Detecting neoplasm

• US 10,590,489 B2
• Filed: 10/04/2017
• Issued: 03/17/2020
• Est. Priority Date: 02/15/2008
• Status: Active Grant

• Current Assignee: Mayo Foundation For Medical Education And Research (Mayo Clinic)
• Original Assignee: Mayo Foundation For Medical Education And Research (Mayo Clinic)
• Inventors: Taylor, William R., Harrington, Jonathan J., Quint, Patrick S., Zou, Hongzhi, Bergen, III, Harold R., Smith, David I., Ahlquist, David A.
• Primary Examiner(s): Aeder, Sean E
• Application Number:
  US15/724,890
• Publication Number:
  US 20180105886A1
• Time in Patent Office: 895 Days
• Field of Search: 536 231
• CPC Class Codes: C12Q 1/37 involving peptidase or proteinase
• CPC Class Codes: C12Q 1/40 involving amylase
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Y 302/01001 Alpha-amylase (3.2.1.1)
• CPC Class Codes: C12Y 304/2107 Pancreatic endopeptidase E (3.4.21.70)
• CPC Class Codes: G01N 2333/928 acting on alpha -1, 4-glucosidic bonds, e.g. hyaluronidase, invertase, amylase
• CPC Class Codes: G01N 2333/966 Elastase
• CPC Class Codes: G01N 2560/00 Chemical aspects of mass spectrometric analysis of biological material
• CPC Class Codes: G01N 33/57407 Specifically defined cancers
• CPC Class Codes: G01N 33/57419 of colon
• CPC Class Codes: G01N 33/57438 of liver, pancreas or kidney

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.

Claims

1. A method, comprising:

(a) extracting genomic DNA from a biological sample of a human individual suspected of having precancer or colorectal cancer, wherein the biological sample is a stool sample;

(b) amplifying a portion of the extracted genomic DNA with primers specific for K-ras, and

measuring a K-ras mutation score by performing a digital melt curve analysis or quantitative allele-specific PCR; and

(c) treating a portion of the extracted genomic DNA with bisulfite;

amplifying the bisulfite-treated genomic DNA with primers specific for BMP3; and

measuring the methylation level of one or more CpG sites in BMP3 by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, or bisulfite genomic sequencing PCR.

2. The method of claim 1, wherein the primers specific for K-ras are selected from SEQ ID NOs:

2, 3, 4, 5, 6, 7 and 8.