An evaluation protocol for subtype-specific breast cancer event prediction

An evaluation protocol for subtype-specific breast cancer event prediction

Sontrop, H.M.J.
Verhaegh, W.F.J.
Reinders, M.J.T.
Moerland, P.D.

Electrical Engineering, Mathematics and Computer Science

Mediamatics

2011-07-08

In recent years increasing evidence appeared that breast cancer may not constitute a single disease at the molecular level, but comprises a heterogeneous set of subtypes. This suggests that instead of building a single monolithic predictor, better predictors might be constructed that solely target samples of a designated subtype, which are believed to represent more homogeneous sets of samples. An unavoidable drawback of developing subtype-specific predictors, however, is that a stratification by subtype drastically reduces the number of samples available for their construction. As numerous studies have indicated sample size to be an important factor in predictor construction, it is therefore questionable whether the potential benefit of subtyping can outweigh the drawback of a severe loss in sample size. Factors like unequal class distributions and differences in the number of samples per subtype, further complicate comparisons. We present a novel experimental protocol that facilitates a comprehensive comparison between subtype-specific predictors and predictors that do not take subtype information into account. Emphasis lies on careful control of sample size as well as class and subtype distributions. The methodology is applied to a large breast cancer compendium involving over 1500 arrays, using a state-of-the-art subtyping scheme. We show that the resulting subtype-specific predictors outperform those that do not take subtype information into account, especially when taking sample size considerations into account.

http://resolver.tudelft.nl/uuid:1c7803ec-fef6-4275-9e70-12c7a450d335

Public Library of Science

1932-6203

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021681

PLoS One, 6 (7), 2011

Institutional Repository

journal article

(c) 2011 Sontrop et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.