Cohort generation and data extraction

The Children’s Hospital of Philadelphia (CHOP) network is both an international referral center and a provider of primary and sub-specialty care services to patients residing in the greater Delaware Valley. Our primary care network, consisting of 31 sites, has been validated as an accurate tool for estimating disease rates across our broader community population.⁽²⁰⁾ The Allergy Section at Children’s Hospital of Philadelphia (CHOP), which includes six care locations, is the largest provider of sub-specialty allergy care services in the region. In addition, it is an international referral center for eosinophilic esophagitis and has developed one of the largest pediatric cohorts for this condition through the Center for Pediatric Eosinophilic Diseases.

To examine the epidemiologic relationship between EoE and members of the allergic march, we extracted electronic medical record (EMR) data from 1/1/2001 to 12/31/2017 for patients seen in the CHOP primary care network. A single outpatient EMR system was used during this time period (EMR; Epic Systems, Verona, WI). Direct patient identifiers (e.g., medical record numbers and names) were removed to create a dataset with only limited identifiers (e.g. date of birth and dates of healthcare encounters). Data analyses were completed using R version 3.3.2. (R Foundation, Vienna, Austria). We identified an EMR-based virtual primary care birth cohort of 130,435 children who established care in our primary care network before their first birthday, and between 1/1/2001 and 12/31/2015. To ensure adequate follow-up to assess the outcomes of interest, we excluded individuals who received primary care from a CHOP-affiliated practice for less than 2 years (i.e., their last office visit occurred less than 2 years after their first office visit). Observation time for children was censored on the date of their last face-to-face outpatient healthcare encounter in our health system prior to their 17^th birthday, and we assumed patients were observed continuously until they were censored.