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Kurki MI, Karjalainen J, Palta P, Sipilä TP, Kristiansson K, Donner KM, Reeve MP, Laivuori H, Aavikko M, Kaunisto MA, Loukola A, Lahtela E, Mattsson H, Laiho P, Della Briotta Parolo P, Lehisto AA, Kanai M, Mars N, Rämö J, Kiiskinen T, Heyne HO, Veerapen K, Rüeger S, Lemmelä S, Zhou W, Ruotsalainen S, Pärn K, Hiekkalinna T, Koskelainen S, Paajanen T, Llorens V, Gracia-Tabuenca J, Siirtola H, Reis K, Elnahas AG, Sun B, Foley CN, Aalto-Setälä K, Alasoo K, Arvas M, Auro K, Biswas S, Bizaki-Vallaskangas A, Carpen O, Chen CY, Dada OA, Ding Z, Ehm MG, Eklund K, Färkkilä M, Finucane H, Ganna A, Ghazal A, Graham RR, Green EM, Hakanen A, Hautalahti M, Hedman ÅK, Hiltunen M, Hinttala R, Hovatta I, Hu X, Huertas-Vazquez A, Huilaja L, Hunkapiller J, Jacob H, Jensen JN, Joensuu H, John S, Julkunen V, Jung M, Junttila J, Kaarniranta K, Kähönen M, Kajanne R, Kallio L, Kälviäinen R, Kaprio J, Kerimov N, Kettunen J, Kilpeläinen E, Kilpi T, Klinger K, Kosma VM, Kuopio T, Kurra V, Laisk T, Laukkanen J, Lawless N, Liu A, Longerich S, Mägi R, Mäkelä J, Mäkitie A, Malarstig A, Mannermaa A, Maranville J, Matakidou A, Meretoja T, Mozaffari SV, Niemi MEK, Niemi M, Niiranen T, O Donnell CJ, Obeidat ME, Okafo G, Ollila HM, Palomäki A, Palotie T, Partanen J, Paul DS, Pelkonen M, Pendergrass RK, Petrovski S, Pitkäranta A, Platt A, Pulford D, Punkka E, Pussinen P, Raghavan N, Rahimov F, Rajpal D, Renaud NA, Riley-Gillis B, Rodosthenous R, Saarentaus E, Salminen A, Salminen E, Salomaa V, Schleutker J, Serpi R, Shen HY, Siegel R, Silander K, Siltanen S, Soini S, Soininen H, Sul JH, Tachmazidou I, Tasanen K, Tienari P, Toppila-Salmi S, Tukiainen T, Tuomi T, Turunen JA, Ulirsch JC, Vaura F, Virolainen P, Waring J, Waterworth D, Yang R, Nelis M, Reigo A, Metspalu A, Milani L, Esko T, Fox C, Havulinna AS, Perola M, Ripatti S, Jalanko A, Laitinen T, Mäkelä TP, Plenge R, McCarthy M, Runz H, Daly MJ, Palotie A. FinnGen provides genetic insights from a well-phenotyped isolated population. Nature 2023; 613:508-518. [PMID: 36653562 PMCID: PMC9849126 DOI: 10.1038/s41586-022-05473-8] [Citation(s) in RCA: 1069] [Impact Index Per Article: 1069.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 10/21/2022] [Indexed: 01/20/2023]
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 explored1,2. 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.
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Affiliation(s)
- Mitja I Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Juha Karjalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Kati M Donner
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mary P Reeve
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Center for Child, Adolescent and Maternal Health, University of Tampere, Tampere, Finland
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Mari A Kaunisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Loukola
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Elisa Lahtela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Hannele Mattsson
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Päivi Laiho
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Pietro Della Briotta Parolo
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Arto A Lehisto
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Masahiro Kanai
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nina Mars
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Joel Rämö
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Henrike O Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Digital Health Center, Hasso Plattner Institute for Digital Engineering, University of Potsdam Potsdam, Potsdam, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kumar Veerapen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sina Rüeger
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Susanna Lemmelä
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Wei Zhou
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Kalle Pärn
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tero Hiekkalinna
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sami Koskelainen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Teemu Paajanen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Vincent Llorens
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Javier Gracia-Tabuenca
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Harri Siirtola
- TAUCHI Research Center, Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, Finland
| | - Kadri Reis
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Benjamin Sun
- Translational Biology, Research and Development, Biogen, Cambridge, MA, USA
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Christopher N Foley
- Optima Partners, Edinburgh, UK
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Mikko Arvas
- Finnish Red Cross Blood Service, Helsinki, Finland
| | | | | | | | - Olli Carpen
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | | | - Oluwaseun A Dada
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Zhihao Ding
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | | | - Kari Eklund
- Division of Rheumatology, Department of Medicine, Helsinki University Central Hospital, Helsinki, Finland
- Orton Orthopedic Hospital, Helsinki, Finland
| | - Martti Färkkilä
- Abdominal Center, Helsinki University Hospital, Helsinki University, Helsinki, Finland
| | - Hilary Finucane
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | - Antti Hakanen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Åsa K Hedman
- Pfizer, New York, NY, USA
- Department of Medicine, Karolinska Institute, Solna, Sweden
| | - Mikko Hiltunen
- Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Iiris Hovatta
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- SleepWell Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | - Laura Huilaja
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | | | | | | | - Heikki Joensuu
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Valtteri Julkunen
- Neuro Center, Neurology, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Marc Jung
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Juhani Junttila
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mika Kähönen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
| | - Risto Kajanne
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Lila Kallio
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Reetta Kälviäinen
- Epilepsy Center, Kuopio University Hospital, Kuopio, Finland
- Department of Neurology, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Johannes Kettunen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Computational Medicine, Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Terhi Kilpi
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | | | - Veli-Matti Kosma
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Teijo Kuopio
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
| | - Venla Kurra
- Department of Clinical Genetics, Tampere University Hospital, Tampere, Finland
- Department of Clinical Genetics, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Triin Laisk
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Jari Laukkanen
- Central Finland Biobank, Central Finland Health Care District, Jyväskylä, Finland
- Department of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Antti Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki, Helsinki, Finland
- Helsinki University Hospital, Helsinki, Finland
| | - Anders Malarstig
- Pfizer, Cambridge, MA, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - Arto Mannermaa
- Biobank of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | | | - Athena Matakidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Tuomo Meretoja
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Mari E K Niemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Marianna Niemi
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- TAUCHI Research Center & Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Teemu Niiranen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- Turku University Hospital and University of Turku, Turku, Finland
| | | | - Ma En Obeidat
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - George Okafo
- Boehringer Ingelheim, Ingelheim am Rhein, Germany
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Antti Palomäki
- Turku University Hospital and University of Turku, Turku, Finland
| | - Tuula Palotie
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital, Helsinki, Finland
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Jukka Partanen
- Finnish Red Cross Blood Service, Helsinki, Finland
- Finnish Hematological Biobank, Helsinki, Finland
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Margit Pelkonen
- Department of Pulmonary Diseases, Kuopio University Hospital, Kuopio, Finland
| | | | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Anne Pitkäranta
- Department of Otorhinolaryngology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Eero Punkka
- Helsinki Biobank, University of Helsinki and Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Pirkko Pussinen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | | | | | - Deepak Rajpal
- Translational Sciences, Sanofi R&D, Framingham, MA, USA
| | - Nicole A Renaud
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rodosthenis Rodosthenous
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Elmo Saarentaus
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Aino Salminen
- Department of Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Eveliina Salminen
- Helsinki University Hospital, Helsinki, Finland
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki, Helsinki, Finland
| | - Veikko Salomaa
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Johanna Schleutker
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | - Raisa Serpi
- Northern Finland Biobank Borealis, University of Oulu, Northern Ostrobothnia Hospital District, Oulu, Finland
| | - Huei-Yi Shen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Richard Siegel
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Kaisa Silander
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Sanna Siltanen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Sirpa Soini
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Hilkka Soininen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | | | - Ioanna Tachmazidou
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Kaisa Tasanen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland
- Department of Dermatology and Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Pentti Tienari
- Department of Neurology, Helsinki University Hospital, Helsinki, Finland
- Translational Immunology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Sanna Toppila-Salmi
- Department of Allergy, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Abdominal Center, Endocrinology, Helsinki University Hospital, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
- Research Program of Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Joni A Turunen
- Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Eye Genetics Group, Folkhälsan Research Center, Helsinki, Finland
| | - Jacob C Ulirsch
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Felix Vaura
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
- University of Turku, Turku, Finland
| | - Petri Virolainen
- Auria Biobank, University of Turku and Turku University Hospital, Turku, Finland
| | | | | | | | - Mari Nelis
- Genomics Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | | | - Aki S Havulinna
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Anu Jalanko
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Tarja Laitinen
- Finnish Clinical Biobank Tampere, Tampere University and Tampere University Hospital, Tampere, Finland
| | - Tomi P Mäkelä
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | | | | | | | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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Schubert R, Geoffroy E, Gregga I, Mulford AJ, Aguet F, Ardlie K, Gerszten R, Clish C, Van Den Berg D, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy R, Conomos M, Blackwell T, Papanicolaou G, Lappalainen T, Mikhaylova AV, Thornton TA, Cho MH, Gignoux CR, Lange L, Lange E, Rich SS, Rotter JI, Manichaikul A, Im HK, Wheeler HE. Protein prediction for trait mapping in diverse populations. PLoS One 2022; 17:e0264341. [PMID: 35202437 PMCID: PMC8870552 DOI: 10.1371/journal.pone.0264341] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Genetically regulated gene expression has helped elucidate the biological mechanisms underlying complex traits. Improved high-throughput technology allows similar interrogation of the genetically regulated proteome for understanding complex trait mechanisms. Here, we used the Trans-omics for Precision Medicine (TOPMed) Multi-omics pilot study, which comprises data from Multi-Ethnic Study of Atherosclerosis (MESA), to optimize genetic predictors of the plasma proteome for genetically regulated proteome-wide association studies (PWAS) in diverse populations. We built predictive models for protein abundances using data collected in TOPMed MESA, for which we have measured 1,305 proteins by a SOMAscan assay. We compared predictive models built via elastic net regression to models integrating posterior inclusion probabilities estimated by fine-mapping SNPs prior to elastic net. In order to investigate the transferability of predictive models across ancestries, we built protein prediction models in all four of the TOPMed MESA populations, African American (n = 183), Chinese (n = 71), European (n = 416), and Hispanic/Latino (n = 301), as well as in all populations combined. As expected, fine-mapping produced more significant protein prediction models, especially in African ancestries populations, potentially increasing opportunity for discovery. When we tested our TOPMed MESA models in the independent European INTERVAL study, fine-mapping improved cross-ancestries prediction for some proteins. Using GWAS summary statistics from the Population Architecture using Genomics and Epidemiology (PAGE) study, which comprises ∼50,000 Hispanic/Latinos, African Americans, Asians, Native Hawaiians, and Native Americans, we applied S-PrediXcan to perform PWAS for 28 complex traits. The most protein-trait associations were discovered, colocalized, and replicated in large independent GWAS using proteome prediction model training populations with similar ancestries to PAGE. At current training population sample sizes, performance between baseline and fine-mapped protein prediction models in PWAS was similar, highlighting the utility of elastic net. Our predictive models in diverse populations are publicly available for use in proteome mapping methods at https://doi.org/10.5281/zenodo.4837327.
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Affiliation(s)
- Ryan Schubert
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, IL, United States of America
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Elyse Geoffroy
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Isabelle Gregga
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Ashley J. Mulford
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Francois Aguet
- Broad Institute, Cambridge, MA, United States of America
| | - Kristin Ardlie
- Broad Institute, Cambridge, MA, United States of America
| | - Robert Gerszten
- Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Clary Clish
- Broad Institute, Cambridge, MA, United States of America
| | - David Van Den Berg
- University of Southern California, Los Angeles, CA, United States of America
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Peter Durda
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - W. Craig Johnson
- Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, United States of America
| | - Elaine Cornell
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Yongmei Liu
- Department of Medicine, Duke University School of Medicine, Durham, NC, United States of America
| | - Russell Tracy
- Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, United States of America
| | - Matthew Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Tom Blackwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, United States of America
| | - George Papanicolaou
- Epidemiology Branch, National Heart, Lung and Blood Institute, Bethesda, MD, United States of America
| | - Tuuli Lappalainen
- New York Genome Center and Department of Systems Biology, Columbia University, New York, NY United States of America
| | - Anna V. Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Timothy A. Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Christopher R. Gignoux
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Leslie Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Ethan Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States of America
| | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Heather E. Wheeler
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
- * E-mail:
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