Large-scale exome analyses reveal new rare variant contributions in amyotrophic lateral sclerosis
Hop, Paul J; Kooyman, Maarten; Kenna, Brendan J; Zwamborn, Ramona A J; van Eijk, Kristel R; Wang, Yan; van Dijk, Charlotte H; Bekema, Erwin; van Rheenen, Wouter; Beele, Paul; van Vugt, Joke J F A; ,; ,; ,; ,; Khleifat, Ahmad Al; Iacoangeli, Alfredo; Cooper-Knock, Johnathan; Smith, Bradley N; Topp, Simon; van der Kooi, Anneke J; Fominykh, Vera; Drory, Vivian; Lerner, Yossef; Shovman, Yehuda; Rowe, Dominic B; Williams, Kelly L; McLaughlin, Russell L; Hurt, Jessica; Huang, Yunfeng; Chen, Chia-Yen; Tsai, Ellen; Runz, Heiko; Aronica, Eleonora; Groen, Ewout J N; van Es, Michael A; Pasterkamp, R Jeroen; Farhan, Sali M K; Garton, Fleur C; McRae, Allan F; McCombe, Pamela A; Henderson, Robert D; Fan, Dongsheng; Šlachtová, Lenka; Høyer, Helle; Nishimura, Agnes L; Cauchi, Ruben J; Brylev, Lev; Rogelj, Boris; Koritnik, Blaž; Zidar, Janez; Salas, Teresa; Mora Pardina, Jesus S; Gotkine, Marc; Povedano, Monica; Corcia, Philippe; Vourc'h, Patrick; Couratier, Philippe; Weber, Markus; Kiernan, Matthew C; Pamphlett, Roger; Blair, Ian P; de Carvalho, Mamede; Başak, Nazli A; Ingre, Caroline; Andersen, Peter M; Zinman, Lorne; Rogaeva, Ekaterina; MacKenzie, Ian R; Dupre, Nicolas; Rouleau, Guy A; Traynor, Bryan J; Ticozzi, Nicola; Chiò, Adriano; Silani, Vincenzo; Hardiman, Orla; Phatnani, Hemali; Harms, Matthew B; Dalgard, Clifton L; Glass, Jonathan D; Landers, John E; Van Damme, Philip; Morrison, Karen E; Shaw, Pamela J; Shaw, Chris E; Al-Chalabi, Ammar; van den Berg, Leonard H; Kenna, Kevin P; Veldink, Jan H
Amyotrophic lateral sclerosis (ALS) is a heritable disorder where rare variants with low-to-moderate penetrance are thought to dominate genetic risk. To identify such rare variants, we harmonized and analyzed exome data from 22 cohorts, totaling 17,919 individuals with ALS and 200,703 controls across discovery and replication phases. Rare variant analyses identified several new risk genes, with replication confirming association of YKT6 and supporting HTR3C, GBGT1 and KNTC1. We also provide strong, independent validation for genes with limited previous evidence: ARPP21, DNAJC7 and CFAP410. Notably, in ARPP21, we identified a new high-effect variant (p.P747L) and confirmed that p.P563L is an ALS-associated variant leading to an aggressive disease course. Beyond new discoveries, our analyses largely recapitulated the known genetic architecture of ALS, identifying risk variants in over 20% of cases and supporting a cumulative oligogenic risk model. These findings highlight new translational targets and show that rare variant analyses capture substantially more genetic risk than common variant genome-wide association studies.
PMCID:13083253
PMID: 41917433
ISSN: 1546-1718
CID: 6041162
Investigating the analytical robustness of the social and behavioural sciences
Aczel, Balazs; Szaszi, Barnabas; Clelland, Harry T; Kovacs, Marton; Holzmeister, Felix; van Ravenzwaaij, Don; Schulz-Kümpel, Hannah; Hoffmann, Sabine; Nilsonne, Gustav; Kosa, Livia; Torma, Zoltan A; Abdelfatah, Yousuf; Aberson, Christopher L; Acar, Oguz A; Acem, Ensar; Adamkovic, Matus; Adamovich, Timofey; Adiasto, Krisna; Ahnström, Love; Akil, Atakan M; Al-Busaidi, Adil S; Al-Hoorie, Ali H; Albers, Casper J; Allen, Peter J; Alsalti, Taym; Altman, Micah; Alzahawi, Shilaan; Ambrosini, Ettore; Anafinova, Saule; Anand, Rahul; Angerer, Martin; Angulo-Brunet, Ariadna; Antonietti, Alberto; Arato, Jozsef; Arenas, Andreu; Aviña, Marco M; Azevedo, Flavio; Bachl, Marko; Bago, Bence; Bahník, Štěpán; Baker, Bradley J; Balayan, Elza; Baldwin, Cassandra L; Banai, Benjamin; Banas, Kasia; Bartoš, František; Baskin, Ernest; Bastiaansen, Jojanneke A; Bault, Nadège; Bauman, Christopher W; Beazer, Quintin H; Behnke, Maciej; Bendixen, Theiss; Berger, Sebastian; Bernard, Anna; Bernardic, Ursa; Bloom, Paul A; Boldt, Annika; Bosch-Rosa, Ciril; Botvinik-Nezer, Rotem; Bouyamourn, Adam; Bozkurt, Ozge; Brehm, Laurel; Breuer, Johannes; Briggs, Ryan; Brohmer, Hilmar; Buchanan, Erin; Buckenmaier, Johannes; Buckley, Jeffrey; Buczny, Jacek; Burghart, Matthias; Butt, Bilal H; Byrd, Nick; Cafarelli, Valentina; Callahan, Patrick; Capitán, Tabaré; Carriere, Kevin; Cataldo, Andrea M; Cepaluni, Gabriel; Chan, Eugene; Chandler, Jesse J; Chang, Chia-Chen; Chen, Xi; Chen, Shirley Shuo; Chen, Fadong; Chen, Hao; Chirkov, Valerii; Cialfi, Daniela; Clarke, Beth; Coelho, Sophie G; Cohen, Clara; Collins, Jason; Cook, Susan W; Corlazzoli, Gaia; Cummins, Jamie; Czymara, Christian; D'hondt, Jonathan; Rosa, Anna Dalla; Davis, Abi M B; Davis, Charles P; Day, Martin V; De Keyzer, Freya; de Leeuw, Joshua R; de Vries, Tjeerd Rudmer; Debnath, Ramit; Dechterenko, Filip; Demiral, Elif E; Desgroseilliers, Marc; Dianovics, Dominik; Diveica, Veronica; Dochow-Sondershaus, Stephan; Dohle, Simone; Dong, LiChen; Dora, Jonas; Dorrough, Angela R; Dreber, Anna; Du, Hongfei; Edlund, John E; Eerland, Anita; Efendić, Emir; Elder, Jacob; Elsherif, Mahmoud M; Ernst, Mareike; Estrada, Eduardo; Eudave, Luis; Evans, Thomas R; Farrera, Arodi; Ferrouhi, El Mehdi; Fiala, Lenka; Fialho, Fabrício M; Fiechter, Joshua L; Fišar, Miloš; Flores-Kanter, Pablo Ezequiel; Folwarczny, Michał; Fossum, Jessica L; Franco, Vithor R; Freichel, René; Freire, Danilo; Frese, Joris; Furnas, Alexander C; Gaebler, Johann D; Gajary, Lisa C; Galang, Carl Michael; Ganschow, Benjamin; Garrison, S Mason; Gasiorowska, Agata; Ponne, Bruno Gasparotto; Gauriot, Romain; Geminiani, Alice; Geraldes, Diogo; Gernsbacher, Morton Ann; Giani, Cinzia; Glerean, Enrico; Gligorić, Vukašin; Gnambs, Timo; Godefroidt, Amélie; González-Bustamante, Bastián; Goreis, Andreas; Graf-Vlachy, Lorenz; Grieder, Manuel; Grigoryev, Dmitry; Grinschgl, Sandra; Grüning, David J; Guassi Moreira, João F; Guichet, Clément; Gurgand, Lilas; Habibnia, Hooman; Hafenbrack, Andrew C; Hafenbrädl, Sebastian; Häffner, Carolin; Hagemeister, Felix; Haigh, Matthew; Hajdu, Nandor; Hajimoladarvish, Narges; Hall, Jonathan D; Hamjediers, Maik; Hardwick, Robert M; Harma, Mehmet; Harp, Nicholas R; Hartvig, Áron D; Heiberger, Raphael H; Heim, Arthur; Hernæs, Øystein; Hernaus, Dennis; Heyman, Tom; Hicks, Joshua; Hogeveen, Jeremy; Höpler, Julia; Houlihan, Sean Dae; Huber, Christoph; Hughes, Conor; Hummler, Teresa; Huth, Karoline; Ingendahl, Moritz; Ishii, Tatsunori; Isler, Ozan; Izydorczak, Kamil; Jackson, Iain R; Jahn, Andrew; Jain, Maitri; Jakubow, Alexander; Jang, Daisung; Jang, JunHyeok; Jekel, Marc; Jia, Fanli; Jiménez-Leal, William; Johnson, Rebecca; Jones, Alex; Jungkunz, Sebastian; Kačmár, Pavol; Kaiser, Caspar; Kalaycı, Yağmur; Kantorowicz, Jaroslaw; Karabulut, Anıl; Karch, Julian D; Karimi-Rouzbahani, Hamid; Karl, Johannes A; Kažemekaitytė, Austėja; Kazlou, Aliaksandr; Kekecs, Zoltan; Kim, Jin; Kirchler, Michael H; Kiss-Dobronyi, Bence; Klasmeier, Kai N; Klein, Jack W; Koba, Cemal; Kołczyńska, Marta; Kolias, Pavlos; Kolouch Grabovský, Matěj; Korbmacher, Max; Korda, Živa; Kowal, Marta; Kretzschmar, André; Krivoshchekov, Vladislav; Krypotos, Angelos-Miltiadis; Kubsch, Marcus; Kunisato, Yoshihiko; Lacko, David; Landwehr, Jan R; Lange, Martin; Lee, Hongmi; Lee, Daniel; Lee, Sangil; Lemay, Edward P; Lempert, Daniel; Leo, Andrea; Lesage, Elise; Levin, Joel M; Li, Peng; Lin, Jing; Lindsay, Luke; Lisovoj, Daria; Liu, Meng; Liu, Sihong; Liu, Tingshu; Iacono, Sergio Lo; Lodder, Paul; López-Bueno, Rubén; Lopez-Nicolas, Ruben; Loter, Katharina; Lou, Nigel Mantou; Lovakov, Andrey; Lu, Jackson G; Ludwig, Jonas; Luebber, Finn; Lukavský, Jiří; Luo, Charles Q; Lyu, Xuanyu; Maassen, Esther; Máčel, Martin; Mack, Michael L; Madan, Christopher R; Mädebach, Andreas; Maffly-Kipp, Joseph; Mallinson, Daniel J; Marchetti, Igor; Marghetis, Tyler; Marini, Matteo M; Fages, Diego Marino; Martínez, Mayte; Martinoli, Mario; Masiliunas, Aidas; Massoni, Sébastien; Mathieu, Kaleb C; Mayer, Stefan; Mayer, Duncan J; Mayer, Maren; McCormick, Ethan M; McDonough, Ian M; McGowan, Amanda L; McIntyre, Miranda M; McKee, Paul; Meier, Armando N; Meier, Pascal F; Melero, Helena; Merkle, Christoph; Merz, Raphael; Michaelides, Michalis P; Michaelsen, Patrik; Mikolajczak, Gosia; Mill, Wladislaw; Millroth, Philip; Miroshnik, Kirill G; Misiak, Michal; Mora, Youri L; Moreau, David; Moreh, Chris; Morvinski, Coby; Mushtaq, Faisal; Nagy, Tamás; Nater, Christa; Naumann, Elias; Navarrete, Gorka; Nebe, Stephan; Nedderhoff, Andre; Nennstiel, Richard; Neugebauer, Martin; Nicolaisen-Sobesky, Eliana; Nielsen, Yngwie A; Niso, Guiomar; Nowak, Benjamin; Okan, Mehmet; Ong, Kenneth; Onicas, Adrian I; Oswald, Christian; Otten, Kasper; Pandey, Shubham; Pantazi, Myrto; Papale, Paolo; Pärnamets, Philip; Pauer, Shiva; Pavlov, Yuri G; Pawel, Samuel; Peelle, Jonathan E; Peetz, Hannah K; Peez, Anton; Pesciarelli, Francesca; Peterson, Brenton D; Petruželka, Benjamin; Petter, Jonas; Pfänder, Jan; Pfuhl, Gerit; Phillips, Joseph; Pietryka, Matthew T; Pirrone, Angelo; Pit, Ilse L; Plachti, Anna; Plank, Irene Sophia; Ploner, Matteo; Poldrack, Russell A; Pollmann, Monique M H; Porcher, Simon; Präg, Patrick; Pua, Andrew Adrian Y; Pugel, Jessica; Puri, Rohan; Püski, Marcell; Radkani, Setayesh; Raes, Louis; Rafaï, Ismaël; Raiber, Klara; Rathje, Steve; Rehms, Raphael; Reshetnikov, Mikhail; Reynolds, Caleb J; Reynolds, James P; Rigaud, Kévin; Rioux, Charlie; Rivera, Sebastian; Robertson, Olly; Román-Caballero, Rafael; Ropovik, Ivan; Röseler, Lukas; Ross, Robert M; Rotella, Amanda; Rüffer, Franziska F; Rusche, Felix; Rusconi, Massimo; Russo, Irene; Sahm, Alexander H J; Salamon, Janos; Samahita, Margaret; Sanaei, Ali; Sangchooli, Arshiya; Sarafoglou, Alexandra; Scandola, Michele; Schaak, Henning; Schaerer, Michael; Schares, Eric; Schilling, Hayden T; Schmalz, Xenia; Schmidt, Kathleen; Schonberg, Tom; Schreiner, Marcel R; Schröder, Joris M; Schubert, Anna-Lena; Schuetze, Brendan; Schultz, Douglas H; Schulze, Lars; Schwartz, Shawn T; Schwitter, Nicole; Scoggins, Bermond; Seetahul, Yashvin; Seri, Raffaello; Shanks, David R; Shaw, Stacy T; Shaw, Joseph; Shen, Qiang; Siemroth, Christoph; Sladekova, Martina; Somo, Angela; Sondhi, Arjun; Sonmez, Burak; Spantig, Lisa; Speekenbrink, Maarten; Stamos, Angelos; Stasielowicz, Lukasz; Steckermeier, Leonie C; Steinkamp, Simon R; Stoevenbelt, Andrea H; Street, Chris N H; Suchow, Jordan W; Sunde, Hans Fredrik; Sundquist, James; Suschevskiy, Vsevolod; Swain, Scott D; Szecsi, Peter; Szekely-Copîndean, Raluca D; Szumowska, Ewa; Tacconelli, Alessandro; Talbert, Eli; Tang, John P; Tendeiro, Jorge N; Testori, Martina; Toffalini, Enrico; Tomašević, Aleksandar; Topel, Selin; Torkkeli, Lasse; Tozzi, Leonardo; Traczyk, Jakub; Trinidad, Alexander; Trübutschek, Darinka; Turek, Konrad; Uhlich, Maximiliane; Uhlmann, Eric L; Urbanska, Karolina; Van Assche, Jasper; van Assen, Marcel A L M; van Dongen, Noah N N; van Lieshout, Kenny; van Veldhuizen, Roel; Varga, Marton A; Vaughn, Leigh Ann; Venczel, Fruzsina; Vezzoli, Michela; Vierus, Paul; Visalli, Antonino; Voldal, Emily; Votta, Fabio; Wagenmakers, Eric-Jan; Waldendorf, Anica; Walker, Matthew J; Wall, Matthew B; Wallen, Henri; Wang, Ke; Wang, Iris; Wang, Y Andre; Weinmann, Markus; Weiß, Martin; Westheide, Christian; Wichman, Aaron; Wilcke, Juliane C; Williams, Benedict J; Wisniewski, David; Woiczyk, Thomas K A; Woźniak, Mateusz; Wright, Joshua D; Youyou, Wu; Wulff, Jesper N; Yang, Tao; Yeung, Siu Kit; Yuen, Kenneth S L; Zawistowski, Michał; Zein, Rizqy A; Zhao, Xian; Zheng, Zefan; Zhou, Steven; Ziller, Conrad; Zimmerman, David; Zogmaister, Cristina; Zultan, Ro'i; Fox, Nicholas; Errington, Timothy M; Nosek, Brian A
The same dataset can be analysed in different justifiable ways to answer the same research question, potentially challenging the robustness of empirical science1-3. In this crowd initiative, we investigated the degree to which research findings in the social and behavioural sciences are contingent on analysts' choices. We examined a stratified random sample of 100 studies published between 2009 and 2018, in which, for one claim per study, at least five reanalysts independently reanalysed the original data. The statistical appropriateness of the reanalyses was assessed in peer evaluations, and the robustness indicators were inspected along a range of research characteristics and study designs. We found that 34% of the independent reanalyses yielded the same result (within a tolerance region of ±0.05 Cohen's d) as the original report; with a four times broader tolerance region, this indicator increased to 57%. Of the reanalyses conducted, 74% reached the same conclusion as the original investigation, 24% yielded no effects or inconclusive results and 2% reported the opposite effect. This exploratory study indicates that the common single-path analyses in social and behavioural research should not be simply assumed to be robust to alternative analyses4. Therefore, we recommend the development and use of practices to explore and communicate this neglected source of uncertainty.
PMID: 41922703
ISSN: 1476-4687
CID: 6041172