US 12,442,819 B2
Methods of predicting progression of Barrett's esophagus
Rebecca J. Thorne, Pittsburgh, PA (US)
Assigned to CERNOSTICS, INC., Bethlehem, PA (US)
Filed by Cernostics, Inc., Bethlehem, PA (US)
Filed on Mar. 12, 2021, as Appl. No. 17/200,260.
Application 17/200,260 is a continuation of application No. 15/778,403, granted, now 10,962,544, previously published as PCT/US2016/063482, filed on Nov. 23, 2016.
Claims priority of provisional application 62/260,010, filed on Nov. 25, 2015.
Prior Publication US 2022/0034894 A1, Feb. 3, 2022
This patent is subject to a terminal disclaimer.
Int. Cl. G01N 33/574 (2006.01)
CPC G01N 33/57484 (2013.01) [G01N 33/57446 (2013.01); G01N 2800/56 (2013.01)] 13 Claims
 
1. A method comprising:
a) labeling cell nuclei in an upper gastrointestinal sample from a subject with a panel of reagents;
b) labeling a plurality of biomarkers in the sample, wherein the plurality of biomarkers are p53, HIF-1α, COX2, p16, alpha-methylacyl-CoA racemase (AMACR), CD68, CD45RO, K20, and HER2/neu;
c) detecting the labeled plurality of biomarkers and cell nuclei with an optical scanner;
d) generating digital image data from the detected labeled plurality of biomarkers and cell nuclei;
e) analyzing the labeled sample using a digital image platform for multi-channel fluorescence whole slide imaging to produce high dimensional quantitative image analysis features; and
f) analyzing the image analysis features associated with the plurality of biomarkers and cell nuclei, wherein the image analysis features are p53 nuclear sum intensity, p53 nuclear mean intensity, ratio of mean HER2/neu intensity:mean K20 intensity in nuclei clusters, ratio of 95th quantile HER2/neu intensity:95th quantile K20 intensity in nuclei clusters, coexpression cellular COX2 and CD68, p53 mean intensity in nuclei clusters, nuclear solidity in p53-overexpressing p16-negative cells, CD45RO plasma membrane sum intensity, AMACR microenvironment standard deviation, COX2 texture in cytoplasm, HIF-1α microenvironment cell mean intensity, HIF-1α microenvironment cell moment (product of mean and standard deviation), p16 cytoplasm mean intensity, nuclear area in p53-overexpressing p16-negative cells, and Hoechst nuclear 95th quantile intensity.