{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T02:29:47Z","timestamp":1775874587207,"version":"3.50.1"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T00:00:00Z","timestamp":1687392000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006196","name":"University of Oulu","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006196","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020 research and innovation programme"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Genome-wide association studies (GWAS) have been successful in identifying genomic loci associated with complex traits. Genetic fine-mapping aims to detect independent causal variants from the GWAS-identified loci, adjusting for linkage disequilibrium patterns.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present \u201cFiniMOM\u201d (fine-mapping using a product inverse-moment prior), a novel Bayesian fine-mapping method for summarized genetic associations. For causal effects, the method uses a nonlocal inverse-moment prior, which is a natural prior distribution to model non-null effects in finite samples. A beta-binomial prior is set for the number of causal variants, with a parameterization that can be used to control for potential misspecifications in the linkage disequilibrium reference. The results of simulations studies aimed to mimic a typical GWAS on circulating protein levels show improved credible set coverage and power of the proposed method over current state-of-the-art fine-mapping method SuSiE, especially in the case of multiple causal variants within a locus.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/vkarhune.github.io\/finimom\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad396","type":"journal-article","created":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T21:43:50Z","timestamp":1687470230000},"source":"Crossref","is-referenced-by-count":7,"title":["Genetic fine-mapping from summary data using a nonlocal prior improves the detection of multiple causal variants"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6064-1588","authenticated-orcid":false,"given":"Ville","family":"Karhunen","sequence":"first","affiliation":[{"name":"Research Unit of Mathematical Sciences, University of Oulu , Oulu, P.O.Box 8000 , FI-90014, Finland"},{"name":"Research Unit of Population Health, University of Oulu , Oulu, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilkka","family":"Launonen","sequence":"additional","affiliation":[{"name":"Research Unit of Mathematical Sciences, University of Oulu , Oulu, P.O.Box 8000 , FI-90014, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marjo-Riitta","family":"J\u00e4rvelin","sequence":"additional","affiliation":[{"name":"Research Unit of Population Health, University of Oulu , Oulu, Finland"},{"name":"Department of Epidemiology and Biostatistics, Imperial College London , London, United Kingdom"},{"name":"Department of Life Sciences, College of Health and Life Sciences, Brunel University , London, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvain","family":"Sebert","sequence":"additional","affiliation":[{"name":"Research Unit of Population Health, University of Oulu , Oulu, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2808-2768","authenticated-orcid":false,"given":"Mikko J","family":"Sillanp\u00e4\u00e4","sequence":"additional","affiliation":[{"name":"Research Unit of Mathematical Sciences, University of Oulu , Oulu, P.O.Box 8000 , FI-90014, Finland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,6,22]]},"reference":[{"key":"2023070705251246600_btad396-B1","doi-asserted-by":"crossref","first-page":"1247","DOI":"10.1126\/science.abj5117","article-title":"Multiple causal variants underlie genetic associations in humans","volume":"375","author":"Abell","year":"2022","journal-title":"Science"},{"key":"2023070705251246600_btad396-B2","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.ajhg.2016.11.007","article-title":"Genome-wide association study identifies 27 loci influencing concentrations of circulating cytokines and growth factors","volume":"100","author":"Ahola-Olli","year":"2017","journal-title":"Am J Hum Genet"},{"key":"2023070705251246600_btad396-B3","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/j.jaci.2010.11.050","article-title":"Interleukins, from 1 to 37, and interferon-gamma: receptors, functions, and roles in diseases","volume":"127","author":"Akdis","year":"2011","journal-title":"J Allergy Clin Immunol"},{"key":"2023070705251246600_btad396-B4","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/j.ajhg.2022.01.002","article-title":"Redefining tissue specificity of genetic regulation of gene expression in the presence of allelic heterogeneity","volume":"109","author":"Arvanitis","year":"2022","journal-title":"Am J Hum Genet"},{"key":"2023070705251246600_btad396-B5","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1071\/PH650119","article-title":"Monte Carlo calculations of the radial distribution functions for a proton\u2013electron plasma","volume":"18","author":"Barker","year":"1965","journal-title":"Aust J Phys"},{"key":"2023070705251246600_btad396-B6","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1093\/bioinformatics\/btw018","article-title":"FINEMAP: efficient variable selection using summary data from genome-wide association studies","volume":"32","author":"Benner","year":"2016","journal-title":"Bioinformatics"},{"key":"2023070705251246600_btad396-B7","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.ajhg.2017.08.012","article-title":"Prospects of fine-mapping trait-associated genomic regions by using summary statistics from genome-wide association studies","volume":"101","author":"Benner","year":"2017","journal-title":"Am J Hum Genet"},{"key":"2023070705251246600_btad396-B8","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1093\/biomet\/asq017","article-title":"The horseshoe estimator for sparse signals","volume":"97","author":"Carvalho","year":"2010","journal-title":"Biometrika"},{"key":"2023070705251246600_btad396-B9","doi-asserted-by":"crossref","DOI":"10.1214\/12-AOS1029","article-title":"Needles and straw in a haystack: posterior concentration for possibly sparse sequences","volume":"40","author":"Castillo","year":"2012","journal-title":"Ann Statist"},{"key":"2023070705251246600_btad396-B10","doi-asserted-by":"crossref","first-page":"1986","DOI":"10.1214\/15-AOS1334","article-title":"Bayesian linear regression with sparse priors","volume":"43","author":"Castillo","year":"2015","journal-title":"Ann Statist"},{"key":"2023070705251246600_btad396-B11","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1534\/genetics.115.176107","article-title":"Fine mapping causal variants with an approximate bayesian method using marginal test statistics","volume":"200","author":"Chen","year":"2015","journal-title":"Genetics"},{"key":"2023070705251246600_btad396-B12","volume-title":"bioRxiv","author":"Cui","year":"2022"},{"key":"2023070705251246600_btad396-B13","first-page":"101","article-title":"A selective overview of variable selection in high dimensional feature space","volume":"20","author":"Fan","year":"2010","journal-title":"Stat Sin"},{"key":"2023070705251246600_btad396-B14","doi-asserted-by":"crossref","first-page":"1712","DOI":"10.1038\/s41588-021-00978-w","article-title":"Large-scale integration of the plasma proteome with genetics and disease","volume":"53","author":"Ferkingstad","year":"2021","journal-title":"Nat Genet"},{"key":"2023070705251246600_btad396-B15","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1038\/s42255-020-00287-2","article-title":"Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals","volume":"2","author":"Folkersen","year":"2020","journal-title":"Nat Metab"},{"key":"2023070705251246600_btad396-B16","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/j.ajhg.2018.04.002","article-title":"The post-GWAS era: from association to function","volume":"102","author":"Gallagher","year":"2018","journal-title":"Am J Hum Genet"},{"key":"2023070705251246600_btad396-B17","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1093\/biomet\/82.4.711","article-title":"Reversible jump Markov chain Monte Carlo computation and Bayesian model determination","volume":"82","author":"Green","year":"1995","journal-title":"Biometrika"},{"key":"2023070705251246600_btad396-B18","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1534\/genetics.114.167908","article-title":"Identifying causal variants at loci with multiple signals of association","volume":"198","author":"Hormozdiari","year":"2014","journal-title":"Genetics"},{"key":"2023070705251246600_btad396-B19","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1111\/j.1471-0528.1993.tb12971.x","article-title":"Labour induction policy in hospitals of different levels of specialisation","volume":"100","author":"J\u00e4rvelin","year":"1993","journal-title":"Br J Obstet Gynaecol"},{"key":"2023070705251246600_btad396-B20","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1111\/j.1467-9868.2009.00730.x","article-title":"On the use of non-local prior densities in Bayesian hypothesis tests","volume":"72","author":"Johnson","year":"2010","journal-title":"J R Stat Soc B Stat Methodol"},{"key":"2023070705251246600_btad396-B21","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1080\/01621459.2012.682536","article-title":"Bayesian model selection in high-dimensional settings","volume":"107","author":"Johnson","year":"2012","journal-title":"J Am Stat Assoc"},{"key":"2023070705251246600_btad396-B22","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1002\/oby.23060","article-title":"The role of inflammatory cytokines as intermediates in the pathway from increased adiposity to disease","volume":"29","author":"Kalaoja","year":"2021","journal-title":"Obesity (Silver Spring)"},{"key":"2023070705251246600_btad396-B23","doi-asserted-by":"crossref","first-page":"100210","DOI":"10.1016\/j.xgen.2022.100210","article-title":"Meta-analysis fine-mapping is often miscalibrated at single-variant resolution","volume":"2","author":"Kanai","year":"2022","journal-title":"Cell Genomics"},{"key":"2023070705251246600_btad396-B24","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.ajhg.2015.06.007","article-title":"Leveraging functional-annotation data in trans-ethnic fine-mapping studies","volume":"97","author":"Kichaev","year":"2015","journal-title":"Am J Hum Genet"},{"key":"2023070705251246600_btad396-B25","doi-asserted-by":"crossref","first-page":"e1004722","DOI":"10.1371\/journal.pgen.1004722","article-title":"Integrating functional data to prioritize causal variants in statistical fine-mapping studies","volume":"10","author":"Kichaev","year":"2014","journal-title":"PLoS Genet"},{"key":"2023070705251246600_btad396-B26","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1017\/S0016672311000164","article-title":"Genetic analysis of complex traits via Bayesian variable selection: the utility of a mixture of uniform priors","volume":"93","author":"Kn\u00fcrr","year":"2011","journal-title":"Genet Res (Camb)"},{"key":"2023070705251246600_btad396-B27","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/1297-9686-45-24","article-title":"Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait mapping and genomic prediction","volume":"45","author":"Kn\u00fcrr","year":"2013","journal-title":"Genet Sel Evol"},{"key":"2023070705251246600_btad396-B28","volume-title":"bioRxiv","author":"Lee","year":"2018"},{"key":"2023070705251246600_btad396-B29","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1016\/j.ajhg.2022.07.002","article-title":"Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies","volume":"109","author":"Lu","year":"2022","journal-title":"Am J Hum Genet"},{"key":"2023070705251246600_btad396-B30","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1002\/gepi.21953","article-title":"JAM: a scalable Bayesian framework for joint analysis of marginal SNP effects","volume":"40","author":"Newcombe","year":"2016","journal-title":"Genet Epidemiol"},{"key":"2023070705251246600_btad396-B31","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.1093\/bioinformatics\/btv764","article-title":"Bayesian variable selection for binary outcomes in high-dimensional genomic studies using non-local priors","volume":"32","author":"Nikooienejad","year":"2016","journal-title":"Bioinformatics"},{"key":"2023070705251246600_btad396-B32","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1214\/20-AOAS1325","article-title":"Bayesian variable selection for survival data using inverse moment priors","volume":"14","author":"Nikooienejad","year":"2020","journal-title":"Ann Appl Stat"},{"key":"2023070705251246600_btad396-B33","doi-asserted-by":"crossref","first-page":"1786","DOI":"10.1093\/ije\/dyab109","article-title":"Cohort profile: 46 years of follow-up of the Northern Finland birth cohort 1966 (NFBC1966)","volume":"50","author":"Nordstr\u00f6m","year":"2022","journal-title":"Int J Epidemiol"},{"key":"2023070705251246600_btad396-B34","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1214\/09-BA403","article-title":"A review of Bayesian variable selection methods: what, how and which","volume":"4","author":"O'Hara","year":"2009","journal-title":"Bayesian Anal"},{"key":"2023070705251246600_btad396-B35","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nrg.2016.142","article-title":"Dissecting the genetics of complex traits using summary association statistics","volume":"18","author":"Pasaniuc","year":"2017","journal-title":"Nat Rev Genet"},{"key":"2023070705251246600_btad396-B36","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1080\/01621459.2015.1130634","article-title":"Nonlocal priors for high-dimensional estimation","volume":"112","author":"Rossell","year":"2017","journal-title":"J Am Stat Assoc"},{"key":"2023070705251246600_btad396-B37","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1111\/rssb.12466","article-title":"Approximate laplace approximations for scalable model selection","volume":"83","author":"Rossell","year":"2021","journal-title":"J R Stat Soc B Stat Methodol"},{"key":"2023070705251246600_btad396-B38","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/ng.271","article-title":"Genome-wide association analysis of metabolic traits in a birth cohort from a founder population","volume":"41","author":"Sabatti","year":"2009","journal-title":"Nat Genet"},{"key":"2023070705251246600_btad396-B39","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bioinformatics\/bty472","article-title":"GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies","volume":"35","author":"Sanyal","year":"2019","journal-title":"Bioinformatics"},{"key":"2023070705251246600_btad396-B40","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/s41576-018-0016-z","article-title":"From genome-wide associations to candidate causal variants by statistical fine-mapping","volume":"19","author":"Schaid","year":"2018","journal-title":"Nat Rev Genet"},{"key":"2023070705251246600_btad396-B41","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/s41467-019-08424-6","article-title":"Quantification of frequency-dependent genetic architectures in 25 UK biobank traits reveals action of negative selection","volume":"10","author":"Schoech","year":"2019","journal-title":"Nat Commun"},{"key":"2023070705251246600_btad396-B42","first-page":"1053","article-title":"Scalable Bayesian variable selection using nonlocal prior densities in ultrahigh-dimensional settings","volume":"28","author":"Shin","year":"2018","journal-title":"Stat Sin"},{"key":"2023070705251246600_btad396-B43","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1038\/ng.2435","article-title":"Bayesian refinement of association signals for 14 loci in 3 common diseases","volume":"44","author":"The Wellcome Trust Case Control Consortium","year":"2012","journal-title":"Nat Gen"},{"key":"2023070705251246600_btad396-B44","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/s43586-021-00056-9","article-title":"Genome-wide association studies","volume":"1","author":"Uffelmann","year":"2021","journal-title":"Nat Rev Methods Primers"},{"key":"2023070705251246600_btad396-B45","author":"University of Oulu","year":"2022"},{"key":"2023070705251246600_btad396-B46","author":"University of Oulu","year":"2022"},{"key":"2023070705251246600_btad396-B47","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.ajhg.2017.06.005","article-title":"10 Years of GWAS discovery: biology, function, and translation","volume":"101","author":"Visscher","year":"2017","journal-title":"Am J Hum Genet"},{"key":"2023070705251246600_btad396-B48","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1002\/gepi.20359","article-title":"Bayes factors for genome-wide association studies: comparison with P-values","volume":"33","author":"Wakefield","year":"2009","journal-title":"Genet Epidemiol"},{"key":"2023070705251246600_btad396-B49","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1002\/gepi.22212","article-title":"Using GWAS top hits to inform priors in Bayesian fine-mapping association studies","volume":"43","author":"Walters","year":"2019","journal-title":"Genet Epidemiol"},{"key":"2023070705251246600_btad396-B50","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1111\/rssb.12388","article-title":"A simple new approach to variable selection in regression, with application to genetic fine mapping","volume":"82","author":"Wang","year":"2020","journal-title":"J R Stat Soc B Stat Methodol"},{"key":"2023070705251246600_btad396-B51","volume-title":"bioRxiv","author":"Wharrie","year":"2022"},{"key":"2023070705251246600_btad396-B52","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/ng.2213","article-title":"Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits","volume":"44","author":"Yang","year":"2012","journal-title":"Nat Gen"},{"key":"2023070705251246600_btad396-B53","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1080\/01621459.2019.1585255","article-title":"Informed proposals for local MCMC in discrete spaces","volume":"115","author":"Zanella","year":"2020","journal-title":"J Am Stat Assoc"},{"key":"2023070705251246600_btad396-B54","doi-asserted-by":"crossref","DOI":"10.1214\/17-AOAS1046","article-title":"Bayesian large-scale multiple regression with summary statistics from genome-wide association studies","volume":"11","author":"Zhu","year":"2017","journal-title":"Ann Appl Stat"},{"key":"2023070705251246600_btad396-B55","doi-asserted-by":"crossref","first-page":"e1010299","DOI":"10.1371\/journal.pgen.1010299","article-title":"Fine-mapping from summary data with the \u201csum of single effects\u201d model","volume":"18","author":"Zou","year":"2022","journal-title":"PLoS Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad396\/50682132\/btad396.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/7\/btad396\/50836038\/btad396.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/7\/btad396\/50836038\/btad396.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,15]],"date-time":"2023-12-15T09:44:26Z","timestamp":1702633466000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad396\/7205323"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,6,22]]},"references-count":55,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2023,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad396","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.12.02.518898","asserted-by":"object"}]},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,1]]},"published":{"date-parts":[[2023,6,22]]},"article-number":"btad396"}}