A catalog of genetic loci associated with kidney function from analyses of a million individuals
Wuttke, Matthias; Li, Yong; Li, Man; Sieber, Karsten B; Feitosa, Mary F; Gorski, Mathias; Tin, Adrienne; Wang, Lihua; Chu, Audrey Y; Hoppmann, Anselm; Kirsten, Holger; Giri, Ayush; Chai, Jin-Fang; Sveinbjornsson, Gardar; Tayo, Bamidele O; Nutile, Teresa; Fuchsberger, Christian; Marten, Jonathan; Cocca, Massimiliano; Ghasemi, Sahar; Xu, Yizhe; Horn, Katrin; Noce, Damia; van der Most, Peter J; Sedaghat, Sanaz; Yu, Zhi; Akiyama, Masato; Afaq, Saima; Ahluwalia, Tarunveer S; Almgren, Peter; Amin, Najaf; Ärnlöv, Johan; Bakker, Stephan J L; Bansal, Nisha; Baptista, Daniela; Bergmann, Sven; Biggs, Mary L; Biino, Ginevra; Boehnke, Michael; Boerwinkle, Eric; Boissel, Mathilde; Bottinger, Erwin P; Boutin, Thibaud S; Brenner, Hermann; Brumat, Marco; Burkhardt, Ralph; Butterworth, Adam S; Campana, Eric; Campbell, Archie; Campbell, Harry; Canouil, Mickaël; Carroll, Robert J; Catamo, Eulalia; Chambers, John C; Chee, Miao-Ling; Chee, Miao-Li; Chen, Xu; Cheng, Ching-Yu; Cheng, Yurong; Christensen, Kaare; Cifkova, Renata; Ciullo, Marina; Concas, Maria Pina; Cook, James P; Coresh, Josef; Corre, Tanguy; Sala, Cinzia Felicita; Cusi, Daniele; Danesh, John; Daw, E Warwick; de Borst, Martin H; De Grandi, Alessandro; de Mutsert, Renée; de Vries, Aiko P J; Degenhardt, Frauke; Delgado, Graciela; Demirkan, Ayse; Di Angelantonio, Emanuele; Dittrich, Katalin; Divers, Jasmin; Dorajoo, Rajkumar; Eckardt, Kai-Uwe; Ehret, Georg; Elliott, Paul; Endlich, Karlhans; Evans, Michele K; Felix, Janine F; Foo, Valencia Hui Xian; Franco, Oscar H; Franke, Andre; Freedman, Barry I; Freitag-Wolf, Sandra; Friedlander, Yechiel; Froguel, Philippe; Gansevoort, Ron T; Gao, He; Gasparini, Paolo; Gaziano, J Michael; Giedraitis, Vilmantas; Gieger, Christian; Girotto, Giorgia; Giulianini, Franco; Gögele, Martin; Gordon, Scott D; Gudbjartsson, Daniel F; Gudnason, Vilmundur; Haller, Toomas; Hamet, Pavel; Harris, Tamara B; Hartman, Catharina A; Hayward, Caroline; Hellwege, Jacklyn N; Heng, Chew-Kiat; Hicks, Andrew A; Hofer, Edith; Huang, Wei; Hutri-Kähönen, Nina; Hwang, Shih-Jen; Ikram, M Arfan; Indridason, Olafur S; Ingelsson, Erik; Ising, Marcus; Jaddoe, Vincent W V; Jakobsdottir, Johanna; Jonas, Jost B; Joshi, Peter K; Josyula, Navya Shilpa; Jung, Bettina; Kähönen, Mika; Kamatani, Yoichiro; Kammerer, Candace M; Kanai, Masahiro; Kastarinen, Mika; Kerr, Shona M; Khor, Chiea-Chuen; Kiess, Wieland; Kleber, Marcus E; Koenig, Wolfgang; Kooner, Jaspal S; Körner, Antje; Kovacs, Peter; Kraja, Aldi T; Krajcoviechova, Alena; Kramer, Holly; Krämer, Bernhard K; Kronenberg, Florian; Kubo, Michiaki; Kühnel, Brigitte; Kuokkanen, Mikko; Kuusisto, Johanna; La Bianca, Martina; Laakso, Markku; Lange, Leslie A; Langefeld, Carl D; Lee, Jeannette Jen-Mai; Lehne, Benjamin; Lehtimäki, Terho; Lieb, Wolfgang; Lim, Su-Chi; Lind, Lars; Lindgren, Cecilia M; Liu, Jun; Liu, Jianjun; Loeffler, Markus; Loos, Ruth J F; Lucae, Susanne; Lukas, Mary Ann; Lyytikäinen, Leo-Pekka; Mägi, Reedik; Magnusson, Patrik K E; Mahajan, Anubha; Martin, Nicholas G; Martins, Jade; März, Winfried; Mascalzoni, Deborah; Matsuda, Koichi; Meisinger, Christa; Meitinger, Thomas; Melander, Olle; Metspalu, Andres; Mikaelsdottir, Evgenia K; Milaneschi, Yuri; Miliku, Kozeta; Mishra, Pashupati P; Mohlke, Karen L; Mononen, Nina; Montgomery, Grant W; Mook-Kanamori, Dennis O; Mychaleckyj, Josyf C; Nadkarni, Girish N; Nalls, Mike A; Nauck, Matthias; Nikus, Kjell; Ning, Boting; Nolte, Ilja M; Noordam, Raymond; O'Connell, Jeffrey; O'Donoghue, Michelle L; Olafsson, Isleifur; Oldehinkel, Albertine J; Orho-Melander, Marju; Ouwehand, Willem H; Padmanabhan, Sandosh; Palmer, Nicholette D; Palsson, Runolfur; Penninx, Brenda W J H; Perls, Thomas; Perola, Markus; Pirastu, Mario; Pirastu, Nicola; Pistis, Giorgio; Podgornaia, Anna I; Polasek, Ozren; Ponte, Belen; Porteous, David J; Poulain, Tanja; Pramstaller, Peter P; Preuss, Michael H; Prins, Bram P; Province, Michael A; Rabelink, Ton J; Raffield, Laura M; Raitakari, Olli T; Reilly, Dermot F; Rettig, Rainer; Rheinberger, Myriam; Rice, Kenneth M; Ridker, Paul M; Rivadeneira, Fernando; Rizzi, Federica; Roberts, David J; Robino, Antonietta; Rossing, Peter; Rudan, Igor; Rueedi, Rico; Ruggiero, Daniela; Ryan, Kathleen A; Saba, Yasaman; Sabanayagam, Charumathi; Salomaa, Veikko; Salvi, Erika; Saum, Kai-Uwe; Schmidt, Helena; Schmidt, Reinhold; Schöttker, Ben; Schulz, Christina-Alexandra; Schupf, Nicole; Shaffer, Christian M; Shi, Yuan; Smith, Albert V; Smith, Blair H; Soranzo, Nicole; Spracklen, Cassandra N; Strauch, Konstantin; Stringham, Heather M; Stumvoll, Michael; Svensson, Per O; Szymczak, Silke; Tai, E-Shyong; Tajuddin, Salman M; Tan, Nicholas Y Q; Taylor, Kent D; Teren, Andrej; Tham, Yih-Chung; Thiery, Joachim; Thio, Chris H L; Thomsen, Hauke; Thorleifsson, Gudmar; Toniolo, Daniela; Tönjes, Anke; Tremblay, Johanne; Tzoulaki, Ioanna; Uitterlinden, André G; Vaccargiu, Simona; van Dam, Rob M; van der Harst, Pim; van Duijn, Cornelia M; Velez Edward, Digna R; Verweij, Niek; Vogelezang, Suzanne; Völker, Uwe; Vollenweider, Peter; Waeber, Gerard; Waldenberger, Melanie; Wallentin, Lars; Wang, Ya Xing; Wang, Chaolong; Waterworth, Dawn M; Bin Wei, Wen; White, Harvey; Whitfield, John B; Wild, Sarah H; Wilson, James F; Wojczynski, Mary K; Wong, Charlene; Wong, Tien-Yin; Xu, Liang; Yang, Qiong; Yasuda, Masayuki; Yerges-Armstrong, Laura M; Zhang, Weihua; Zonderman, Alan B; Rotter, Jerome I; Bochud, Murielle; Psaty, Bruce M; Vitart, Veronique; Wilson, James G; Dehghan, Abbas; Parsa, Afshin; Chasman, Daniel I; Ho, Kevin; Morris, Andrew P; Devuyst, Olivier; Akilesh, Shreeram; Pendergrass, Sarah A; Sim, Xueling; Böger, Carsten A; Okada, Yukinori; Edwards, Todd L; Snieder, Harold; Stefansson, Kari; Hung, Adriana M; Heid, Iris M; Scholz, Markus; Teumer, Alexander; Köttgen, Anna; Pattaro, Cristian
Chronic kidney disease (CKD) is responsible for a public health burden with multi-systemic complications. Through trans-ancestry meta-analysis of genome-wide association studies of estimated glomerular filtration rate (eGFR) and independent replication (n = 1,046,070), we identified 264 associated loci (166 new). Of these, 147 were likely to be relevant for kidney function on the basis of associations with the alternative kidney function marker blood urea nitrogen (n = 416,178). Pathway and enrichment analyses, including mouse models with renal phenotypes, support the kidney as the main target organ. A genetic risk score for lower eGFR was associated with clinically diagnosed CKD in 452,264 independent individuals. Colocalization analyses of associations with eGFR among 783,978 European-ancestry individuals and gene expression across 46 human tissues, including tubulo-interstitial and glomerular kidney compartments, identified 17 genes differentially expressed in kidney. Fine-mapping highlighted missense driver variants in 11 genes and kidney-specific regulatory variants. These results provide a comprehensive priority list of molecular targets for translational research.
PMID: 31152163
ISSN: 1546-1718
CID: 3936112
Genome-wide analyses as part of the international FTLD-TDP whole-genome sequencing consortium reveals novel disease risk factors and increases support for immune dysfunction in FTLD
Pottier, Cyril; Ren, Yingxue; Perkerson, Ralph B; Baker, Matt; Jenkins, Gregory D; van Blitterswijk, Marka; DeJesus-Hernandez, Mariely; van Rooij, Jeroen G J; Murray, Melissa E; Christopher, Elizabeth; McDonnell, Shannon K; Fogarty, Zachary; Batzler, Anthony; Tian, Shulan; Vicente, Cristina T; Matchett, Billie; Karydas, Anna M; Hsiung, Ging-Yuek Robin; Seelaar, Harro; Mol, Merel O; Finger, Elizabeth C; Graff, Caroline; Öijerstedt, Linn; Neumann, Manuela; Heutink, Peter; Synofzik, Matthis; Wilke, Carlo; Prudlo, Johannes; Rizzu, Patrizia; Simon-Sanchez, Javier; Edbauer, Dieter; Roeber, Sigrun; Diehl-Schmid, Janine; Evers, Bret M; King, Andrew; Mesulam, M Marsel; Weintraub, Sandra; Geula, Changiz; Bieniek, Kevin F; Petrucelli, Leonard; Ahern, Geoffrey L; Reiman, Eric M; Woodruff, Bryan K; Caselli, Richard J; Huey, Edward D; Farlow, Martin R; Grafman, Jordan; Mead, Simon; Grinberg, Lea T; Spina, Salvatore; Grossman, Murray; Irwin, David J; Lee, Edward B; Suh, EunRan; Snowden, Julie; Mann, David; Ertekin-Taner, Nilufer; Uitti, Ryan J; Wszolek, Zbigniew K; Josephs, Keith A; Parisi, Joseph E; Knopman, David S; Petersen, Ronald C; Hodges, John R; Piguet, Olivier; Geier, Ethan G; Yokoyama, Jennifer S; Rissman, Robert A; Rogaeva, Ekaterina; Keith, Julia; Zinman, Lorne; Tartaglia, Maria Carmela; Cairns, Nigel J; Cruchaga, Carlos; Ghetti, Bernardino; Kofler, Julia; Lopez, Oscar L; Beach, Thomas G; Arzberger, Thomas; Herms, Jochen; Honig, Lawrence S; Vonsattel, Jean Paul; Halliday, Glenda M; Kwok, John B; White, Charles L; Gearing, Marla; Glass, Jonathan; Rollinson, Sara; Pickering-Brown, Stuart; Rohrer, Jonathan D; Trojanowski, John Q; Van Deerlin, Vivianna; Bigio, Eileen H; Troakes, Claire; Al-Sarraj, Safa; Asmann, Yan; Miller, Bruce L; Graff-Radford, Neill R; Boeve, Bradley F; Seeley, William W; Mackenzie, Ian R A; van Swieten, John C; Dickson, Dennis W; Biernacka, Joanna M; Rademakers, Rosa
Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) represents the most common pathological subtype of FTLD. We established the international FTLD-TDP whole-genome sequencing consortium to thoroughly characterize the known genetic causes of FTLD-TDP and identify novel genetic risk factors. Through the study of 1131 unrelated Caucasian patients, we estimated that C9orf72 repeat expansions and GRN loss-of-function mutations account for 25.5% and 13.9% of FTLD-TDP patients, respectively. Mutations in TBK1 (1.5%) and other known FTLD genes (1.4%) were rare, and the disease in 57.7% of FTLD-TDP patients was unexplained by the known FTLD genes. To unravel the contribution of common genetic factors to the FTLD-TDP etiology in these patients, we conducted a two-stage association study comprising the analysis of whole-genome sequencing data from 517 FTLD-TDP patients and 838 controls, followed by targeted genotyping of the most associated genomic loci in 119 additional FTLD-TDP patients and 1653 controls. We identified three genome-wide significant FTLD-TDP risk loci: one new locus at chromosome 7q36 within the DPP6 gene led by rs118113626 (p value = 4.82e - 08, OR = 2.12), and two known loci: UNC13A, led by rs1297319 (p value = 1.27e - 08, OR = 1.50) and HLA-DQA2 led by rs17219281 (p value = 3.22e - 08, OR = 1.98). While HLA represents a locus previously implicated in clinical FTLD and related neurodegenerative disorders, the association signal in our study is independent from previously reported associations. Through inspection of our whole-genome sequence data for genes with an excess of rare loss-of-function variants in FTLD-TDP patients (n ≥ 3) as compared to controls (n = 0), we further discovered a possible role for genes functioning within the TBK1-related immune pathway (e.g., DHX58, TRIM21, IRF7) in the genetic etiology of FTLD-TDP. Together, our study based on the largest cohort of unrelated FTLD-TDP patients assembled to date provides a comprehensive view of the genetic landscape of FTLD-TDP, nominates novel FTLD-TDP risk loci, and strongly implicates the immune pathway in FTLD-TDP pathogenesis.
PMID: 30739198
ISSN: 1432-0533
CID: 3691682