A Diagnostic Tool for Assessment of Genetic Abnormalities as Indicators of Malignancy

Identification of Barrett’s esophagus (BE) patients at greatest risk for having or progressing to esophageal adenocarcinoma (EAC) is complicated. Difficulties related to histological diagnosis by endoscopic biopsy include incomplete sampling, lengthy procedure time, and variability between clinics and pathologists in classifying dysplasia at both the high-grade and low-grade ends of the spectrum.1-3 Histology does not precisely predict progression.2 Further, some EAC develops without detection of earlier stages of dysplasia.4 NeoGenomics employs Vysis FISH probes in a four-probe panel to detect gains and losses of MYC (8q24), p16 (CDKN2A at 9p21), HER2 (ERBB2 at 17q12), and ZNF217 (20q13) associated with higher-risk disease.

  • NeoSITE B.E. is a FISH assay performed on cytology brushings from Barrett’s esophagus to differentiate cases at high risk of cancer from those at low risk. It is available as a global or tech-only test.
  • It compares patterns of chromosomal gain and loss in the patient’s sample to known patterns suggestive of either esophageal adenocarcinoma and high-grade dysplasia (EAC/HGD) or low-grade dysplasia and non-dysplasia (LGD/ND).
  • This test has sensitivity of 86% and specificity of 67% for differentiating the high-risk from the low-risk groups.

Numerous studies over the last decade have confirmed the associations of each of the four loci tested with progression of BE. The ability of this combined four-probe set to distinguish various grades of BE was firmly established in 2006 by Brankley et al.2 This group and others, including NeoGenomics, have demonstrated that the frequency and variety of chromosome abnormalities are not only correlated with the general level of dysplasia,2,5-8 but that they increase within individual patients as the lesions progress.7,9 This indicates a patient-specific FISH result can be useful to assess an individual’s risk.


Uses and Benefits of NeoSITE B.E.

NeoSITE B.E. serves as an ancillary test that adds the discriminatory power of genetic data to these critical tasks in managing BE:

  • Determining the risk of having HGD or EAC NeoSITE B.E. enhances the morphologic diagnosis of EAC or HGC.

Positive test results with concordant morphology together support aggressive treatment decisions. NeoSITE B.E. confirms histology when results are concordant, and suggests further investigation is needed when results differ from histology.

  • Determining the prognosis of BE

NeoSITE B.E. identifies genetic abnormalities in patients with BE, and provides indication of progression requiring additional procedures and specific management.

  • Differentiating between patients with low-grade dysplasia and high-grade dysplasia

NeoSITE B.E. provides an objective means for determining whether the patient has LGD vs. HGD when making decisions about aggressive treatment options.

Because NeoSITE B.E. is performed on cytology brushings rather than biopsies, collection is rapid and a larger area of BE can be sampled.


NeoSite B.E

A normal esophageal cell nucleus
with the expected two signals from each probe

NeoSite BE

Normal FISH results in nuclei of an
esophageal cytology brushing


NeoSite BE

An abnormal esophageal cell nucleus
with one p16 signal missing an extra
signal from all other probe

NeoSite BE

Esophageal brushing with majority of nuclei
demonstrating FISH abnormalities

Testing Process

Clients are encouraged to collect separate brushings from nodular areas of BE, if present, and the complete affected area (pan brushing). The sample brushed from the nodules will be analyzed first, and reported as the final result if positive. If negative, the pan brushing will be analyzed and both results will be reported.

Signals from all probes are counted and interpreted with an internally-derived algorithm. Sensitivity is 86% and specificity is 67% for differentiating high-risk EAC/HGD samples from low-risk LGD/ND samples according to NeoGenomics’ validation in specimens of all grades of BE. Sensitivity and specificity are higher when only nodules rather than the entire Barrett’s area are brushed. Data collection is continuing and test performance data will be updated periodically.


Ordering Information


Specimen Collection and Processing:

Two vials of PreservCyt are required and may be requested from NeoGenomics in the NeoSITE B.E. Collection Kit. Please see detailed collection and processing instructions in the kit, or in the printable Specimen Requirements or Test Guide below.


Turnaround Time:

3-5 days


Level of Service:

NeoSITE B.E. can be ordered as a global or tech-only test.
Print Test Description & Specimen Requirements
Contact us for more information about this test


Notes on Test Use:

  • Cytology studies are not performed at NeoGenomics and should be performed, if needed, by the referring institution on additional samples.
  • This test does not differentiate high-grade dysplasia from adenocarcinoma, nor does it differentiate between normal mucosa, intestinal metaplasia, and low-grade dysplasia.
  • This test is also not for determining likelihood of response to trastuzumab in gastroesophageal junction cancer. NeoGenomics offers separate HER2 FISH testing on FFPE biopsy specimens for this purpose. Please see details here.


  • Bennett C, Vakil N, Bergman J, et al. Consensus statements for management of Barrett’s dysplasia and early-stage esophageal adenocarcinoma, based on a Delphi process. Gastroent. 2012;143:336-346.
  • Brankley SM, Wang KK, Harwood AR, et al. The development of a fluorescence in situ hybridization assay for the detection of dysplasia and adenocardinoma in Barrett’s esophagus. J Mol Diag. 2006;8(2):260-267.
  • Voltaggio L, Montgomery EA, Lam-Himlin Dora. A clinical and histopathologic focus on Barrett esophgagus and Barrett-related dysplasia.Arch Pathol Lab Med. 2011;135:1249-1260.
  • Wiseman EA, Ang YS. Risk factors for neoplastic progression in Barrett’s esophagus. World J Gastroenterol. 2011;17(32):3672-3683.
  • Bulsiewicz W, Carlson G, Chouinard T, et al. Detection of esophageal adenocarcinoma (EAC) by a four-probe fluorescence in situ hybridization (FISH) assay. Am J Gastroent. 2011;106:S584-S611, abstract 59.
  • Phillips WA, Lord RV, Nancarrow DJ, et al. Barrett’s esophagus. J Gastroent Hep. 2011;26:639-648.
  • Barr Fritcher EG, Brankley SM, Kipp BR, et al. A comparison of conventional cytology, DNA ploidy analysis, and fluorescence in situ hybridization for the detection of dysplasia and adenocarcinoma in patients with Barrett’s esophagus. Hum Pathol. 2008;39(8):1128-1135.
  • Brankley SM, Barr Fritcher EG, Smyrk TC, et al. Fluorescence in situ hybridization mapping of esophagectomy specimens from patients with Barrett’s esophagus with high-grade dysplasia or adenocarcinoma. Hum Pathol. 2012;43:172-179.
  • Bulsiewicz W, Carlson G, Chouinard T, et al. DNA abnormalities in benign Barrett’s esophagus (BE) are associated with subsequent progression to esophageal adenocarcinoma (EAC). Am J Gastroent. 2011;106:S584-S611, abstract 79.