Text data extraction for a prospective, research-focused data mart: implementation and validation.

BACKGROUND: Translational research typically requires data abstracted from medical records as well as data collected specifically for research. Unfortunately, many data within electronic health records are represented as text that is not amenable to aggregation for analyses. We present a scalable open source SQL Server Integration Services package, called Regextractor, for including regular expression parsers into a classic extract, transform, and load workflow. We have used Regextractor to abstract discrete data from textual reports from a number of 'machine generated' sources. To validate this package, we created a pulmonary function test data mart and analyzed the quality of the data mart versus manual chart review. METHODS: Eleven variables from pulmonary function tests performed closest to the initial clinical evaluation date were studied for 100 randomly selected subjects with scleroderma. One research assistant manually reviewed, abstracted, and entered relevant data into a database. Correlation with data obtained from the automated pulmonary function test data mart within the Northwestern Medical Enterprise Data Warehouse was determined. RESULTS: There was a near perfect (99.5%) agreement between results generated from the Regextractor package and those obtained via manual chart abstraction. The pulmonary function test data mart has been used subsequently to monitor disease progression of patients in the Northwestern Scleroderma Registry. In addition to the pulmonary function test example presented in this manuscript, the Regextractor package has been used to create cardiac catheterization and echocardiography data marts. The Regextractor package was released as open source software in October 2009 and has been downloaded 552 times as of 6/1/2012. CONCLUSIONS: Collaboration between clinical researchers and biomedical informatics experts enabled the development and validation of a tool (Regextractor) to parse, abstract and assemble structured data from text data contained in the electronic health record. Regextractor has been successfully used to create additional data marts in other medical domains and is available to the public.

Longitudinal evaluation of PROMIS-29 and FACIT-dyspnea short forms in systemic sclerosis.

OBJECTIVE: To assess the sensitivity of the Patient-Reported Outcomes Measurement Information System 29-item Health Profile (PROMIS-29) and the Functional Assessment of Chronic Illness Therapy-Dyspnea 10-item short form (FACIT-Dyspnea) for measuring change in health status and dyspnea in systemic sclerosis (SSc). METHODS: One hundred patients with SSc completed the PROMIS-29, FACIT-Dyspnea, and traditional instruments [Medical Research Council Dyspnea Score, St. George's Respiratory Questionnaire (SGRQ), Health Assessment Questionnaire-Disability Index (HAQ-DI), and Medical Outcomes Study Short Form-36 (SF-36)] at baseline and 1-year visits. PROMIS-29, FACIT-Dyspnea, and traditional instrument change scores were compared across composite modified Medsger Disease Severity and modified Rodnan Skin score (mRSS) change groups. RESULTS: Moderately high Spearman correlation coefficients were observed between FACIT-Dyspnea and SGRQ (r = 0.57), FACIT-Dyspnea functional limitations and SF-36 physical component summary (PCS; r = 0.51), PROMIS-29 physical functioning and HAQ-DI (r = 0.50), and SF-36 PCS (r = 0.52) change scores. In most validity comparisons, PROMIS-29, FACIT-Dyspnea, HAQ-DI, and SF-36 scores performed similarly. While PROMIS-29 covers more content areas than SF-36 (e.g., sleep), it may do so at the expense of responsiveness of its 4-item physical function scale as compared to the multiitem-derived SF-36 PCS. Statistically significant increases in SF-36 role physical (p = 0.01) and physical component scale (p = 0.016), but not PROMIS-29, were observed in patients with mRSS improvement. CONCLUSION: PROMIS-29 and FACIT-Dyspnea are valid instruments to measure health status and dyspnea in patients with SSc. In physical function assessment, longer PROMIS short forms or computer adaptive testing should be considered to improve responsiveness to the effect of skin disease changes on physical function in patients with SSc.

Serum amyloid A is a marker for pulmonary involvement in systemic sclerosis.

Inflammation in systemic sclerosis (SSc) is a prominent, but incompletely characterized feature in early stages of the disease. The goal of these studies was to determine the circulating levels, clinical correlates and biological effects of the acute phase protein serum amyloid A (SAA), a marker of inflammation, in patients with SSc. Circulating levels of SAA were determined by multiplex assays in serum from 129 SSc patients and 98 healthy controls. Correlations between SAA levels and clinical and laboratory features of disease were analyzed. The effects of SAA on human pulmonary fibroblasts were studied ex vivo. Elevated levels of SAA were found in 25% of SSc patients, with the highest levels in those with early-stage disease and diffuse cutaneous involvement. Significant negative correlations of SAA were found with forced vital capacity and diffusion capacity for carbon monoxide. Patients with elevated SAA had greater dyspnea and more frequent interstitial lung disease, and had worse scores on patient-reported outcome measures. Incubation with recombinant SAA induced dose-dependent stimulation of IL-6 and IL-8 in normal lung fibroblasts in culture. Serum levels of the inflammatory marker SAA are elevated in patients with early diffuse cutaneous SSc, and correlate with pulmonary involvement. In lung fibroblasts, SAA acts as a direct stimulus for increased cytokine production. These findings suggest that systemic inflammation in SSc may be linked to lung involvement and SAA could serve as a potential biomarker for this complication.

A candidate gene study reveals association between a variant of the Peroxisome Proliferator-Activated Receptor Gamma (PPAR-γ) gene and systemic sclerosis.

INTRODUCTION: The multifunctional nuclear receptor peroxisome proliferator-activated receptor gamma (PPAR-γ) has potent anti-fibrotic effects, and its expression and activity are impaired in patients with systemic sclerosis (SSc). We investigated PPAR-γ gene (PPARG) single nucleotide polymorphisms (SNPs) associated with SSc. METHODS: Tag SNPs spanning PPARG were genotyped in a European ancestry US discovery cohort comprising 152 SSc patients and 450 controls, with replication of our top signal in a European cohort (1031 SSc patients and 1014 controls from France). Clinical parameters and disease severity were analyzed to evaluate clinical associations with PPARG variants. RESULTS: In the discovery cohort, a single PPARG intronic SNP (rs10865710) was associated with SSc (p=0.010; odds ratio=1.52 per C allele, 95% confidence interval 1.10-2.08). This association was replicated in the French validation cohort (p=0.052; odds ratio=1.16 per C allele, 95% confidence interval 1.00-1.35). Meta-analysis of both cohorts indicated stronger evidence for association (p=0.002; odds ratio=1.22 per C allele, 95% confidence interval 1.07-1.40). The rs10865710 C allele was also associated with pulmonary arterial hypertension in the French SSc cohort (p=0.002; odds ratio=2.33 per C allele, 95% confidence interval 1.34-4.03). CONCLUSIONS: A PPARG variant is associated with susceptibility to SSc, consistent with a role of PPAR-γ in the pathogenesis of SSc.

Molecular signatures in skin associated with clinical improvement during mycophenolate treatment in systemic sclerosis.

Heterogeneity in systemic sclerosis (SSc) confounds clinical trials. We previously identified "intrinsic" gene expression subsets by analysis of SSc skin. Here we test the hypotheses that skin gene expression signatures including intrinsic subset are associated with modified Rodnan skin score (MRSS) improvement during mycophenolate mofetil (MMF) treatment. Gene expression and intrinsic subset assignment were measured in 12 SSc patients' biopsies and 10 controls at baseline, and from serial biopsies of 1 cyclophosphamide-treated patient and 9 MMF-treated patients. Gene expression changes during treatment were determined using paired t-tests corrected for multiple hypothesis testing. MRSS improved in four of seven MMF-treated patients classified as the inflammatory intrinsic subset. Three patients without MRSS improvement were classified as normal-like or fibroproliferative intrinsic subsets. A total of 321 genes (false discovery rate (FDR)<5%) were differentially expressed at baseline between patients with and without MRSS improvement during treatment. The expression of 571 genes (FDR<10%) changed between pre- and post-MMF treatment biopsies for patients showing MRSS improvement. Gene expression changes in skin are only seen in patients with MRSS improvement. Baseline gene expression in skin, including intrinsic subset assignment, may identify SSc patients whose MRSS will improve during MMF treatment, suggesting that gene expression in skin may allow targeted treatment in SSc.

The pulmonary fibrosis-associated MUC5B promoter polymorphism does not influence the development of interstitial pneumonia in systemic sclerosis.

BACKGROUND: More than 80% of patients with systemic sclerosis (SSc) develop lung involvement, most commonly interstitial pneumonia (IP). We recently identified a common variant in the promoter region of MUC5B (rs35705950) that has a significant effect on the risk of developing both familial and sporadic forms of IP. We hypothesized that this MUC5B promoter polymorphism is also associated with IP in subjects with SSc. METHODS: We examined the minor allele frequency of the MUC5B polymorphism among 231 subjects with SSc, 109 with IP, and 122 without IP. IP diagnosis was confirmed by HRCT imaging and defined as the presence of reticular infiltrates and/or honeycomb cysts. FVC and diffusing capacity of the lung for carbon monoxide (Dlco) were also assessed. RESULTS: We found no association between IP and the MUC5B polymorphism among subjects with SSc (OR = 1.1, P = .80). The frequencies of the MUC5B polymorphism among subjects with SSc with IP (10.6%) and without IP (9.4%) were similar to the frequency observed in a population of unaffected control subjects (9.0%). In secondary analyses, we found the MUC5B polymorphism was not significantly associated with either FVC (P = .42) or Dlco (P = .06). No association with SSc-associated IP was found even when we used a more conservative definition of IP (FVC ≤ 70% and evidence of reticulations or honeycombing vs SSc FVC > 70% and no evidence of reticulation or honeycombing). CONCLUSIONS: Although SSc-associated IP is clinically, radiologically, and histologically similar to other forms of IP, it appears to have distinct genetic risk factors. This study highlights the genetic and phenotypic heterogeneity of IP in general.

Validity of two new patient-reported outcome measures in systemic sclerosis: Patient-Reported Outcomes Measurement Information System 29-item Health Profile and Functional Assessment of Chronic Illness Therapy-Dyspnea short form.

OBJECTIVE: Many patient-reported outcome (PRO) instruments used in systemic sclerosis (SSc) trials are limited by lack of validation, licensing fees, and complicated scoring systems. We assessed the construct validity for discriminative purposes of 2 new PRO instruments, the Patient-Reported Outcomes Measurement Information System 29-item Health Profile (PROMIS-29) and the Functional Assessment of Chronic Illness Therapy-Dyspnea short form (FACIT-Dyspnea), measuring health status and dyspnea in SSc patients. METHODS: Seventy-three patients participated in a cross-sectional study at a tertiary SSc program. PROMIS-29, FACIT-Dyspnea, and legacy PRO instruments used in clinical trials (Medical Research Council Dyspnea Score, St. George's Respiratory Questionnaire, Health Assessment Questionnaire disability index, and Short Form 36) were administered. Composite severity scores using an adaptation of the Medsger Disease Severity Index were generated using clinical, diagnostic, and laboratory information. PROMIS-29 and FACIT-Dyspnea scores were compared with legacy PRO measures and composite severity scores. RESULTS: The mean patient age (84% women) was 51 years (range 22-72 years). The mean SSc disease duration from the onset of the first non-Raynaud's phenomenon symptom was 7.2 years (range 0-45 years). Spearman's correlation coefficients across FACIT-Dyspnea and PROMIS physical functioning scores with legacy PRO instruments were generally high (range 0.50-0.86); those between PROMIS and FACIT-Dyspnea with composite disease severity scores were more modest, but statistically significant (range 0.33-0.48, P < 0.01). CONCLUSION: PROMIS-29 and FACIT-Dyspnea are valid instruments to measure the health status of SSc patients. PROMIS-29 and FACIT-Dyspnea may be preferable to legacy instruments because they are freely available in multiple languages and simple to administer, score, and interpret.