Detecting neoplasm

• US 9,632,093 B2
• Filed: 06/29/2016
• Issued: 04/25/2017
• 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: Bergen, III, Harold S., Taylor, William R., Harrington, Jonathan J., Quint, Patrick S., Zou, Hongzhi, Smith, David I., Ahlquist, David A.
• Primary Examiner(s): AEDER, SEAN E
• Application Number:
  US15/197,105
• Publication Number:
  US 20160305946A1
• Time in Patent Office: 300 Days
• Field of Search: None
• 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 for characterizing a biological sample comprising:

(a) obtaining a biological sample from a human individual;

(b) measuring a K-ras mutation score within the obtained biological sample through exposing a portion of the biological sample to one or more K-ras specific primers and determining the K-ras mutation score by performing a digital melt curve analysis or quantitative allele-specific PCR, wherein the K-ras specific primers comprise a nucleic acid sequence selected from the group consisting of SEQ ID NOs;

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

(c) measuring a methylation level of a CpG site for BMP3 in a portion of the obtained biological sample through

treating genomic DNA in the biological sample with bisulfite;

amplifying the bisulfite-treated genomic DNA using primers specific for BMP3, and determining the methylation level of the CpG site by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, or bisulfite genomic sequencing PCR;

(d) comparing the K-ras mutation score and the BMP3 methylation level to a corresponding set of control samples without colorectal cancer; and

(e) determining that the individual has colorectal cancer when

     1) the measured K-ras mutation score is higher than in the control sample, and

     2) the measured BMP3 methylation level is higher than in the control sample.

2. The method of claim 1, wherein the biological sample is a stool sample, a tissue sample, a blood sample, or a urine sample.