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Synopsis
Perform a genome-wide association (GWA) meta-analysis for comorbid migraine and depression (M+D+) cases versus non-migraine non-depression (M-D-) controls.
Analysis plans and early results
Migraine Depression Study_ Analysis proposal.doc (8 Aug, 2011)
Migraine Depression Study_Analysis proposal_June2016.doc (28 Jun, 2016)
Migraine_depression_TC_Verneri Boukje 050912.pptx (14 Jan, 2014)
Migraine_depression_meta_v4.pptx (13 March, 2014)
Migr-Depr_overview_2016.pptx (2 April, 2016)
MigDep results and replication.xlsx
Draft Migr depr GWAS art_Mei 2013 ML.doc
Replication results of early findings (I think):
data_verneri_GERMANY.assoc
Data_verneri_HUNT.assoc
data_verneri_KCL.assoc
data_verneri_LEIDEN.assoc
map_file.map
Summary of GWA Studies in Migraine_depression_meta_v4.pptx (NB, studies in brackets were not part of the analysis shown in the Migraine_depression_meta_v4.pptx)
NB, final numbers may change from the following due to updated 1KGP SNP/sample filtering.
IHGC 1000 Genomes Project (1KGP) Imputed Migraine GWA meta-analysis (Gormley et al 2016):
Original migraine analysis plan documents:
1KGP_Migraine_GWAMA_OriginalAnalysisPlan_Email.pdf
analysis_plan_10-07-2013.pdf
phenotype_info_sheet.xls
Genotype_info_sheet.xls
Publication:
Gormley P, Anttila V, Winsvold BS, Palta P, Esko T, Pers TH, Farh KH, Cuenca-Leon E, Muona M, Furlotte NA, Kurth T, Ingason A, McMahon G, Ligthart L, Terwindt GM, Kallela M, Freilinger TM, Ran C, Gordon SG, Stam AH, Steinberg S, Borck G, Koiranen M, Quaye L, Adams HH, Lehtimäki T, Sarin AP, Wedenoja J, Hinds DA, Buring JE, Schürks M, Ridker PM, Hrafnsdottir MG, Stefansson H, Ring SM, Hottenga JJ, Penninx BW, Färkkilä M, Artto V, Kaunisto M, Vepsäläinen S, Malik R, Heath AC, Madden PA, Martin NG, Montgomery GW, Kurki MI, Kals M, Mägi R, Pärn K, Hämäläinen E, Huang H, Byrnes AE, Franke L, Huang J, Stergiakouli E, Lee PH, Sandor C, Webber C, Cader Z, Muller-Myhsok B, Schreiber S, Meitinger T, Eriksson JG, Salomaa V, Heikkilä K, Loehrer E, Uitterlinden AG, Hofman A, van Duijn CM, Cherkas L, Pedersen LM, Stubhaug A, Nielsen CS, Männikkö M, Mihailov E, Milani L, Göbel H, Esserlind AL, Christensen AF, Hansen TF, Werge T; International Headache Genetics Consortium, Kaprio J, Aromaa AJ, Raitakari O, Ikram MA, Spector T, Järvelin MR, Metspalu A, Kubisch C, Strachan DP, Ferrari MD, Belin AC, Dichgans M, Wessman M, van den Maagdenberg AM, Zwart JA, Boomsma DI, Smith GD, Stefansson K, Eriksson N, Daly MJ, Neale BM, Olesen J, Chasman DI, Nyholt DR, Palotie A.
Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine.
Nat Genet. 2016 Aug;48(8):856-66. doi: 10.1038/ng.3598.
Phenotype files obtained (20 May, 2016)
LUMINA cases for migraine depr GWAS_final_edited.xls
RS1 and RS2_with HADS data_final_edited.xls
dutch_model1.sample (LUMINA?)
dutch_model2.sample (Rotterdam?)
22-11-2012_LUMINA_cases_and_controles.ped
22-11-2012_spaanse_data_complete.ped
HUNT_migraine_and_depression_phenotypes.xlsx
hunt.migdep.sample
22-11-2012_HUNT_Genotype_and_Fenotype_data.ped
Genotype files obtained (20 May, 2016)
1KGP imputed:
WGHS_migraine_depression_1000G_20130927.txt.gz
23andMe_V2_migraine_with_depression_20131105.txt.gz
23andMe_V3_migraine_with_depression_20131106.txt.gz
HapMap imputed:
KCL_M+D-vsM-D-.gwama
KCL_M+D+vsM-D-.gwama
Current status in obtaining data for comorbid migraine and depression GWA meta-analysis
NB, final numbers may change from the following due to updated 1KGP SNP/sample filtering.
The Summary of IHGC data on FIMM server
Summary of novel datasets (Gormley et al 2016) available on the FIMM server at your disposal for IHGC projects. To acquire the data, fill in the IHGC project proposal form and send it to Risto Kajanne, who will forward it to the IHGC Preparatory Committee (Aarno, Arn and Jes) for evaluation and take care of the subsequent procedures.
IHGC_data_collection_30-Mar-2016.xlsx
Migraine_analysis_proposal_form.docx