Author: Mark J. Daly

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Preprints

Functional screen of Inflammatory Bowel Disease genes reveals key epithelial functions

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Analysis of protein-coding genetic variation in 60,706 humans

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An Atlas of Genetic Correlations across Human Diseases and Traits

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Discovery Of The First Genome-Wide Significant Risk Loci For ADHD

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An open resource of structural variation for medical and population genetics

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Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism

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Regional missense constraint improves variant deleteriousness prediction

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  • Site-wide: 1,141
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Common risk variants identified in autism spectrum disorder

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Genetics of 38 blood and urine biomarkers in the UK Biobank

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LD Score Regression Distinguishes Confounding from Polygenicity in Genome-Wide Association Studies

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New mutations, old statistical challenges

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Current clinical use of polygenic scores will risk exacerbating health disparities

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  • Site-wide: 14,221
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Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia

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Evaluating potential drug targets through human loss-of-function genetic variation

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Genome wide meta-analysis identifies genomic relationships, novel loci, and pleiotropic mechanisms across eight psychiatric disorders.

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Transcript expression-aware annotation improves rare variant discovery and interpretation

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Association mapping of inflammatory bowel disease loci to single variant resolution

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Systematic single-variant and gene-based association testing of 3,700 phenotypes in 281,850 UK Biobank exomes

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Phenome-wide association studies (PheWAS) across large "real-world data" population cohorts support drug target validation

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Medical relevance of protein-truncating variants across 337,208 individuals in the UK Biobank study

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Genome-wide maps of enhancer regulation connect risk variants to disease genes

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Human demographic history impacts genetic risk prediction across diverse populations

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  • Site-wide: 4,784
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Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies

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Scalable generalized linear mixed model for region-based association tests in large biobanks and cohorts

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Bayesian model comparison for rare variant association studies

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Quantifying the impact of rare and ultra-rare coding variation across the phenotypic spectrum

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Limited contribution of rare, noncoding variation to autism spectrum disorder from sequencing of 2,076 genomes in quartet families

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  • Site-wide: 82,843

Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine

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  • Site-wide: 133,351
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Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders

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  • Site-wide: 104,449

Comparative genetic architectures of schizophrenia in East Asian and European populations

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Ultra-rare disruptive and damaging mutations influence educational attainment in the general population

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Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations

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Population histories of the United States revealed through fine-scale migration and haplotype analysis

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Ultra-rare genetic variation in the epilepsies: a whole-exome sequencing study of 17,606 individuals

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Reduced expression of COVID-19 host receptor, ACE2 is associated with small bowel inflammation, more severe disease, and response to anti-TNF therapy in Crohn's disease

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Multi-Ancestry Meta-Analysis yields novel genetic discoveries and ancestry-specific associations

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Abundant contribution of short tandem repeats to gene expression variation in humans

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Predicting Functional Effects of Missense Variants in Voltage-Gated Sodium and Calcium Channels

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ASD and ADHD have a similar burden of rare protein-truncating variants

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  • Site-wide: 10,475
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A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects

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  • Site-wide: 10,628
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Trans-biobank analysis with 676,000 individuals elucidates the association of polygenic risk scores of complex traits with human lifespan

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Whole Genome Sequencing in Psychiatric Disorders: the WGSPD Consortium

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Gene family information facilitates variant interpretation and identification of disease-associated genes

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Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population

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Tractor: A framework allowing for improved inclusion of admixed individuals in large-scale association studies.

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Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population

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Analysis across Taiwan Biobank, Biobank Japan and UK Biobank identifies hundreds of novel loci for 36 quantitative traits

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Refining the role of de novo protein truncating variants in neurodevelopmental disorders using population reference samples

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Genomic dissection of bipolar disorder and schizophrenia including 28 subphenotypes

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An Unexpectedly Complex Architecture for Skin Pigmentation in Africans

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Burden analysis of missense variants in 1,330 disease-associated genes on 3D provides insights into the mutation effects

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Estimating the Selective Effect of Heterozygous Protein Truncating Variants from Human Exome Data

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Genetic predisposition to myeloproliferative neoplasms implicates hematopoietic stem cell biology

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Discovery of an autoimmunity-associated IL2RA enhancer by unbiased targeting of transcriptional activation

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Enrichment of rare protein truncating variants in amyotrophic lateral sclerosis patients

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Genetics of human plasma lipidome: Understanding lipid metabolism and its link to diseases beyond traditional lipids

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A genome-wide association study for shared risk across major psychiatric disorders in a nation-wide birth cohort implicates fetal neurodevelopment as a key mediator

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Sequencing of over 100,000 individuals identifies multiple genes and rare variants associated with Crohns disease susceptibility

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Base-Specific Mutational Intolerance Near Splice-Sites Clarifies Role Of Non-Essential Splice Nucleotides

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The ExAC Browser: Displaying reference data information from over 60,000 exomes

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Rare loss-of-function variants in KMT2F are associated with schizophrenia and developmental disorders

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The rate of false polymorphisms introduced when imputing genotypes from global imputation panels

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Epigenetic aging of classical monocytes from healthy individuals

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Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma

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Polygenic risk, susceptibility genes, and breast cancer over the life course

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Targeted gene sequencing in 6994 individuals with neurodevelopmental disorder with epilepsy

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Schizophrenia risk conferred by protein-coding de novo mutations

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Applicability of the mutation-selection balance model to population genetics of heterozygous protein-truncating variants in humans

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Network analysis of genome-wide selective constraint reveals a gene network active in early fetal brain intolerant of mutation

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A platform for case-control matching enables association studies without genotype sharing

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Mosaic Mutations in Blood DNA Sequence Are Associated with Solid Tumor Cancers

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An expanded analysis framework for multivariate GWAS connects inflammatory biomarkers to functional variants and disease

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The iPSYCH2012 case-cohort sample: New directions for unravelling genetic and environmental architectures of severe mental disorders

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Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

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An efficient and accurate frailty model approach for genome-wide survival association analysis controlling for population structure and relatedness in large-scale biobanks

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Case-control analysis identifies shared properties of rare germline variation in cancer predisposing genes

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CCR5-del32 is not deleterious in the homozygous state in humans

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RICOPILI: Rapid Imputation for COnsortias PIpeLIne

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Novel protective associations with age-related macular degeneration: A common variant near CTRB1 and a rare variant in PELI3

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Identification of shared and differentiating genetic risk for autism spectrum disorder, attention deficit hyperactivity disorder and case subgroups.

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Contribution of rare and common variants to intellectual disability in a high-risk population sub-isolate of Northern Finland

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Evaluation of copy number burden in specific epilepsy types from a genome-wide study of 18,564 subjects

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High heritability of ascending aortic diameter and multi-ethnic prediction of thoracic aortic disease.

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Meta-analysis of Scandinavian Schizophrenia Exomes

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A method to exploit the structure of genetic ancestry space to enhance case-control studies

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Implementation of CYP2D6 copy-number imputation panel and frequency of key pharmacogenetic variants in Finnish individuals with a psychotic disorder

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Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

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Set-based rare variant association tests for biobank scale sequencing data sets

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Target Gene Notebook: Connecting genetics and drug discovery

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Prioritization of disease genes from GWAS using ensemble based positive-unlabeled learning

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The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia

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Reassessment Of Lesion-Associated Gene And Variant Pathogenicity In Focal Human Epilepsies

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Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection

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Chromosome level genome assembly and annotation of highly invasive Japanese stiltgrass (Microstegium vimineum)

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Differences in the genetic architecture of common and rare variants in childhood, persistent and late-diagnosed attention deficit hyperactivity disorder

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Comprehensive genome-wide association study of different forms of hernia identifies more than 80 associated loci

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