Methods to determine carcinogenesis, identify markers for early cancer diagnosis and identify targets of therapy
AssigneeVisible Genomics, LLC
InventorsJames M. Barbeau, John S. DePaolo
Life of this patent
Estimating the term…
Abstract
Methods and techniques to identify carcinogenesis pathways and markers for early cancer diagnosis. Cell sampling is performed on a single tumor with multiple samples being taken from the tumor and outward toward the periphery and beyond. Large scale analysis is performed, such as whole genomic sequencing, to identify the differences between the cells of the various samples. The differences are evaluated to determine which differences represent a change along the carcinogenesis pathway.
Claims14
A method of analyzing carcinogenesis of a tumor, comprising the steps of:
- removing at least a portion of the tumor and a portion of normal tissue surrounding the tumor as a tissue block;
- flash freezing the tissue block;
- sectioning the tissue block into a plurality of vertical sections;
- staining alternating vertical sections with hematoxylin and eosin;
- collecting cell samples from unstained vertical sections using the stained vertical sections as guides and a microdissector, wherein the cell samples are taken from the normal tissue, from a border region between a pre-neoplastic dysplastic region and the normal tissue, from the pre-neoplastic dysplastic region, and from within the tumor;
- isolating DNA from the cell samples;
- preparing a DNA library from the isolated DNA;
- sequencing the DNA library;
- aligning sequences obtained from the sequencing;
- and
- comparing sequences from the cell samples to identify genetic differences between cell samples taken from different tissue regions,
- wherein the cell sample taken from the normal tissue is used as a baseline for the comparison between sequences.
A method of analyzing carcinogenesis of a tumor, comprising:
- taking at least one cell sample at a location within the tumor;
- taking at least one cell sample at a location within a periphery of the tumor;
- performing large scale analysis on all of the cell samples;
- and
- identifying differences between cells of the cell samples.
A method of identifying carcinogenesis mutations, comprising:
- sampling cells within a tumor;
- sampling cells at a periphery of the tumor;
- performing large scale analysis of the samplings of cells;
- and
- identifying differences between cells of the cell samples.
A method of identifying diagnostic markers of cancer, comprising:
- sampling cells at at least one location within a tumor;
- sampling cells at a periphery of the tumor;
- performing large scale analysis of the samplings of cells;
- and
- identifying differences between cells of the cell samples.
A method of identifying therapeutic targets of cancer, comprising:
- sampling cells at at least one location within a tumor;
- sampling cells at a periphery of the tumor;
- performing large scale analysis of the samplings of cells;
- and
- identifying differences between cells of the cell samples.
Dependencies are inferred from the claim text.