Method for predicting prognosis of cancer

Patent metadata

Field	Value
Publication number	US-2017053060-A1
Application number	US-201515118817-A
Country	US
Kind code	A1
Filing date	Jan 9, 2015
Priority date	Feb 18, 2014
Publication date	Feb 23, 2017
Grant date	—

Abstract

Disclosed is a method for predicting cancer prognosis, comprising: forming gene pairs by using a plurality of genes to be tested; determining clusters for the formed gene pairs through a clustering method; calculating a distribution of each gene pair based on the determined cluster; and selecting reference gene pairs for determining a class based on the calculated distribution.

First claim

What is claimed is:

1 . A method for predicting cancer prognosis, the method comprising:
forming gene pairs by using a plurality of genes to be tested; determining clusters for the formed gene pairs through a clustering method; calculating a distribution of each gene pair based on the determined cluster; and selecting reference gene pairs for determining a class based on the calculated distribution.

2 . The method for predicting the cancer prognosis of claim 1 , the method further comprising:
selecting a plurality of genes to be tested in microarray data according to a predetermined reference, before forming the gene pairs.

3 . The method for predicting the cancer prognosis of claim 2 , wherein in the selection of the genes, the plurality of genes to be tested is selected by using at least one of Relief-A and Symmetrical Uncertainty algorithms.

4 . The method for predicting the cancer prognosis of claim 1 , the method further comprising:
receiving a correct answer class for the plurality of genes to be tested, before forming the gene pairs.

5 . The method for predicting the cancer prognosis of claim 4 , wherein in the determining of the clusters for the formed gene pairs, the clusters are determined by clustering for the gene pairs which belong to the same correct answer class.

6 . The method for predicting the cancer prognosis of claim 1 , wherein in the calculating of the distribution of each gene pair, the distribution is calculated by a sum of Euclidean distances for average values of the determined clusters for the gene pairs.

7 . The method for predicting the cancer prognosis of claim 1 , the method further comprising:
receiving expression levels for the gene pairs of the test sample, after selecting the reference gene pairs for determining the class; and predicting a class for each gene pair of the test sample by projecting the expression levels for the gene pairs of the test sample to a 2D image for the reference gene pairs.

8 . The method for predicting the cancer prognosis of claim 7 , wherein in the predicting of the class for each gene pair of the test sample, the class for each gene pair is predicted based on the expression levels for the gene pairs of the test sample projected to the 2D image and Euclidean distances between the plurality of classes.

9 . The method for predicting the cancer prognosis of claim 8 , wherein in the predicting of the class for each gene pair of the test sample, the class for each gene pair of the test sample is predicted as a class having a relatively smaller Euclidean distance.

10 . The method for predicting the cancer prognosis of claim 8 , wherein in the predicting of the class for each gene pair of the test sample, when the Euclidean distances between the gene pairs of the test sample and the plurality of classes are the same as each other, the class for each gene pair is predicted based on a sum of the Euclidean distances between the gene pairs of the test sample and all clusters which belong to each of the plurality of classes.

11 . The method for predicting the cancer prognosis of claim 10 , wherein in the predicting of the class for each gene pair of the test sample, the class for each gene pair of the test sample is predicted as a class having a relatively smaller sum of the Euclidean distances.

12 . The method for predicting the cancer prognosis of claim 7 , the method further comprising:
determining a final class of the test sample, after predicting the class for each gene pair of the test sample.

13 . The method for predicting the cancer prognosis of claim 12 , wherein in the determining of the final class of the test sample, the final class is determined as the most predicted class among the predicted classes for each gene pair of the test sample.

Assignees

• Industry-Academic Cooperation Foundation Yonsei Univ

Inventors

• Park Sang Hyun
• Kim Hyun Jin
• Ahn Jae Gyoon
• Park Chi Hyun
• Yoon Young Mi

Classifications

• C12Q1/6837 Primary

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title

• G06F19/18 Primary

  Physics · mapped topic

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title

• C12Q2600/118

  Prognosis of disease development · CPC title

• C12Q2600/158

  Expression markers · CPC title