without reducing Aβ burden

Author

Haure-Mirande, Jean-Vianney, primary, Wang, Minghui, additional, Audrain, Mickael, additional, Fanutza, Tomas, additional, Kim, Soong Ho, additional, Heja, Szilvia, additional, Readhead, Ben, additional, Dudley, Joel T., additional, Blitzer, Robert D., additional, Schadt, Eric E., additional, Zhang, Bin, additional, Gandy, Sam, additional, and Ehrlich, Michelle E., additional

Published
2018
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42. Integrative approach to sporadic Alzheimer’s disease: deficiency of TYROBP in a tauopathy mouse model reduces C1q and normalizes clinical phenotype while increasing spread and state of phosphorylation of tau

Author

Audrain, Mickael, primary, Haure-Mirande, Jean-Vianney, additional, Wang, Minghui, additional, Kim, Soong Ho, additional, Fanutza, Tomas, additional, Chakrabarty, Paramita, additional, Fraser, Paul, additional, St George-Hyslop, Peter H., additional, Golde, Todd E., additional, Blitzer, Robert D., additional, Schadt, Eric E., additional, Zhang, Bin, additional, Ehrlich, Michelle E., additional, and Gandy, Sam, additional

Published
2018
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44. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease

Author

Wang, Minghui, primary, Beckmann, Noam D., additional, Roussos, Panos, additional, Wang, Erming, additional, Zhou, Xianxiao, additional, Wang, Qian, additional, Ming, Chen, additional, Neff, Ryan, additional, Ma, Weiping, additional, Fullard, John F., additional, Hauberg, Mads E., additional, Bendl, Jaroslav, additional, Peters, Mette A., additional, Logsdon, Ben, additional, Wang, Pei, additional, Mahajan, Milind, additional, Mangravite, Lara M., additional, Dammer, Eric B., additional, Duong, Duc M., additional, Lah, James J., additional, Seyfried, Nicholas T., additional, Levey, Allan I., additional, Buxbaum, Joseph D., additional, Ehrlich, Michelle, additional, Gandy, Sam, additional, Katsel, Pavel, additional, Haroutunian, Vahram, additional, Schadt, Eric, additional, and Zhang, Bin, additional

Published
2018
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45. iPSC-derived familial Alzheimer’s PSEN2 N141I cholinergic neurons exhibit mutation-dependent molecular pathology corrected by insulin signaling

Author

Moreno, Cesar L., primary, Della Guardia, Lucio, additional, Shnyder, Valeria, additional, Ortiz-Virumbrales, Maitane, additional, Kruglikov, Ilya, additional, Zhang, Bin, additional, Schadt, Eric E., additional, Tanzi, Rudolph E., additional, Noggle, Scott, additional, Buettner, Christoph, additional, and Gandy, Sam, additional

Published
2018
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49. Integrated biology approach reveals molecular and pathological interactions among Alzheimer’s Aβ42, Tau, TREM2, and TYROBP in Drosophila models

Author

Sekiya, Michiko, primary, Wang, Minghui, additional, Fujisaki, Naoki, additional, Sakakibara, Yasufumi, additional, Quan, Xiuming, additional, Ehrlich, Michelle E., additional, De Jager, Philip L., additional, Bennett, David A., additional, Schadt, Eric E., additional, Gandy, Sam, additional, Ando, Kanae, additional, Zhang, Bin, additional, and Iijima, Koichi M., additional

Published
2018
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