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 clinician features not captured in coded data alone. We performed sentiment analysis on 2,484 hospital discharge notes for 2,010 individuals from a psychiatric inpatient unit, as well as 20,859 hospital discharges for 15,011 individuals from general medical units, in a large New England health system between January 2011 and 2014. The primary measures of sentiment captured intensity of subjective positive or negative sentiment expressed in the discharge notes. Mean scores were contrasted between sociodemographic and clinical groups in mixed effects regression models. Discharge note sentiment was then examined for association with risk for readmission in Cox regression models. Discharge notes for individuals with greater medical comorbidity were modestly but significantly lower in positive sentiment among both psychiatric and general medical cohorts (p<0.001 in each). Greater positive sentiment at discharge was associated with significantly decreased risk of hospital readmission in each cohort (~12% decrease per standard deviation above the mean). Automated characterization of discharge notes in terms of sentiment identifies differences between sociodemographic groups, as well as in clinical outcomes, and is not explained by differences in diagnosis. Clinician sentiment merits investigation to understand why and how it reflects or impacts outcomes.
Typically, algorithms to classify phenotypes using electronic medical record (EMR) data were developed to perform well in a specific patient population. There is increasing interest in analyses which ...can allow study of a specific outcome across different diseases. Such a study in the EMR would require an algorithm that can be applied across different patient populations. Our objectives were: (1) to develop an algorithm that would enable the study of coronary artery disease (CAD) across diverse patient populations; (2) to study the impact of adding narrative data extracted using natural language processing (NLP) in the algorithm. Additionally, we demonstrate how to implement CAD algorithm to compare risk across 3 chronic diseases in a preliminary study.
We studied 3 established EMR based patient cohorts: diabetes mellitus (DM, n = 65,099), inflammatory bowel disease (IBD, n = 10,974), and rheumatoid arthritis (RA, n = 4,453) from two large academic centers. We developed a CAD algorithm using NLP in addition to structured data (e.g. ICD9 codes) in the RA cohort and validated it in the DM and IBD cohorts. The CAD algorithm using NLP in addition to structured data achieved specificity >95% with a positive predictive value (PPV) 90% in the training (RA) and validation sets (IBD and DM). The addition of NLP data improved the sensitivity for all cohorts, classifying an additional 17% of CAD subjects in IBD and 10% in DM while maintaining PPV of 90%. The algorithm classified 16,488 DM (26.1%), 457 IBD (4.2%), and 245 RA (5.0%) with CAD. In a cross-sectional analysis, CAD risk was 63% lower in RA and 68% lower in IBD compared to DM (p<0.0001) after adjusting for traditional cardiovascular risk factors.
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 was low. Preliminary data suggest that CAD risk was significantly lower in RA and IBD compared to DM.
Abstract
Background
The gut-selective nature of vedolizumab has raised questions regarding increased joint pain or arthralgia with its use in inflammatory bowel disease (IBD) patients. As arthralgias ...are seldom coded and thus difficult to study, few studies have examined the comparative risk of arthralgia between vedolizumab and tumor necrosis factor inhibitor (TNFi). Our objectives were to evaluate the application of natural language processing (NLP) to identify arthralgia in the clinical notes and to compare the risk of arthralgia between vedolizumab and TNFi in IBD.
Methods
We performed a retrospective study using a validated electronic medical record (EMR)-based IBD cohort from 2 large tertiary care centers. The index date was the first date of vedolizumab or TNFi prescription. Baseline covariates were assessed 1 year before the index date; patients were followed 1 year after the index date. The primary outcome was arthralgia, defined using NLP. Using inverse probability of treatment weight to balance the cohorts, we then constructed Cox regression models to calculate the hazard ratio (HR) for arthralgia in the vedolizumab and TNFi groups.
Results
We studied 367 IBD patients on vedolizumab and 1218 IBD patients on TNFi. Patients on vedolizumab were older (mean age, 41.2 vs 34.9 years) and had more prevalent use of immunomodulators (52.3% vs 31.9%) than TNFi users. Our data did not observe a significantly increased risk of arthralgia in the vedolizumab group compared with TNFi (HR, 1.20; 95% confidence interval, 0.97-1.49).
Conclusions
In this large observational study, we did not find a significantly increased risk of arthralgia associated with vedolizumab use compared with TNFi.
The availability of monoclonal antibodies to tumor necrosis factor α has revolutionized management of Crohn's disease (CD) and ulcerative colitis. However, limited data exist regarding comparative ...effectiveness of these agents to inform clinical practice.
This study consisted of patients with CD or ulcerative colitis initiation either infliximab (IFX) or adalimumab (ADA) between 1998 and 2010. A validated likelihood of nonresponse classification score using frequency of narrative mentions of relevant symptoms in the electronic health record was applied to assess comparative effectiveness at 1 year. Inflammatory bowel disease-related surgery, hospitalization, and use of steroids were determined during this period.
Our final cohort included 1060 new initiations of IFX (68% for CD) and 391 of ADA (79% for CD). In CD, the likelihood of nonresponse was higher in ADA than IFX (odds ratio, 1.62 and 95% CI, 1.21-2.17). Similar differences favoring efficacy of IFX were observed for the individual symptoms of diarrhea, pain, bleeding, and fatigue. However, there was no difference in inflammatory bowel disease-related surgery, hospitalizations, or prednisone use within 1 year after initiation of IFX or ADA in CD. There was no difference in narrative or codified outcomes between the 2 agents in ulcerative colitis.
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 these treatments are broadly comparable in effectiveness in routine clinical practice.
To optimally leverage the scalability and unique features of the electronic health records (EHR) for research that would ultimately improve patient care, we need to accurately identify patients and ...extract clinically meaningful measures. Using multiple sclerosis (MS) as a proof of principle, we showcased how to leverage routinely collected EHR data to identify patients with a complex neurological disorder and derive an important surrogate measure of disease severity heretofore only available in research settings.
In a cross-sectional observational study, 5,495 MS patients were identified from the EHR systems of two major referral hospitals using an algorithm that includes codified and narrative information extracted using natural language processing. In the subset of patients who receive neurological care at a MS Center where disease measures have been collected, we used routinely collected EHR data to extract two aggregate indicators of MS severity of clinical relevance multiple sclerosis severity score (MSSS) and brain parenchymal fraction (BPF, a measure of whole brain volume).
The EHR algorithm that identifies MS patients has an area under the curve of 0.958, 83% sensitivity, 92% positive predictive value, and 89% negative predictive value when a 95% specificity threshold is used. The correlation between EHR-derived and true MSSS has a mean R(2) = 0.38±0.05, and that between EHR-derived and true BPF has a mean R(2) = 0.22±0.08. To illustrate its clinical relevance, derived MSSS captures the expected difference in disease severity between relapsing-remitting and progressive MS patients after adjusting for sex, age of symptom onset and disease duration (p = 1.56×10(-12)).
Incorporation of sophisticated codified and narrative EHR data accurately identifies MS patients and provides estimation of a well-accepted indicator of MS severity that is widely used in research settings but not part of the routine medical records. Similar approaches could be applied to other complex neurological disorders.
Summary
Background
The prevalence of older adults with inflammatory bowel diseases (IBD) is increasing. Frailty is an important predictor of outcomes in many chronic disease states. The implications ...of frailty have not been well‐delineated in IBD.
Aims
To report the prevalence of a frailty‐associated diagnosis and determine the association between frailty and mortality in a cohort of IBD patients.
Methods
In a cohort of 11 001 IBD patients, we applied a validated definition of frailty using International Classification of Disease codes. We compared frail IBD patients to those without a frailty‐related code (“fit”). We constructed multivariable logistic regression models adjusting for clinically pertinent confounders (age, gender, race, IBD type, follow‐up, IBD‐related surgery, ≥1 comorbidity in the Charlson comorbidity index CCI, and immunosuppression use) to determine whether frailty predicts mortality.
Results
A total of 675 (6%) IBD patients had a frailty‐related diagnosis. The prevalence of frailty increased with age, rising from 4% in 20‐29 year olds to 25% in patients 90 years or older. The most prevalent frailty diagnosis was protein‐energy malnutrition. The strongest predictors of frailty were non‐IBD comorbidity, all‐cause and IBD‐related, hospitalisations. Frailty remained independently associated with mortality after adjusting for age, sex, duration of follow‐up, comorbidity, need for IBD‐related surgery and immunosuppression (OR: 2.90, 95% CI: 2.29‐3.68).
Conclusions
Frailty is prevalent in IBD patients and increases with age. Frailty nearly triples the odds of mortality for IBD patients. Risk stratifying patients by frailty may improve outcomes.
Infections are an important adverse effect of immunosuppression for treatment of inflammatory bowel diseases (IBDs). However, risk of infection cannot be sufficiently determined based on patients’ ...ages or comorbidities. Frailty has been associated with outcomes of patients with other inflammatory diseases. We aimed to determine the association between frailty and risk of infections after immunosuppression for IBD.
We performed a cohort study of 11,001 patients with IBD, using a validated frailty definition based on International Classification of Disease codes to identify patients who were frail vs fit in the 2 years before initiation of an anti–tumor necrosis factor (TNF) or immunomodulator therapy, from 1996 through 2010. Our primary outcome was an infection in the first year after treatment. We constructed multivariable logistic regression models, adjusting for clinically pertinent confounders (age, comorbidities, steroid use, and combination therapy) to determine the association between frailty and posttreatment infections.
There were 1299 patients treated with an anti-TNF agent and 2676 patients treated with an immunomodulator. In this cohort, 5% of patients who received anti-TNF therapy and 7% of patients who received an immunomodulator were frail in the 2 years before immunosuppression. Frail patients were older and had more comorbidities. Higher proportions of frail patients developed infections after treatment (19% after TNF and 17% after immunomodulators) compared with fit patients (9% after TNF and 7% after immunomodulators; P < .01 for frail vs fit in both groups). Frail patients had an increased risk of infection after we adjusted for age, comorbidities, and concomitant medications (anti-TNF adjusted odds ratio, 2.05 95% confidence interval, 1.07–3.93 and immunomodulator adjusted odds ratio, 1.81 95% confidence interval, 1.22–2.70).
Frailty was associated with infections after immunosuppression in patients with IBD after we adjust for age and comorbidities. Systematic assessment and strategies to improve frailty might reduce infection risk in patients with IBD.
Display omitted
Introduction
Crohn’s disease (CD) and ulcerative colitis (UC) are associated with considerable direct healthcare costs. There have been few comprehensive analyses of all IBD- and non-IBD ...comorbidities that determine direct costs in this population.
Methods
We used data from a validated cohort of patients with inflammatory bowel disease (IBD). Total healthcare costs were estimated as a sum of costs associated with IBD-related hospitalizations and surgery, imaging (CT or MR scans), outpatient visits, endoscopic evaluation, and emergency room (ER) care. All ICD-9 codes were extracted for each patient and clustered into 1804 distinct phecode clusters representing individual phenotypes. A phenome-wide association analysis (PheWAS) was performed using logistic regression to identify predictors of being in the top decile of costs.
Results
Our cohort is comprised of 10,721 patients with IBD among whom 50% had CD. The median age was 46 years. The median total cost per patient is $11,203 (IQR $2396–30,563). The strongest association with total healthcare costs was intestinal obstruction without mention of hernia (
p
= 5.93 × 10
−156
) and other intestinal obstruction (
p
= 9.24 × 10
−131
). In addition, strong associations were observed for symptoms consistent with severity of IBD including the presence of fluid–electrolyte imbalance (
p
= 1.90 × 10
−130
), hypovolemia (
p
= 1.65 × 10
−114
), abdominal pain (
p
= 7.29 × 10
−60
), and anemia (
p
= 1.90–10
−83
). Cardiopulmonary diseases and psychological comorbidity also demonstrated significant associations with total costs with the latter being more strongly associated with ER visit-related costs.
Conclusions
Surrogate markers suggesting possible irreversible bowel damage and active disease demonstrate the greatest influence on IBD-related healthcare costs.
PDF
