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https://www.readbyqxmd.com/read/29023970/phenotype-validation-in-electronic-health-records-based-genetic-association-studies
#1
Lu Wang, Scott M Damrauer, Hong Zhang, Alan X Zhang, Rui Xiao, Jason H Moore, Jinbo Chen
The linkage between electronic health records (EHRs) and genotype data makes it plausible to study the genetic susceptibility of a wide range of disease phenotypes. Despite that EHR-derived phenotype data are subjected to misclassification, it has been shown useful for discovering susceptible genes, particularly in the setting of phenome-wide association studies (PheWAS). It is essential to characterize discovered associations using gold standard phenotype data by chart review. In this work, we propose a genotype stratified case-control sampling strategy to select subjects for phenotype validation...
October 11, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28867356/relationship-of-sult1a1-copy-number-variation-with-estrogen-metabolism-and-human-health
#2
Jixia Liu, Ran Zhao, Zhan Ye, Alexander J Frey, Emily R Schriver, Nathaniel W Snyder, Scott J Hebbring
Human cytosolic sulfotransferase 1A1 (SULT1A1) is considered to be one of the most important SULT isoforms for metabolism, detoxification, and carcinogenesis. This theory is driven by observations that SULT1A1 is widely expressed in multiple tissues and acts on a wide range of phenolic substrates. SULT1A1 is subject to functional common copy number variation (CNV) including deletions or duplications. However, it is less clear how SULT1A1 CNV impacts health and disease. To better understand the biological role of SULT1A1 in human health, we genotyped CNV in 14,275 Marshfield Clinic patients linked to an extensive electronic health record...
November 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28736474/phenotype-analysis-of-early-risk-factors-from-electronic-medical-records-improves-image-derived-diagnostic-classifiers-for-optic-nerve-pathology
#3
Shikha Chaganti, Kunal P Nabar, Katrina M Nelson, Louise A Mawn, Bennett A Landman
We examine imaging and electronic medical records (EMR) of 588 subjects over five major disease groups that affect optic nerve function. An objective evaluation of the role of imaging and EMR data in diagnosis of these conditions would improve understanding of these diseases and help in early intervention. We developed an automated image-processing pipeline that identifies the orbital structures within the human eyes from computed tomography (CT) scans, calculates structural size, and performs volume measurements...
February 11, 2017: Proceedings of SPIE
https://www.readbyqxmd.com/read/28711146/drug-repositioning-strategies-for-the-identification-of-novel-therapies-for-rheumatic-autoimmune-inflammatory-diseases
#4
REVIEW
Amrie C Grammer, Peter E Lipsky
Rheumatic Autoimmune Inflammatory Diseases such as Sjögren's and lupus lack modern treatments. Less than 5% of drugs approved by the FDA from 2014 to mid-2016 had a RAID indication. Many RAID standard-of-care drugs were repurposed based on serendipitous observations, similarity-of-disease categorization, and/or off-target effects. Recently, drug repurposing has become more intentional, relying on an evolving awareness of molecular underpinnings, as well as a better understanding of drug-target interactions by computational modeling...
August 2017: Rheumatic Diseases Clinics of North America
https://www.readbyqxmd.com/read/28686612/evaluating-phecodes-clinical-classification-software-and-icd-9-cm-codes-for-phenome-wide-association-studies-in-the-electronic-health-record
#5
Wei-Qi Wei, Lisa A Bastarache, Robert J Carroll, Joy E Marlo, Travis J Osterman, Eric R Gamazon, Nancy J Cox, Dan M Roden, Joshua C Denny
OBJECTIVE: To compare three groupings of Electronic Health Record (EHR) billing codes for their ability to represent clinically meaningful phenotypes and to replicate known genetic associations. The three tested coding systems were the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) codes, the Agency for Healthcare Research and Quality Clinical Classification Software for ICD-9-CM (CCS), and manually curated "phecodes" designed to facilitate phenome-wide association studies (PheWAS) in EHRs...
2017: PloS One
https://www.readbyqxmd.com/read/28602423/a-fast-and-accurate-algorithm-to-test-for-binary-phenotypes-and-its-application-to-phewas
#6
Rounak Dey, Ellen M Schmidt, Goncalo R Abecasis, Seunggeun Lee
The availability of electronic health record (EHR)-based phenotypes allows for genome-wide association analyses in thousands of traits and has great potential to enable identification of genetic variants associated with clinical phenotypes. We can interpret the phenome-wide association study (PheWAS) result for a single genetic variant by observing its association across a landscape of phenotypes. Because a PheWAS can test thousands of binary phenotypes, and most of them have unbalanced or often extremely unbalanced case-control ratios (1:10 or 1:600, respectively), existing methods cannot provide an accurate and scalable way to test for associations...
July 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28557243/the-use-of-electronic-health-records-for-psychiatric-phenotyping-and-genomics
#7
REVIEW
Jordan W Smoller
The widespread adoption of electronic health record (EHRs) in healthcare systems has created a vast and continuously growing resource of clinical data and provides new opportunities for population-based research. In particular, the linking of EHRs to biospecimens and genomic data in biobanks may help address what has become a rate-limiting study for genetic research: the need for large sample sizes. The principal roadblock to capitalizing on these resources is the need to establish the validity of phenotypes extracted from the EHR...
May 30, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28495862/the-diagnosis-wide-landscape-of-hospital-acquired-aki
#8
Anne-Sophie Jannot, Anita Burgun, Eric Thervet, Nicolas Pallet
BACKGROUND AND OBJECTIVES: The exploration of electronic hospital records offers a unique opportunity to describe in-depth the prevalence of conditions associated with diagnoses at an unprecedented level of comprehensiveness. We used a diagnosis-wide approach, adapted from phenome-wide association studies (PheWAS), to perform an exhaustive analysis of all diagnoses associated with hospital-acquired AKI (HA-AKI) in a French urban tertiary academic hospital over a period of 10 years. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS: We retrospectively extracted all diagnoses from an i2b2 (Informatics for Integrating Biology and the Bedside) clinical data warehouse for patients who stayed in this hospital between 2006 and 2015 and had at least two plasma creatinine measurements performed during the first week of their stay...
June 7, 2017: Clinical Journal of the American Society of Nephrology: CJASN
https://www.readbyqxmd.com/read/28422977/defining-the-complex-phenotype-of-severe-systemic-loxoscelism-using-a-large-electronic-health-record-cohort
#9
Jamie R Robinson, Vanessa E Kennedy, Youssef Doss, Lisa Bastarache, Joshua Denny, Jeremy L Warner
OBJECTIVE: Systemic loxoscelism is a rare illness resulting from the bite of the recluse spider and, in its most severe form, can lead to widespread hemolysis, coagulopathy, and death. We aim to describe the clinical features and outcomes of the largest known cohort of individuals with moderate to severe loxoscelism. METHODS: We performed a retrospective, cross sectional study from January 1, 1995, to December 31, 2015, at a tertiary-care academic medical center, to determine individuals with clinical records consistent with moderate to severe loxoscelism...
2017: PloS One
https://www.readbyqxmd.com/read/28229460/phenome-wide-association-studies-a-new-method-for-functional-genomics-in-humans
#10
Dan M Roden
In experimental physiological research, a common study design for examining the functional role of a gene or a genetic variant is to introduce that genetic variant into a model organism (such as yeast or mouse) and then to search for phenotypic consequences. The development of DNA biobanks linked to dense phenotypic information enables such an experiment to be applied to human subjects in the form of a phenome-wide association study (PheWAS). The PheWAS paradigm takes advantage of a curated medical phenome, often derived from electronic health records, to search for associations between 'input functions' and phenotypes in an unbiased fashion...
June 15, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28060329/drug-repurposing-hypothesis-generation-using-the-re-fine-drugs-system
#11
Kelly Regan, Soheil Moosavinasab, Philip Payne, Simon Lin
The promise of drug repurposing is that existing drugs may be used for new disease indications in order to curb the high costs and time for approval. The goal of computational methods for drug repurposing is to enable solutions for safer, cheaper and faster drug discovery. Towards this end, we developed a novel method that integrates genetic and clinical phenotype data from large-scale GWAS and PheWAS studies with detailed drug information on the concept of transitive Drug-Gene-Disease triads. We created "RE:fine Drugs," a freely available, interactive dashboard that automates gene, disease and drug-based searches to identify drug repurposing candidates...
December 11, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27919371/a-machine-learning-based-framework-to-identify-type-2-diabetes-through-electronic-health-records
#12
Tao Zheng, Wei Xie, Liling Xu, Xiaoying He, Ya Zhang, Mingrong You, Gong Yang, You Chen
OBJECTIVE: To discover diverse genotype-phenotype associations affiliated with Type 2 Diabetes Mellitus (T2DM) via genome-wide association study (GWAS) and phenome-wide association study (PheWAS), more cases (T2DM subjects) and controls (subjects without T2DM) are required to be identified (e.g., via Electronic Health Records (EHR)). However, existing expert based identification algorithms often suffer in a low recall rate and could miss a large number of valuable samples under conservative filtering standards...
January 2017: International Journal of Medical Informatics
https://www.readbyqxmd.com/read/27897004/identifying-genetic-associations-with-variability-in-metabolic-health-and-blood-count-laboratory-values-diving-into-the-quantitative-traits-by-leveraging-longitudinal-data-from-an-ehr
#13
Shefali S Verma, Anastasia M Lucas, Daniel R Lavage, Joseph B Leader, Raghu Metpally, Sarathbabu Krishnamurthy, Frederick Dewey, Ingrid Borecki, Alexander Lopez, John Overton, John Penn, Jeffrey Reid, Sarah A Pendergrass, Gerda Breitwieser, Marylyn D Ritchie
A wide range of patient health data is recorded in Electronic Health Records (EHR). This data includes diagnosis, surgical procedures, clinical laboratory measurements, and medication information. Together this information reflects the patient's medical history. Many studies have efficiently used this data from the EHR to find associations that are clinically relevant, either by utilizing International Classification of Diseases, version 9 (ICD-9) codes or laboratory measurements, or by designing phenotype algorithms to extract case and control status with accuracy from the EHR...
2017: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27792870/phenome-wide-association-study-of-autoantibodies-to-citrullinated-and-noncitrullinated-epitopes-in-rheumatoid-arthritis
#14
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
OBJECTIVE: Patients with rheumatoid arthritis (RA) develop autoantibodies against a spectrum of antigens, but the clinical significance of these autoantibodies is unclear. Using a phenome-wide association study (PheWAS) approach, we examined the association between autoantibodies and clinical subphenotypes of RA. METHODS: This study was conducted in a cohort of RA patients identified from the electronic medical records (EMRs) of 2 tertiary care centers. Using a published multiplex bead assay, we measured 36 autoantibodies targeting epitopes implicated in RA...
April 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27589350/phenome-wide-association-study-of-rheumatoid-arthritis-subgroups-identifies-association-between-seronegative-disease-and-fibromyalgia
#15
Jayanth Doss, Huan Mo, Robert J Carroll, Leslie J Crofford, Joshua C Denny
OBJECTIVE: The differences between seronegative and seropositive rheumatoid arthritis (RA) have not been widely reported. We performed electronic health record (EHR)-based phenome-wide association studies (PheWAS) to identify disease associations in seropositive and seronegative RA. METHODS: A validated algorithm identified RA subjects from the de-identified version of the Vanderbilt University Medical Center EHR. Serotypes were determined by rheumatoid factor (RF) and anti-cyclic citrullinated peptide antibody (ACPA) values...
February 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/27535653/emerge-phenome-wide-association-study-phewas-identifies-clinical-associations-and-pleiotropy-for-stop-gain-variants
#16
Anurag Verma, Shefali S Verma, Sarah A Pendergrass, Dana C Crawford, David R Crosslin, Helena Kuivaniemi, William S Bush, Yuki Bradford, Iftikhar Kullo, Suzette J Bielinski, Rongling Li, Joshua C Denny, Peggy Peissig, Scott Hebbring, Mariza De Andrade, Marylyn D Ritchie, Gerard Tromp
BACKGROUND: We explored premature stop-gain variants to test the hypothesis that variants, which are likely to have a consequence on protein structure and function, will reveal important insights with respect to the phenotypes associated with them. We performed a phenome-wide association study (PheWAS) exploring the association between a selected list of functional stop-gain genetic variants (variation resulting in truncated proteins or in nonsense-mediated decay) and an extensive group of diagnoses to identify novel associations and uncover potential pleiotropy...
August 12, 2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27508393/phenome-wide-association-study-to-explore-relationships-between-immune-system-related-genetic-loci-and-complex-traits-and-diseases
#17
Anurag Verma, Anna O Basile, Yuki Bradford, Helena Kuivaniemi, Gerard Tromp, David Carey, Glenn S Gerhard, James E Crowe, Marylyn D Ritchie, Sarah A Pendergrass
We performed a Phenome-Wide Association Study (PheWAS) to identify interrelationships between the immune system genetic architecture and a wide array of phenotypes from two de-identified electronic health record (EHR) biorepositories. We selected variants within genes encoding critical factors in the immune system and variants with known associations with autoimmunity. To define case/control status for EHR diagnoses, we used International Classification of Diseases, Ninth Revision (ICD-9) diagnosis codes from 3,024 Geisinger Clinic MyCode® subjects (470 diagnoses) and 2,899 Vanderbilt University Medical Center BioVU biorepository subjects (380 diagnoses)...
2016: PloS One
https://www.readbyqxmd.com/read/27189611/-re-fine-drugs-an-interactive-dashboard-to-access-drug-repurposing-opportunities
#18
Soheil Moosavinasab, Jeremy Patterson, Robert Strouse, Majid Rastegar-Mojarad, Kelly Regan, Philip R O Payne, Yungui Huang, Simon M Lin
The process of discovering new drugs has been extremely costly and slow in the last decades despite enormous investment in pharmaceutical research. Drug repurposing enables researchers to speed up the process of discovering other conditions that existing drugs can effectively treat, with low cost and fast FDA approval. Here, we introduce 'RE:fine Drugs', a freely available interactive website for integrated search and discovery of drug repurposing candidates from GWAS and PheWAS repurposing datasets constructed using previously reported methods in Nature Biotechnology...
2016: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/27187070/phenome-wide-association-study-for-alcohol-and-nicotine-risk-alleles-in-26394-women
#19
Renato Polimanti, Henry R Kranzler, Joel Gelernter
To identify novel traits associated with alleles known to predispose to alcohol and nicotine use, we conducted a phenome-wide association study (PheWAS) in a large multi-population cohort. We investigated 7688 African-Americans, 1133 Asian-Americans, 14 081 European-Americans, and 3492 Hispanic-Americans from the Women's Health Initiative, analyzing alleles at the CHRNA3-CHRNA5 locus, ADH1B, and ALDH2 with respect to phenotypic traits related to anthropometric characteristics, dietary habits, social status, psychological traits, reproductive history, health conditions, and nicotine/alcohol use...
October 2016: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/27147087/phenome-wide-association-studies-as-a-tool-to-advance-precision-medicine
#20
REVIEW
Joshua C Denny, Lisa Bastarache, Dan M Roden
Beginning in the early 2000s, the accumulation of biospecimens linked to electronic health records (EHRs) made possible genome-phenome studies (i.e., comparative analyses of genetic variants and phenotypes) using only data collected as a by-product of typical health care. In addition to disease and trait genetics, EHRs proved a valuable resource for analyzing pharmacogenetic traits and developing reverse genetics approaches such as phenome-wide association studies (PheWASs). PheWASs are designed to survey which of many phenotypes may be associated with a given genetic variant...
August 31, 2016: Annual Review of Genomics and Human Genetics
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