ArticleNature genetics2023
Phenotype integration improves power and preserves specificity in biobank-based genetic studies of major depressive disorder.
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 50 citations in OpenAlex.
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- Unveiling the enigma of anxiety disorders and depression: from pathogenesis to treatment.Science China. Life sciences · 2026Review
- Transfer learning enhances clinical utility of polygenic scores with small, phenotypically refined cohorts.Genome research · 2026Article
- Pleiotropic shared heritability quantifies the shared genetic variance of common diseases.Nature genetics · 2026Article
- DOMAIN-AWARE MATRIX COMPLETION FOR PHENOTYPE IMPUTATION USING ELECTRONIC HEALTH RECORD DATA WITH APPLICATIONS IN GENOMIC RESEARCH.The annals of applied statistics · 2026Article
- Can Psychiatric Genetics Advance Without Incorporating a Life Course Perspective?Biological psychiatry · 2026Review
- A machine learning framework reveals key drivers of cytokine responses in a healthy human cohort.NPJ systems biology and applications · 2026Article
- The predicament of heritable confounders.Nature genetics · 2026Review
- Choice of phenotype scale is critical in biobank-based G×E tests.bioRxiv : the preprint server for biology · 2026Article
- Replication of COPD susceptibility loci in a large Chinese elderly population using a validated, multi-setting EHR phenotype.BMC pulmonary medicine · 2026Article
- Specificity of Polygenic Scores for Psychiatric Disorders Beyond Transdiagnostic Genetic Risk.JAMA network open · 2026Article
- The broad structure of psychopathology in the All of Us Research Program.Psychological medicine · 2025Article
- Liability threshold model-based disease risk prediction based on electronic health record phenotypes.Nature genetics · 2025Article
- Exploiting pleiotropy to enhance variant discovery with functional false discovery rates.Nature computational science · 2025Article
- Genetic analyses of eight complex diseases using predicted continuous representations of disease.Cell reports methods · 2025Article
- Genetic risk effects on psychiatric disorders act in sets.medRxiv : the preprint server for health sciences · 2025Article
- Multitrait Genetic Analysis Identifies Novel Pleiotropic Loci for Depression and Schizophrenia in East Asians.Schizophrenia bulletin · 2025Article
- Review
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Authors and funding
13 authors at 7 institutions in 3 countries.
Funding
Abstract
Biobanks often contain several phenotypes relevant to diseases such as major depressive disorder (MDD), with partly distinct genetic architectures. Researchers face complex tradeoffs between shallow (large sample size, low specificity/sensitivity) and deep (small sample size, high specificity/sensitivity) phenotypes, and the optimal choices are often unclear. Here we propose to integrate these phenotypes to combine the benefits of each. We use phenotype imputation to integrate information across hundreds of MDD-relevant phenotypes, which significantly increases genome-wide association study (GWAS) power and polygenic risk score (PRS) prediction accuracy of the deepest available MDD phenotype in UK Biobank, LifetimeMDD. We demonstrate that imputation preserves specificity in its genetic architecture using a novel PRS-based pleiotropy metric. We further find that integration via summary statistics also enhances GWAS power and PRS predictions, but can introduce nonspecific genetic effects depending on input. Our work provides a simple and scalable approach to improve genetic studies in large biobanks by integrating shallow and deep phenotypes.
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