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INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES

Anurag Verma, Joseph B Leader, Shefali S Verma, Alex Frase, John Wallace, Scott Dudek, Daniel R Lavage, Cristopher V Van Hout, Frederick E Dewey, John Penn, Alex Lopez, John D Overton (+5 others)
2016 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
We found the majority of the PheWAS ICD-9 diagnoses highly related to the clinical lab measures associated with same SNPs.  ...  Phenome-Wide Association studies (PheWAS) provide a way to explore the association between genetic variants and comprehensive phenotypic measurements, generating new hypotheses and also exposing the complex  ...  In this study we started with SNPs highly associated with clinical lab measures, thus have compared and contrasted what the ICD-9 diagnoses were also associated with these clinical lab measures.  ... 
pmid:26776183 pmcid:PMC4718547 fatcat:5oqejwyfozcmjpqk3hp6efdssa

INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES

ANURAG VERMA, JOSEPH B. LEADER, SHEFALI S. VERMA, ALEX FRASE, JOHN WALLACE, SCOTT DUDEK, DANIEL R. LAVAGE, CRISTOPHER V. VAN HOUT, FREDERICK E. DEWEY, JOHN PENN, ALEX LOPEZ, JOHN D. OVERTON (+5 others)
2015 Biocomputing 2016  
We found the majority of the PheWAS ICD-9 diagnoses highly related to the clinical lab measures associated with same SNPs.  ...  Phenome-Wide Association studies (PheWAS) provide a way to explore the association between genetic variants and comprehensive phenotypic measurements, generating new hypotheses and also exposing the complex  ...  In this study we started with SNPs highly associated with clinical lab measures, thus have compared and contrasted what the ICD-9 diagnoses were also associated with these clinical lab measures.  ... 
doi:10.1142/9789814749411_0016 fatcat:uh5cyykon5cpjhzczpjcjd2tce

PheWAS and Beyond: The Landscape of Associations with Medical Diagnoses and Clinical Measures across 38,662 Individuals from Geisinger

Anurag Verma, Anastasia Lucas, Shefali S. Verma, Yu Zhang, Navya Josyula, Anqa Khan, Dustin N. Hartzel, Daniel R. Lavage, Joseph Leader, Marylyn D. Ritchie, Sarah A. Pendergrass
2018 American Journal of Human Genetics  
and 25 median clinical laboratory measures.  ...  Most phenome-wide association studies (PheWASs) to date have used a small to moderate number of SNPs for association with phenotypic data.  ...  Acknowledgments This project is funded, in part, under a grant with the Pennsylvania  ... 
doi:10.1016/j.ajhg.2018.02.017 pmid:29606303 pmcid:PMC5985339 fatcat:s7dq6miwjzeohbqfy7ebfts6lm

Phenome-Wide Association Studies: Leveraging Comprehensive Phenotypic and Genotypic Data for Discovery

S. A. Pendergrass, Marylyn D. Ritchie
2015 Current Genetic Medicine Reports  
These networks can be identified through Phenome-Wide Association Studies (PheWAS) where the association between a collection of genetic variants, or in some cases a particular clinical lab variable, and  ...  a wide and diverse range of phenotypes, diagnoses, traits, and/or outcomes are evaluated.  ...  Acknowledgments MD Ritchie has received research grants from the NIH and Geisinger Health Systems.  ... 
doi:10.1007/s40142-015-0067-9 pmid:26146598 pmcid:PMC4489156 fatcat:szd2u6dukndnpoaewjxtskbz2q

Using phenome-wide association studies to examine the effect of environmental exposures on human health

Joseph M. Braun, Geetika Kalloo, Samantha L. Kingsley, Nan Li
2019 Environment International  
By conducting Phenome Wide Association Studies (PheWAS), we can generate new hypotheses about new or poorly understood exposures, identify novel associations for established toxicants, and better understand  ...  In this article, we provide a conceptual framework for conducting PheWAS in environmental epidemiology and summarize some of the advantages and challenges to using the PheWAS to study environmental pollutant  ...  Grant Funding: This work was supported by grants from the National Institute of Environmental Health Sciences grants (R01 ES025214, R01 ES024381, and R01 ES027408) and National Institutes of Health (UG3  ... 
doi:10.1016/j.envint.2019.05.071 pmid:31200158 pmcid:PMC6682449 fatcat:pvoacgnh55caracyhq4b7hga7e

Phenome-Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis

Katherine P. Liao, Jeffrey A. Sparks, Boris P. Hejblum, I-Hsin Kuo, Jing Cui, Lauren J. Lahey, Andrew Cagan, Vivian S. Gainer, Weidong Liu, T. Tony Cai, Jeremy Sokolove, Tianxi Cai
2017 Arthritis & Rheumatology  
† Value for the association between the autoantibody and the phenome-wide association study (PheWAS) code.  ...  Figure 1 . 1 Phenome-wide significant associations between autoantibodies (grouped by epitope target) and phenome-wide association study (PheWAS) codes (false discovery rate [FDR] #10%).  ...  Liao, Sparks, and T. Cai had full access to all of the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.  ... 
doi:10.1002/art.39974 pmid:27792870 pmcid:PMC5378622 fatcat:otpxk55qn5c4bhdyeg2jj3fuhe

PREDICTIVE MODELING OF HOSPITAL READMISSION RATES USING ELECTRONIC MEDICAL RECORD-WIDE MACHINE LEARNING: A CASE-STUDY USING MOUNT SINAI HEART FAILURE COHORT

KHADER SHAMEER, KIPP W JOHNSON, ALEXANDRE YAHI, RICCARDO MIOTTO, LI LI, DORAN RICKS, JEBAKUMAR JEBAKARAN, PATRICIA KOVATCH, PARTHO P. SENGUPTA, SENGUPTA GELIJNS, ALAN MOSKOVITZ, BRUCE DARROW (+5 others)
2016 Biocomputing 2017  
A total of 4,205 variables were extracted from EMR including diagnosis codes (n=1,763), medications (n=1,028), laboratory measurements (n=846), surgical procedures (n=564) and vital signs (n=4).  ...  Compared to existing predictive models for HF readmission rates (AUCs in the range of 0.6-0.7), results from our EMR-wide predictive model (AUC=0.78; Accuracy=83.19%) and phenome-wide feature selection  ...  and JTD.  ... 
doi:10.1142/9789813207813_0027 pmid:27896982 pmcid:PMC5362124 fatcat:bk7swgilcrd55pb4gjjzcqem34

Temporal phenome analysis of a large electronic health record cohort enables identification of hospital-acquired complications

Jeremy L Warner, Amin Zollanvari, Quan Ding, Peijin Zhang, Graham M Snyder, Gil Alterovitz
2013 JAMIA Journal of the American Medical Informatics Association  
Contributors JLW had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. JLW and GA conceived the study design.  ...  Acknowledgements The authors would like to extend special thanks to Peter Szolovits, Leo Celi, Federico Cismondi, Daniel Scott, Tom Lasko, and Josh Denny, for their support and advice in regards to MIMIC  ...  defined by the prevalence of International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) codes or aggregations of such codes, can be used to calculate a phenome-wide association  ... 
doi:10.1136/amiajnl-2013-001861 pmid:23907284 pmcid:PMC3861919 fatcat:d4crzrrfzned7nfhbtaxllvjny

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization

Jeremy L Warner, Joshua C Denny, David A Kreda, Gil Alterovitz
2014 JAMIA Journal of the American Medical Informatics Association  
In the middle panel B, the user has selected to display phenome-wide association study (PheWAS) codes and the aggregate counts are recalculated accordingly.  ...  Not surprisingly, therefore, the Manhattan Plot, the visualization tool widely adopted in genome-wide association studies, has emerged as the best-known visualization tool for phenome exploration.  ...  PROVENANCE AND PEER REVIEW Not commissioned; externally peer reviewed. DATA SHARING Data was all from MIMIC II, a publicly available de-identified EMR database.  ... 
doi:10.1136/amiajnl-2014-002965 pmid:25336590 pmcid:PMC6080728 fatcat:6f3vfnzobveevnknnzkcb3rtju

An exploratory phenome wide association study linking asthma and liver disease genetic variants to electronic health records from the Estonian Biobank

Glen James, Sulev Reisberg, Kaido Lepik, Nicholas Galwey, Paul Avillach, Liis Kolberg, Reedik Mägi, Tõnu Esko, Myriam Alexander, Dawn Waterworth, A. Katrina Loomis, Jaak Vilo (+1 others)
2019 PLoS ONE  
To explore the utility of data available in the Biobank, we conducted a phenome-wide association study (PheWAS) in two areas of interest to healthcare researchers; asthma and liver disease.  ...  We used 11 asthma and 13 liver disease-associated single nucleotide polymorphisms (SNPs), identified from published genome-wide association studies, to test our ability to detect established associations  ...  ICD-10 diagnostic codes were used to determine clinical diagnoses.  ... 
doi:10.1371/journal.pone.0215026 pmid:30978214 pmcid:PMC6461350 fatcat:pxp32tf7azd3xolseu73xjixme

Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics

Antoine Neuraz, Laurent Chouchana, Georgia Malamut, Christine Le Beller, Denis Roche, Philippe Beaune, Patrice Degoulet, Anita Burgun, Marie-Anne Loriot, Paul Avillach, Donna K. Slonim
2013 PLoS Computational Biology  
Phenome-Wide Association Studies (PheWAS) investigate whether genetic polymorphisms associated with a phenotype are also associated with other diagnoses.  ...  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.  ...  Acknowledgments Eric Zapletal: installation and management of the i2b2 HEGP CDW. Author Contributions  ... 
doi:10.1371/journal.pcbi.1003405 pmid:24385893 pmcid:PMC3873228 fatcat:6hsqwm4ohnfqxa22micmi5u5by

Exome-by-phenome-wide rare variant gene burden association with electronic health record phenotypes [article]

Joseph Park, Nathan Katz, Xinyuan Zhang, Anastasia M Lucas, Anurag Verma, Renae L Judy, Rachel L Kember, Jinbo Chen, Scott M Damrauer, Marylyn D Ritchie, Daniel J Rader, Regeneron Genetics Center
2019 bioRxiv   pre-print
variants in each gene with diverse EHR phenotypes using a phenome-wide association study (PheWAS) approach.  ...  However, this methodology has not yet been applied on both an exome-wide and phenome-wide scale, and the clinical ontologies of rare loss-of-function variants in many genes have yet to be described.  ...  Clinical imaging and laboratory measurements To build upon our successfully evaluated exome-by-phenome-wide gene-phenotype associations, we took a deeper dive into the cardiovascular imaging and laboratory  ... 
doi:10.1101/798330 fatcat:b37rqvuqcbbf7iyay3qincu7vy

Rare variants in drug target genes contributing to complex diseases, phenome-wide

Shefali Setia Verma, Navya Josyula, Anurag Verma, Xinyuan Zhang, Yogasudha Veturi, Frederick E. Dewey, Dustin N. Hartzel, Daniel R. Lavage, Joe Leader, Marylyn D. Ritchie, Sarah A. Pendergrass
2018 Scientific Reports  
Phenome Wide Association Studies (PheWAS) have been successful in identifying genetic associations across hundreds of thousands of diseases.  ...  these genes and 541 diagnoses and 35 quantitative clinical lab measures using a gene burden-based approach.  ...  While genome wide association studies (GWAS) and Phenome Wide Association Studies (PheWAS) studies have identified novel and replicating associations for many common genetic variants and complex traits  ... 
doi:10.1038/s41598-018-22834-4 pmid:29545597 pmcid:PMC5854600 fatcat:o6yu43rlu5dlzl5l64utzdrc4y

Mining the human phenome using semantic web technologies: a case study for Type 2 Diabetes

Jyotishman Pathak, Richard C Kiefer, Suzette J Bielinski, Christopher G Chute
2012 AMIA Annual Symposium Proceedings  
In this work, we study how emerging Semantic Web technologies can be applied in conjunction with clinical and genotype data stored at the Mayo Clinic Biobank to mine the phenotype data for genetic associations  ...  The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology.  ...  the entire set of ICD-9-CM billing and diagnoses codes for each eligible subject.  ... 
pmid:23304343 pmcid:PMC3540447 fatcat:jsqjif53rzdfbfhhp6ec7s6wli

Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank

Jyotishman Pathak, Richard C Kiefer, Suzette J Bielinski, Christopher G Chute
2012 Journal of Biomedical Semantics  
The ability to conduct genome-wide association studies (GWAS) has enabled new exploration of how genetic variations contribute to health and disease etiology.  ...  Results: In this work, we study how emerging Semantic Web technologies can be applied in conjunction with clinical and genotype data stored at the Mayo Clinic Biobank to mine the phenotype data for genetic  ...  retrieving the entire set of ICD-9-CM billing and diagnoses codes for each eligible subject.  ... 
doi:10.1186/2041-1480-3-10 pmid:23244446 pmcid:PMC3554594 fatcat:3iozhejznvgcfbhvfn2axufso4
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