Detecting neoplasm

Patent metadata

Field	Value
Publication number	US-12043871-B2
Application number	US-202218062419-A
Country	US
Kind code	B2
Filing date	Dec 6, 2022
Priority date	Feb 15, 2008
Publication date	Jul 23, 2024
Grant date	Jul 23, 2024

Abstract

This document relates to methods and materials for detecting premalignant and malignant neoplasms. For example, methods and materials for determining whether or not a stool sample from a mammal contains nucleic acid markers or polypeptide markers of a neoplasm are provided.

First claim

What is claimed is:

1. A method comprising:
(a) obtaining a stool sample from a subject that has or is suspected of having colorectal cancer;
(b) extracting genomic DNA from the stool sample; and
(c) using the extracted genomic DNA from the stool sample to determine a K-ras mutation score and BMP methylation status.

2. The method of claim 1 , wherein the K-ras mutation score is determined using digital melt curve analysis.

3. The method of claim 1 , wherein the K-ras mutation score is determined using quantitative allele-specific PCR.

4. The method of claim 1 , wherein the K-ras mutation score is determined by amplifying a region of the extracted genomic DNA using primers specific for one or more K-ras mutations.

5. The method of claim 4 , wherein the primers specific for one or more K-ras mutations are selected from SEQ ID NOs: 2, 3, 4, 5, 6, 7, and 8.

6. The method of claim 4 , wherein the primers detect a K-ras mutation corresponding to amino acid number 12 .

7. The method of claim 1 , wherein the BMP methylation status is determined by measuring a methylation level of one or more CpG sites in BMP3.

8. The method of claim 7 , wherein measuring a methylation level of one or more CpG sites in BMP3 comprises using one or more of methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, and bisulfite genomic sequencing PCR.

9. The method of claim 1 , wherein the BMP methylation status is determined by treating the extracted genomic DNA with a bisulfite reagent.

10. The method of claim 9 , wherein the bisulfite reagent is sodium bisulfite.

11. The method of claim 9 , wherein the BMP methylation status is determined by amplifying a region of the extracted bisulfite-treated genomic DNA using primers specific for one or more CpG sites in BMP3.

12. The method of claim 1 , wherein extracting the genomic DNA from the stool sample comprises using a DNA stabilization buffer.

13. The method of claim 1 , wherein extracting the genomic DNA from the stool sample comprises using DNA extraction reagents.

Assignees

• Mayo Found Medical Education & Res

Inventors

• Taylor William R
• Harrington Jonathan J
• Quint Patrick S
• Zou Hongzhi
• Bergen Iii Harold R
• Smith David I
• Ahlquist David A

Classifications

• G01N33/57557

  of other specific parts of the body, e.g. brain · CPC title

• G01N33/57535

  of the large intestine, e.g. colon, rectum or anus · CPC title

• G01N33/57525

  of the liver or pancreas · CPC title

• C12Q2600/158

  Expression markers · CPC title

• G01N2560/00

  Chemical aspects of mass spectrometric analysis of biological material · CPC title