Label-free assessment of biomarker expression using vibration spectroscopy

A biomarker, vibrational spectroscopy technique for label-free assessment of biomarker expression using vibrational spectroscopy

Pending Publication Date: 2022-04-01
VENTANA MEDICAL SYST INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

To make matters worse, unpredictable borderline cases of disease and the like can further lead to potential problems when evaluating samples

Method used

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  • Label-free assessment of biomarker expression using vibration spectroscopy
  • Label-free assessment of biomarker expression using vibration spectroscopy
  • Label-free assessment of biomarker expression using vibration spectroscopy

Examples

Experimental program
Comparison scheme
Effect test

example 1

[0198] The expression and fixation time of three different biomarkers (BCL2, FOXP3, and ki67) are presented here. Stain each fixed time tissue block for each biomarker and quantify expression across the slide using an image analysis algorithm (e.g., an algorithm suitable for quantitatively determining the expression level of each stain, For example, an automated algorithm that first segments the tissue on a slide and then identifies regions of the tissue that are not of interest; the algorithm will then automatically determine whether the tissue is positive or negative for a given protein biomarker). Figures 9A, 9B, and 9C show summary results for BCL2, ki-67, and FOXP3, respectively, in the form of box-and-whisker plots and at fixed times. BCL2 and FOXP3 were found to be particularly unstable and susceptible to inappropriate fixation, with their expression levels increasing steadily and monotonically with fixation time.

[0199] On the other hand, ki-67 was found to be relat...

example 2

[0202] MirrIR microscope slides (Kevley Technologies, Chesterland, OH) for reflectance infrared studies were used for mid-IR spectroscopy measurements. Four-micron serial sections of formalin-fixed, paraffin-embedded (FFPE) tonsil tissue were mounted on pretreated MirrIR slides. Dewax the tonsil tissue manually according to OP2100-025. Briefly, after the xylene step, slides were hydrated through a decreasing gradient of ethanol and then transferred to a Rapid Antigen Retrieval (RAR) bench in VENTANA Cell Conditioner 1 (CC1) solution.

[0203] Perform antigen retrieval in CC1 solution in the RAR chamber, which is prepressurized to 30 psi before turning on the heater. The total heating time for any given experiment consists of a 90 s ramp up time and a 2 min cool down time. After the antigen retrieval step, slides were gently washed in deionized water and air dried at room temperature. Dried slides with intact tonsil tissue were used for mid-IR measurements. Single antigen r...

example 3

[0207] Example 3 – Estimating Biomarker Expression Using a Trained Biomarker Expression Estimation Engine

[0208] the summary of instruction

[0209] This experiment utilizes mid-infrared (mid-IR) spectroscopy to examine the vibrational state of molecules in histological tissue sections. In this work, changes in mid-IR spectra caused by differential repair of tonsil tissue are investigated and used to train a biomarker expression estimation engine. Identified shifts in the Mid-IR spectrum correlate with immunohistochemical (IHC) staining for Ki-67 and C4d proteins.

[0210] introduce

[0211] Mid-infrared spectroscopy (mid-IR) is a powerful optical technique that probes the vibrational states of individual molecules in tissues and is very sensitive to the conformational state of proteins. This extreme sensitivity makes mid-IR spectroscopy ideal for microscopy applications, as the presence of endogenous and exogenous materials and even conformational states can be rev...

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Abstract

The present disclosure relates to automated systems and methods for predicting expression of one or more biomarkers in a sample of biological samples. In some embodiments, the sample is a sample having an unknown immobilization state, or a sample subjected to an unknown immobilization duration. In some embodiments, the predicted expression is a quantitative estimate of a positive percentage of one or more biomarkers. In other embodiments, the predicted expression is a quantitative estimate of staining intensity of one or more biomarkers. In some embodiments, the systems and methods utilize a trained biomarker expression estimation engine that has been trained with a plurality of training samples, where the trained biomarker expression estimation engine is adapted to derive biomarker expression characteristics from the samples. In some embodiments, the trained biomarker expression estimation engine includes a machine learning algorithm based on projection to a potential structure regression model. In some embodiments, the trained biomarker expression estimation engine includes a neural network.

Description

[0001] Cross references to related patent applications [0002] This application claims the benefit of the filing date of U.S. Patent Application Serial No. 62 / 892,680, filed August 28, 2019, the disclosure of which is incorporated herein by reference in its entirety. Background technique [0003] Disease diagnosis based on the interpretation of tissue or cell samples taken from diseased organisms has grown enormously over the past few years. In situ techniques such as in situ hybridization (ISH) and in situ polymerase chain reaction are now used to help diagnose human disease states and elucidate genes in tissue sites, in addition to traditional tissue staining techniques and immunohistochemical (IHC) assays expression site. Therefore, there are a variety of techniques to assess not only cell morphology, but also the presence of specific molecules (for example, DNA, RNA, and proteins) within cells and tissues. Each of these techniques requires sample cells or tissues to und...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N21/35G01N21/65
CPCG01N21/65G01N21/35G01N2201/1296G06V20/695G06V10/82G06V10/774G01N21/3577
Inventor D·鲍尔
Owner VENTANA MEDICAL SYST INC
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