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Identification of 370 Genetic Loci for Age at First Sex and Birth

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Identification of 370 Genetic Loci for Age at First Sex and Birth 1 Supplementary Note 2 Identification of 370 genetic loci for age at 3 first sex and birth linked to externalizing 4 behaviour 5 6 Melinda C. Mills1,2,†,*, Felix C. Tropf1,2,3,4,†, David M. Brazel1,2,†, Natalie van Zuydam5, Ahmad Vaez6,7, 7 eQTLGen Consortium, BIOS Consortium, Tune H. Pers8,9, Harold Snieder6, John R.B. Perry10, Ken K. 8 Ong10,†, Marcel den Hoed5,†, Nicola Barban11,†, and Felix R. Day10,†,* on behalf of the Human 9 Reproductive Behaviour Consortium 10 11 1 Leverhulme Centre for Demographic Science, University of Oxford, Oxford, United Kingdom 12 2 Nuffield College, University of Oxford, Oxford, United Kingdom 13 3 École Nationale de la Statistique et de L’administration Économique (ENSAE), Paris, France 14 4 Center for Research in Economics and Statistics (CREST), Paris, France 15 5 The Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University 16 and SciLifeLab, Uppsala, Sweden 17 6 Department of Epidemiology, University of Groningen, University Medical Center Groningen, 18 Groningen, The Netherlands 19 7 Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran 20 8 The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical 21 Sciences, University of Copenhagen, Copenhagen, Denmark 22 9 Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark 23 10 MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, United 24 Kingdom 25 11 Department of Statistical Sciences, University of Bologna, Italy 26 27 † Denotes equal contribution 28 * Correspondence to Melinda C. Mills, [email protected], and Felix R. Day, 29 [email protected] 30 31 32 1 Contents 2 List of Supplementary Figures ................................................................................................................. 4 3 List of Supplementary Tables .................................................................................................................. 5 4 1. Background and Phenotype Definitions ......................................................................................... 7 5 1.1 Background ............................................................................................................................. 7 6 1.2 Phenotype Definitions ............................................................................................................ 7 7 2. Summary of Methods, Purpose of Analysis and Main Results ....................................................... 8 8 3. Phenotypic and genotypic changes in the onset of human reproductive behaviour over time ........ 9 9 3.1 Phenotypic changes in the onset of human reproductive behaviour .............................................. 9 10 3.2 Heterogeneity in heritability across birth cohorts .......................................................................... 13 11 4. Overview of GWAS meta-analysis ..................................................................................................... 16 12 4.1 Participating cohorts ....................................................................................................................... 16 13 4.2 Sample inclusion criteria ................................................................................................................. 17 14 4.3 Genotyping and imputation ............................................................................................................ 17 15 4.4 Models used to test for association ................................................................................................ 18 16 4.5 Analysis of X chromosome .............................................................................................................. 18 17 4.6 Quality Control (QC): filters & diagnostic checks ............................................................................ 18 18 4.6.1 Filters .................................................................................................................................... 19 19 4.6.2 Diagnostic graphs ................................................................................................................. 19 20 4.6.3 SNPs and cohorts excluded .................................................................................................. 19 21 4.7 Meta Analyses ................................................................................................................................. 20 22 4.8 MTAG results ................................................................................................................................. 21 23 4.9 Summary of discovered loci and Manhattan plots ......................................................................... 21 24 5. Polygenic score calculation and prediction .................................................................................. 26 25 5.1 Calculation of polygenic scores ....................................................................................................... 26 26 5.2 Out of sample prediction ................................................................................................................ 26 27 5.3 Accounting for right-censoring and comparing top and bottom 5% PGS ....................................... 27 28 6. Testing population stratification and environmentally mediated parental genetic effects of 29 childhood socioeconomic status ........................................................................................................... 29 30 6.1 Testing Population Stratification: LD Score intercept test .............................................................. 29 31 6.2 Polygenic score prediction by childhood socio-economic status ................................................... 30 32 7. Genetic correlations with related traits ........................................................................................ 32 33 7.1 Genetic correlation with related traits ........................................................................................... 32 1 7.2 Genetic correlations by sex ............................................................................................................. 33 2 8. Uncovering shared genetic etiology with Genomic SEM .............................................................. 36 3 8.1 AFB and AFS regression educational attainment (EA) and trait X .................................................. 36 4 8.2 Reproductive biology and externalizing behaviour explanation of variance ................................. 40 5 9. Bi-directional MR of reproductive behaviour, teenage behavioural disinhibition and onset of later 6 life disease............................................................................................................................................. 43 7 9.1 Background, methods and innovation .................................................................................. 43 8 9.2 Results MR ............................................................................................................................ 43 9 10. Later age at first birth linked to parental longevity .................................................................. 45 10 10.1 Background and innovation .......................................................................................................... 45 11 10.2 Data and measurement ................................................................................................................ 45 12 10.3 Methods of analysis ...................................................................................................................... 45 13 10.4 Results: Later reproductive timing predicts parental longevity ................................................... 46 14 11. Gene prioritization .................................................................................................................... 47 15 11.1 Methods ........................................................................................................................................ 47 16 11.2 Results ................................................................................................................................... 49 17 11.2.1 Candidate genes in brain .............................................................................................. 49 18 11.2.2 Candidate genes in glands ............................................................................................ 50 19 11.2.3 Candidate genes in female reproductive organs .......................................................... 50 20 11.2.4 Candidate genes in male reproductive organs ............................................................. 52 21 12. Sex-specific genetic effects ............................................................................................................. 53 22 12.1 Genetic overlap among sexes: LD score bivariate regression ...................................................... 53 23 12.2 Sex specific loci ............................................................................................................................. 56 24 12.2.1 Methods and identification of 10 additional associations for AFS and 1 for AFB ........ 56 25 12.2.2 Gene Prioritization Results AFS ..................................................................................... 56 26 12.2.3 Gene Prioritization Results AFB ........................................................................................
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