ArticlePLoS computational biology2013
Phenome-wide association studies on a quantitative trait: application to TPMT enzyme activity and thiopurine therapy in pharmacogenomics.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 55 citations in OpenAlex.
- Overcome the Limitation of Phenome-Wide Association Studies (PheWAS): Extension of PheWAS to Efficient and Robust Large-Scale ICD Codes Analysis.medRxiv : the preprint server for health sciences · 2024Article
- Maturation and application of phenome-wide association studies.Trends in genetics : TIG · 2022Review
- Mining Electronic Health Records for Drugs Associated With 28-day Mortality in COVID-19: Pharmacopoeia-wide Association Study (PharmWAS).JMIR medical informatics · 2022Article
- Improving early diagnosis of rare diseases using Natural Language Processing in unstructured medical records: an illustration from Dravet syndrome.Orphanet journal of rare diseases · 2021Article
- Causal Inference Methods to Integrate Omics and Complex Traits.Cold Spring Harbor perspectives in medicine · 2021Review
- Neuroimaging PheWAS (Phenome-Wide Association Study): A Free Cloud-Computing Platform for Big-Data, Brain-Wide Imaging Association Studies.Neuroinformatics · 2021Article
- Mapping ICD-10 and ICD-10-CM Codes to Phecodes: Workflow Development and Initial Evaluation.JMIR medical informatics · 2019Article
- Clinical and Pharmacological Aspects of Hospital-Acquired Acute Kidney Injuries Outside the Intensive Care Unit: A Phenome-Wide Association Study.Kidney diseases (Basel, Switzerland) · 2019Article
- PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison.BMC bioinformatics · 2019Article
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- Body Composition Profiling in the UK Biobank Imaging Study.Obesity (Silver Spring, Md.) · 2018Article
- Predicting the need for a reduced drug dose, at first prescription.Scientific reports · 2018Article
- Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects.Bioinformatics (Oxford, England) · 2018Article
- Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials underInternational journal of molecular sciences · 2018Article
- Genome-wide and Phenome-wide Approaches to Understand Variable Drug Actions in Electronic Health Records.Clinical and translational science · 2018Review
- Association between borderline dysnatremia and mortality insight into a new data mining approach.BMC medical informatics and decision making · 2017Observational
- Phenome-Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis.Arthritis & rheumatology (Hoboken, N.J.) · 2017Article
- Phenome-Wide Association Study of Rheumatoid Arthritis Subgroups Identifies Association Between Seronegative Disease and Fibromyalgia.Arthritis & rheumatology (Hoboken, N.J.) · 2017Article
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Corrections and comments
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Authors and funding
10 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phenome-Wide Association Studies (PheWAS) investigate whether genetic polymorphisms associated with a phenotype are also associated with other diagnoses. In this study, we have developed new methods to perform a PheWAS based on ICD-10 codes and biological test results, and to use a quantitative trait as the selection criterion. We tested our approach on thiopurine S-methyltransferase (TPMT) activity in patients treated by thiopurine drugs. We developed 2 aggregation methods for the ICD-10 codes: an ICD-10 hierarchy and a mapping to existing ICD-9-CM based PheWAS codes. Eleven biological test results were also analyzed using discretization algorithms. We applied these methods in patients having a TPMT activity assessment from the clinical data warehouse of a French academic hospital between January 2000 and July 2013. Data after initiation of thiopurine treatment were analyzed and patient groups were compared according to their TPMT activity level. A total of 442 patient records were analyzed representing 10,252 ICD-10 codes and 72,711 biological test results. The results from the ICD-9-CM based PheWAS codes and ICD-10 hierarchy codes were concordant. Cross-validation with the biological test results allowed us to validate the ICD phenotypes. Iron-deficiency anemia and diabetes mellitus were associated with a very high TPMT activity (p = 0.0004 and p = 0.0015, respectively). We describe here an original method to perform PheWAS on a quantitative trait using both ICD-10 diagnosis codes and biological test results to identify associated phenotypes. In the field of pharmacogenomics, PheWAS allow for the identification of new subgroups of patients who require personalized clinical and therapeutic management.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.