Fine-mapping a genome-wide meta-analysis of 98,374 migraine cases identifies 181 sets of candidate causal variants

Migraine is a highly prevalent neurovascular disorder for which genome-wide association studies (GWAS) have identified over one hundred risk loci, yet the causal variants and genes remain mostly unknown. Here, we meta-analyzed three migraine GWAS including 98,374 cases and 869,160 controls and identified 122 independent risk loci of which 35 were new. Fine-mapping of a meta-analysis is challenging because some variants may be missing from some participating studies and accurate linkage disequilibrium (LD) information of the variants is often not available. Here, using the exact in-sample LD, we first investigated which statistics could reliably capture the quality of fine-mapping when only reference LD was available. We observed that the posterior expected number of causal variants best distinguished between the high- and low-quality results. Next, we performed fine- mapping for 102 autosomal risk regions using FINEMAP. We produced high-quality fine-mapping for 93 regions and defined 181 distinct credible sets. Among the high- quality credible sets were 7 variants with very high posterior inclusion probability (PIP > 0.9) and 2 missense variants with PIP > 0.5 (rs6330 in NGF and rs1133400 in INPP5A ). For 35 association signals, we managed to narrow down the set of potential risk variants to at most 5 variants. ### Competing Interest Statement A.P. is the Scientific Director of the public-private partnership project FinnGen that has 12 industry partners that provide funding for the FinnGen project. ### Funding Statement This work was supported by grants no. 336825, 338507, 352795 from the Research Council of Finland to M.P., by Sigrid Jusélius foundation (M.P. and A.P.) and by the Doctoral School of University of Helsinki (H.H.). The FinnGen project is funded by two grants from Business Finland (HUS 4685/31/2016 and UH 4386/31/2016) and the following industry partners: AbbVie Inc., AstraZeneca UK Ltd, Biogen MA Inc., Bristol Myers Squibb (and Celgene Corporation & Celgene International II Sàrl), Genentech Inc., Merck Sharp & Dohme LCC, Pfizer Inc., GlaxoSmithKline Intellectual Property Development Ltd., Sanofi US Services Inc., Maze Therapeutics Inc., Janssen Biotech Inc, Novartis AG, and Boehringer Ingelheim International GmbH. The genotyping of the Trøndelag Health Study (HUNT) was financed by the National Institute of health (NIH), University of Michigan, The Norwegian Research council, and Central Norway Regional Health Authority and the Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: A human subjects protocol of 23andMe study had been reviewed and approved by Ethical & Independent Review Services, a private institutional review board (). Written informed consent was obtained from all study participants. UK Biobank received ethical approval from the North West Multi-centre Research Ethics Committee (MREC). Written informed consent was obtained from all study participants. The Coordinating Ethics Committee of the Hospital District of Helsinki and Uusimaa (HUS) approved the FinnGen study protocol (Nr HUS/990/2017). FinnGen participants provided informed consent under the Finnish Biobank Act. Older cohorts with study-specific consents were transferred to the Finnish biobanks after approval by Fimea, the National Supervisory Authority for Welfare and Health. Recruitment protocols followed the biobank protocols approved by Fimea. The FinnGen study is approved by Finnish Institute for Health and Welfare (permit numbers: THL/2031/6.02.00/2017, THL/1101/5.05.00/2017, THL/341/6.02.00/2018, THL/2222/6.02.00/2018, THL/283/6.02.00/2019, THL/1721/5.05.00/2019 and THL/1524/5.05.00/2020), Digital and population data service agency (permit numbers: VRK43431/2017-3, VRK/6909/2018-3, VRK/4415/2019-3), the Social Insurance Institution (permit numbers: KELA 58/522/2017, KELA 131/522/2018, KELA 70/522/2019, KELA 98/522/2019, KELA 134/522/2019, KELA 138/522/2019, KELA 2/522/2020, KELA 16/522/2020), Findata permit numbers THL/2364/14.02/2020, THL/4055/14.06.00/2020,,THL/3433/14.06.00/2020, THL/4432/14.06/2020, THL/5189/14.06/2020, THL/5894/14.06.00/2020, THL/6619/14.06.00/2020, THL/209/14.06.00/2021, THL/688/14.06.00/2021, THL/1284/14.06.00/2021, THL/1965/14.06.00/2021, THL/5546/14.02.00/2020, THL/2658/14.06.00/2021, THL/4235/14.06.00/2021 and Statistics Finland (permit numbers: TK-53-1041-17 and TK/143/07.03.00/2020 (earlier TK-53-90-20) TK/1735/07.03.00/2021). The Biobank Access Decisions for FinnGen samples and data utilized in FinnGen Data Freeze 8 include: THL Biobank BB2017\_55, BB2017\_111, BB2018\_19, BB\_2018\_34, BB\_2018\_67, BB2018\_71, BB2019\_7, BB2019\_8, BB2019\_26, BB2020\_1, Finnish Red Cross Blood Service Biobank 7.12.2017, Helsinki Biobank HUS/359/2017, Auria Biobank AB17-5154 and amendment #1 (August 17 2020), AB20-5926 and amendment #1 (April 23 2020), Biobank Borealis of Northern Finland\_2017\_1013, Biobank of Eastern Finland 1186/2018 and amendment 22 # /2020, Finnish Clinical Biobank Tampere MH0004 and amendments (21.02.2020 & 06.10.2020), Central Finland Biobank 1-2017, and Terveystalo Biobank STB 2018001. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes