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Related Experiment Videos

Colon cancer prognosis prediction by gene expression profiling.

Alain Barrier1, Antoinette Lemoine, Pierre-Yves Boelle

  • 1Service de Chirurgie Digestive, Hôpital Tenon, Université Pierre et Marie Curie, Assistance Publique, 75020 Paris, France. barrier@stat.Berkeley.edu

Oncogene
|August 11, 2005
PubMed
Summary

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Accurate prognosis predictors for stage II and III colon cancer were developed using gene expression measures from either tumor or non-neoplastic mucosa. These predictors achieved high accuracy, suggesting a new approach for patient outcome assessment.

Area of Science:

  • Oncology
  • Genomics
  • Bioinformatics

Background:

  • Accurate prognosis prediction is crucial for managing stage II and III colon cancer.
  • Gene expression profiling offers a potential avenue for developing novel prognostic tools.

Purpose of the Study:

  • To assess the feasibility of creating a prognosis predictor for stage II and III colon cancer patients using microarray gene expression data.
  • To determine if gene expression from tumor (T) or non-neoplastic mucosa (NM) is more effective for prognosis prediction.

Main Methods:

  • Microarray gene expression profiling of T and NM mRNA samples from 18 colon cancer patients (9 recurrence, 9 no recurrence).
  • Application of the k-nearest neighbour method for prognosis prediction.
  • Utilized six-fold and double cross-validation for predictor selection and accuracy estimation.

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Main Results:

  • A 30-gene tumor-based predictor and a 70-gene non-neoplastic mucosa-based predictor were developed.
  • Estimated accuracies for the predictors were 78% (T-based) and 83% (NM-based).
  • Both tumor and non-neoplastic mucosa gene expression data proved valuable for prognosis prediction.

Conclusions:

  • It is possible to build accurate prognosis predictors for stage II and III colon cancer patients based on gene expression measures.
  • Both tumor and non-neoplastic mucosa samples can be effectively utilized for developing these prognostic tools.