ArticleMolecular medicine (Cambridge, Mass.)2017
Efficient genome-wide association in biobanks using topic modeling identifies multiple novel disease loci.
Article in Molecular medicine (Cambridge, Mass.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Cardiovascular-kidney-metabolic syndrome: candidate subtypes and genetic risk factors.BMC medical genomics · 2026Article
- Exploring the genetic architecture of multiple long-term conditions using a genome-wide association study in the UK Biobank population.Scientific reports · 2025Article
- Topic modeling identifies novel genetic loci associated with multimorbidities in UK Biobank.Cell genomics · 2023Article
- Pharmacogenomic variation in the Malagasy population: implications for the antimalarial drug primaquine metabolism.Pharmacogenomics · 2023Article
- Leveraging Large-Scale Genetics of PTSD and Cardiovascular Disease to Demonstrate Robust Shared Risk and Improve Risk Prediction Accuracy.The American journal of psychiatry · 2022Article
- A graph-embedded topic model enables characterization of diverse pain phenotypes among UK biobank individuals.iScience · 2022Article
- The Molecular Genetics of Dissociative Symptomatology: A Transdiagnostic Literature Review.Genes · 2022Review
- Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth.iScience · 2021Article
- Assessment of a Prediction Model for Antidepressant Treatment Stability Using Supervised Topic Models.JAMA network open · 2020Article
- Using phenome-wide association to investigate the function of a schizophrenia risk locus at SLC39A8.Translational psychiatry · 2019Article
- Article
- Mapping of Transdiagnostic Neuropsychiatric Phenotypes Across Patients in Two General Hospitals.Journal of the Academy of Consultation-Liaison PsychiatryArticle
- Distribution of agitation and related symptoms among hospitalized patients using a scalable natural language processing method.General hospital psychiatryArticle
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5 authors.
Funding
Abstract
Biobanks and national registries represent a powerful tool for genomic discovery, but rely on diagnostic codes that may be unreliable and fail to capture the relationship between related diagnoses. We developed an efficient means of conducting genome-wide association studies using combinations of diagnostic codes from electronic health records (EHR) for 10845 participants in a biobanking program at two large academic medical centers. Specifically, we applied latent Dirichilet allocation to fit 50 disease topics based on diagnostic codes, then conducted genome-wide common-variant association for each topic. In sensitivity analysis, these results were contrasted with those obtained from traditional single-diagnosis phenome-wide association analysis, as well as those in which only a subset of diagnostic codes are included per topic. In meta-analysis across three biobank cohorts, we identified 23 disease-associated loci with p<1e-15, including previously associated autoimmune disease loci. In all cases, observed significant associations were of greater magnitude than for single phenome-wide diagnostic codes, and incorporation of less strongly-loading diagnostic codes enhanced association. This strategy provides a more efficient means of phenome-wide association in biobanks with coded clinical data.
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