DOI: 10.6084/m9.figshare.19604335.v2
title: Imputation paper summary statistics

description: Here we have summary statistics from GWAS used in the following paper <br> Dahl et al (2022) BioRxiv "Phenotype integration improves power and preserves specificity in biobank-based genetic studies of MDD" <br> All summary statistics are in the .ma format with the following columns: <br> SNP: RSID of SNP A1: effect allele A2: other allele freq: frequency of effect allele b: effect size (beta) of effect allele se: standard error of beta p: P value of association N: sample size (which may differ between different SNPs due to missing genotypes at SNPs, see QC for genotypes in the bioRxiv paper) <br> GWAS summary statistics are available for the following phenotypes <br> A) Observed phenotypes <br> 1. LifetimeMDD: Deepest possible MDD phenotype in 67K individuals in UKBiobank, based on CIDI-SF, as described in Cai et al 2020 Nature Genetics 2. GPpsy: Shallow MDD phenotype in 330K individuals in UKBiobank, based on self-report help-seeking, as described in Cai et al 2020 Nature Genetics 3. PGC29: MDD defined based on structured interviews in 29 core cohorts in the PGC-MDD Working Group, as described in Wray et al 2018 Nature Genetics 4. ipsych: Affective disorders identified through medical registry ICD10 codes in the iPSYCH cohorts, as described in Schork et al 2019 Nature Neuroscience 5. 23andMe: Self-reported diagnosis or treatment of depression from consenting 23andMe users, as described in Hyde et al 2016 Nature Genetics <br> B) Imputed phenotypes <br> 1.SoftImpOnly.LifetimeMDD: Softimpute imputed LifetimeMDD measure in 267K White-British individuals for whom this measure is not observed in UKBiobank 2. SoftImpAll.LifetimeMDD: Softimpute imputed LifetimeMDD measure in 267K White-British individuals for whom this measure is not observed in UKBiobank, combined with the phenotyped measures of LifetimeMDD in 67K individuals 3. AutoImpOnly.LifetimeMDD: Autocomplete imputed LifetimeMDD measure in 267K White-British individuals for whom this measure is not observed in UKBiobank 4. AutoImpAll.LifetimeMDD: Autocomplete imputed LifetimeMDD measure in 267K White-British individuals for whom this measure is not observed in UKBiobank, combined with the phenotyped measures of LifetimeMDD in 67K individuals <br> C) MTAG outputs for LifetimeMDD (See Fig 4A in Dahl et al 2022 BioRxiv) <br> 1. MTAG.GPpsy.LifetimeMDD: MTAG run with LifetimeMDD and GPpsy as described in Cai et al 2020 Nature Genetics as input 2. MTAG.FamHist.LifetimeMDD: MTAG run with LifetimeMDD and phenotypes on family history of depression as input 3. MTAG.Envs.LifetimeMDD: MTAG run with LifetimeMDD and environmental phenotypes such as townsend deprivation index as input 4. MTAG.AllDep.LifetimeMDD: MTAG run with LifetimeMDD and all alternative, shallower definitions of MDD in UKBiobank as described in Cai et al 2020 Nature Genetics as input 5. MTAG.AllDepEnvs.LifetimeMDD: MTAG run with LifetimeMDD and all alternative, shallower definitions of MDD in UKBiobank as described in Cai et al 2020 Nature Genetics as well as environmental factors as input 6. MTAG.All.LifetimeMDD: MTAG run with LifetimeMDD and all alternative, shallower definitions of MDD in UKBiobank as described in Cai et al 2020 Nature Genetics, as well as family history measures of depression and environmental factors as input <br>