FinnGen provides genetic insights from a well-phenotyped isolated population
Mitja Kurki, Juha Karjalainen, Priit Palta, Timo P. Sipilä, Kati Kristiansson, Kati Donner, Mary Pat Reeve, Hannele Laivuori, Mervi Aavikko, Mari Kaunisto, Anu Loukola, Elisa Lahtela, Hannele Mattsson, Päivi Laiho, Pietro Della Briotta Parolo, Arto Lehistö, Masahiro Kanai, Nina Mars, Joel Rämö, Tuomo Kiiskinen, Henrike Heyne, Kumar Veerapen, Sina Rüeger, Susanna Lemmelä, Wei Zhou, Sanni Ruotsalainen, Kalle Pärn, Tero Hiekkalinna, Sami Koskelainen, Teemu Paajanen, Vincent Llorens, Javier Gracia‐Tabuenca, Harri Siirtola, Kadri Reis, Abdelrahman G. Elnahas, Benjamin B. Sun, Christopher N. Foley, Katriina Aalto‐Setälä, Kaur Alasoo, Mikko Arvas, Kirsi Auro, Shameek Biswas, Argyro Bizaki-Vallaskangas, Olli Carpén, Chia‐Yen Chen, Oluwaseun Alexander Dada, Zhihao Ding, Margaret G. Ehm, Kari K. Eklund, Martti Färkkilâ, Hilary K. Finucane, Andrea Ganna, Awaisa Ghazal, Robert Graham, Eric M. Green, Antti Hakanen, Marco Hautalahti, Åsa K. Hedman, Mikko Hiltunen, Reetta Hinttala, Iiris Hovatta, Xinli Hu, Adriana Huertas‐Vázquez, Laura Huilaja, Julie Hunkapiller, Howard J. Jacob, Jan-Nygaard Jensen, Heikki Joensuu, Sally John, Valtteri Julkunen, Marc Jung, Juhani Junttila, Kai Kaarniranta, Mika Kähönen, Risto Kajanne, Lila Kallio, Reetta Kälviäinen, Jaakko Kaprio, FinnGen, Nurlan Kerimov, Johannes Kettunen, Elina Kilpeläinen, Terhi Kilpi, K. Klinger, Veli‐Matti Kosma, Teijo Kuopio, Venla Kurra, Triin Laisk, Jari A. Laukkanen, Nathan Lawless, Aoxing Liu, Simonne Longerich, Reedik Mägi, Johanna Mäkelä, Antti Mäkitie, Anders Mälarstig, Arto Mannermaa, Joseph Maranville, Athena Matakidou, Tuomo J Meretoja
Abstract
Abstract Population isolates such as those in Finland benefit genetic research because deleterious alleles are often concentrated on a small number of low-frequency variants (0.1% ≤ minor allele frequency < 5%). These variants survived the founding bottleneck rather than being distributed over a large number of ultrarare variants. Although this effect is well established in Mendelian genetics, its value in common disease genetics is less explored 1,2 . FinnGen aims to study the genome and national health register data of 500,000 Finnish individuals. Given the relatively high median age of participants (63 years) and the substantial fraction of hospital-based recruitment, FinnGen is enriched for disease end points. Here we analyse data from 224,737 participants from FinnGen and study 15 diseases that have previously been investigated in large genome-wide association studies (GWASs). We also include meta-analyses of biobank data from Estonia and the United Kingdom. We identified 30 new associations, primarily low-frequency variants, enriched in the Finnish population. A GWAS of 1,932 diseases also identified 2,733 genome-wide significant associations (893 phenome-wide significant (PWS), P < 2.6 × 10 –11 ) at 2,496 (771 PWS) independent loci with 807 (247 PWS) end points. Among these, fine-mapping implicated 148 (73 PWS) coding variants associated with 83 (42 PWS) end points. Moreover, 91 (47 PWS) had an allele frequency of <5% in non-Finnish European individuals, of which 62 (32 PWS) were enriched by more than twofold in Finland. These findings demonstrate the power of bottlenecked populations to find entry points into the biology of common diseases through low-frequency, high impact variants.