BIOMARKERS FOR COLORECTAL CANCER

摘要

Biomarkers and methods for predicting the risk of a disease related to microbiota, in particular colorectal cancer (CRC), are described.

主权项

1. A method of obtaining a set of gene markers for predicting the risk of an abnormal condition related to microbiota, comprising:
a) identifying abnormal-associated gene markers by a metagenome-wide association study (MGWAS) strategy comprising:
i) collecting a sample from each subject from a population of subjects with the abnormal condition (abnormal) and subjects without the abnormal condition (controls),ii) extracting DNA from each sample, constructing a DNA library from each sample, and carrying out high-throughput sequencing of each DNA library to obtain sequencing reads for each sample;iii) mapping the sequencing reads to a gene catalog, and deriving a gene profile from the mapping result;iv) performing a Wilcoxon rank-sum test on the gene profile to identify differential metagenomic gene contents between the abnormal and controls; b) ranking all of the abnormal-associated gene markers identified in step a) by a minimum redundancy-maximum relevance (mRMR) method, and identifying/classifying sequential marker sets therefrom; and c) for each sequential marker set, estimating the error rate by leave-one-out cross-validation (LOOCV) of a linear discrimination classifier, and selecting an optimal gene marker set with the lowest error rate as the set of gene markers for predicting the risk of the abnormal condition.