Andrew Cagan
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View article: Genetic sex validation for sample tracking in next-generation sequencing clinical testing
Genetic sex validation for sample tracking in next-generation sequencing clinical testing Open
Objective Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of bot…
View article: Validation of Real-World Case Definitions for COVID-19 Diagnosis and Severe COVID-19 Illness Among Patients Infected with SARS-CoV-2: Translation of Clinical Trial Definitions to Real-World Settings
Validation of Real-World Case Definitions for COVID-19 Diagnosis and Severe COVID-19 Illness Among Patients Infected with SARS-CoV-2: Translation of Clinical Trial Definitions to Real-World Settings Open
Purpose This study assessed the performance of International Classification of Diseases 10th Revision, Clinical Modification (ICD-10-CM) coronavirus disease 2019 (COVID-19) diagnostic code U07.1 against polymerase chain reaction (PCR) test…
View article: Multi-ancestry genome- and phenome-wide association studies of diverticular disease in electronic health records with natural language processing enriched phenotyping algorithm
Multi-ancestry genome- and phenome-wide association studies of diverticular disease in electronic health records with natural language processing enriched phenotyping algorithm Open
Objective Diverticular disease (DD) is one of the most prevalent conditions encountered by gastroenterologists, affecting ~50% of Americans before the age of 60. Our aim was to identify genetic risk variants and clinical phenotypes associa…
View article: The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics
The Mass General Brigham Biobank Portal: an i2b2-based data repository linking disparate and high-dimensional patient data to support multimodal analytics Open
Objective Integrating and harmonizing disparate patient data sources into one consolidated data portal enables researchers to conduct analysis efficiently and effectively. Materials and Methods We describe an implementation of Informatics …
View article: Association Between Inflammation, Incident Heart Failure, and Heart Failure Subtypes in Patients With Rheumatoid Arthritis
Association Between Inflammation, Incident Heart Failure, and Heart Failure Subtypes in Patients With Rheumatoid Arthritis Open
Objective In rheumatoid arthritis (RA), there are limited data on risk factors for the clinical heart failure (HF) subtypes of HF with reduced ejection fraction (HFrEF) and HF with preserved ejection fraction (HFpEF). This study examined t…
View article: Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm
Multi-ancestry Genome- and Phenome-wide Association Studies of Diverticular Disease in Electronic Health Records with Natural Language Processing enriched phenotype algorithm Open
Background and aims Diverticular disease is among the most prevalent conditions encountered by gastroenterologists, affecting ∼50% of Americans before the age of 60. Our aim was to identify genetic risk variants and clinical phenotypes ass…
View article: Impact of ICD10 and secular changes on electronic medical record rheumatoid arthritis algorithms
Impact of ICD10 and secular changes on electronic medical record rheumatoid arthritis algorithms Open
Objective The objective of this study was to compare the performance of an RA algorithm developed and trained in 2010 utilizing natural language processing and machine learning, using updated data containing ICD10, new RA treatments, and a…
View article: The Association Between Arthralgia and Vedolizumab Using Natural Language Processing
The Association Between Arthralgia and Vedolizumab Using Natural Language Processing Open
In this large observational study, we did not find a significantly increased risk of arthralgia associated with vedolizumab use compared with TNFi.
View article: Association Between Anti–Citrullinated Fibrinogen Antibodies and Coronary Artery Disease in Rheumatoid Arthritis
Association Between Anti–Citrullinated Fibrinogen Antibodies and Coronary Artery Disease in Rheumatoid Arthritis Open
Objective Antibodies against citrullinated fibrinogen (anti–Cit‐fibrinogen) have been implicated in rheumatoid arthritis ( RA ) and associated with cardiovascular risk in RA . The objective of this study was to examine the association betw…
View article: Validation of a risk stratification tool for fall-related injury in a state-wide cohort
Validation of a risk stratification tool for fall-related injury in a state-wide cohort Open
Objective A major preventable contributor to healthcare costs among older individuals is fall-related injury. We sought to validate a tool to stratify such risk based on readily available clinical data, including projected medication adver…
View article: Phenome‐Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis
Phenome‐Wide Association Study of Autoantibodies to Citrullinated and Noncitrullinated Epitopes in Rheumatoid Arthritis Open
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 examine…
View article: Comparative Effectiveness of Infliximab and Adalimumab in Crohnʼs Disease and Ulcerative Colitis
Comparative Effectiveness of Infliximab and Adalimumab in Crohnʼs Disease and Ulcerative Colitis Open
We identified a modestly higher likelihood of symptomatic nonresponse at 1 year for ADA compared with IFX in patients with CD. However, there were no differences in inflammatory bowel disease-related surgery or hospitalizations, suggesting…
View article: The Biobank Portal for Partners Personalized Medicine: A Query Tool for Working with Consented Biobank Samples, Genotypes, and Phenotypes Using i2b2
The Biobank Portal for Partners Personalized Medicine: A Query Tool for Working with Consented Biobank Samples, Genotypes, and Phenotypes Using i2b2 Open
We have designed a Biobank Portal that lets researchers request Biobank samples and genotypic data, query associated electronic health records, and design and download datasets containing de-identified attributes about consented Biobank su…
View article: Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort
Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort Open
Narrative data in an electronic health record offer considerable potential to define temporally evolving disease outcomes such as nonresponse to treatment.
View article: Sentiment Measured in Hospital Discharge Notes Is Associated with Readmission and Mortality Risk: An Electronic Health Record Study
Sentiment Measured in Hospital Discharge Notes Is Associated with Readmission and Mortality Risk: An Electronic Health Record Study Open
Natural language processing tools allow the characterization of sentiment--that is, terms expressing positive and negative emotion--in text. Applying such tools to electronic health records may provide insight into meaningful patient or cl…
View article: Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts
Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts Open
We developed and validated a CAD algorithm that performed well across diverse patient populations. The addition of NLP into the CAD algorithm improved the sensitivity of the algorithm, particularly in cohorts where the prevalence of CAD wa…
View article: Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases
Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases Open
EHR cohorts form valuable data sources for examining genotype-phenotype relationships. Vitamin D risk alleles explain 3% of the variance in vitamin D levels in patients with IBD.
View article: Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases
Diabetes and the risk of infections with immunomodulator therapy in inflammatory bowel diseases Open
Summary Background Infections are an important concern in patients using immunosuppressive therapy for their inflammatory bowel disease ( IBD ). Diabetes affects nearly 10% of Americans. Whether it confers an additional risk with immunosup…
View article: TYK2 Protein-Coding Variants Protect against Rheumatoid Arthritis and Autoimmunity, with No Evidence of Major Pleiotropic Effects on Non-Autoimmune Complex Traits
TYK2 Protein-Coding Variants Protect against Rheumatoid Arthritis and Autoimmunity, with No Evidence of Major Pleiotropic Effects on Non-Autoimmune Complex Traits Open
Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challen…
View article: A Clinical Perspective on the Relevance of Research Domain Criteria in Electronic Health Records
A Clinical Perspective on the Relevance of Research Domain Criteria in Electronic Health Records Open
These findings show that a computationally derived tool based on RDoC workgroup reports identifies symptom distributions in clinician notes beyond those captured by ICD-9 codes, and these domains have significant predictive validity. More …