title: A single biopsy is valid for genetic diagnosis of eosinophilic esophagitis regardless of tissue preservation or location in the esophagus.
abstract: OBJECTIVE
  A new gene expression profile test may distinguish eosinophilic esophagitis (EoE) and gastroesophageal reflux disease (GERD), but the optimal tissue preparation and biopsy location are unknown. We aimed to determine if formalin-fixed paraffin-embedded (FFPE) and RNA-later (RNAL) preserved specimens from newly diagnosed EoE patients have equivalent gene expression scores and whether scores vary by esophageal biopsy location.
  
  
  METHODS
  We analyzed prospectively collected and banked esophageal biopsies from EoE patients and GERD controls. Paired FFPE and RNAL samples from the distal, mid, and proximal esophagus were used. RNA was extracted, and gene expression for a previously constructed 96 gene panel was quantified with a summary expression score. Scores were compared between EoE and GERD patients, between FFPE and RNAL samples, and between the different esophageal locations.
  
  
  RESULTS
  A total of 72 samples, representing paired FFPE and RNAL specimens from 9 EoE cases and 3 GERD controls, were analyzed. Overall median gene expression scores were similar between FFPE and RNAL (238 vs 227; p=0.64), correlation was excellent between FFPE and RNAL (Spearman's rho=0.90; p<0.001), and there were no differences by biopsy level. Median gene scores distinguished EoE from controls (134 vs 402; p=0.02), and overall agreement between preservation methods and EoE case status was perfect (kappa=1.0; p<0.001).
  
  
  CONCLUSIONS
  Gene expression scores were equivalent in FFPE and RNAL, and were also similar across three esophageal locations. This implies that a single biopsy in either FFPE or RNAL from anywhere in the esophagus may have the potential for genetic diagnosis of EoE.
authors.affiliation: Center for Esophageal Diseases and Swallowing; Center for Gastrointestinal Biology and Disease, Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA. edellon@med.unc.edu.
authors.forename: Evan S
authors.initials: ES
authors.lastname: Dellon
authors.affiliation: Diagnovus, Nashville, TN, USA.
authors.forename: Vivek
authors.initials: V
authors.lastname: Yellore
authors.affiliation: Diagnovus, Nashville, TN, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Andreatta
authors.affiliation: Diagnovus, Nashville, TN, USA.
authors.forename: James
authors.initials: J
authors.lastname: Stover
mesh_terms: D000328:Adult; D000368:Aged; D001706:Biopsy; D016022:Case-Control Studies; D057765:Eosinophilic Esophagitis / Q000175:diagnosis / Q000235:genetics*; D004947:Esophagus / Q000737:chemistry* / Q000473:pathology; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D006801:Humans; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D011237:Predictive Value of Tests; D011446:Prospective Studies; D055815:Young Adult
chemical_list: D005819:Genetic Markers