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Open Access Highly Accessed Research

Classifying leukemia types with chromatin conformation data

Mathieu Rousseau12, Maria A Ferraiuolo1, Jennifer L Crutchley1, Xue Qing David Wang1, Hisashi Miura1, Mathieu Blanchette2* and Josée Dostie1*

Author Affiliations

1 Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec H3G 1Y6, Canada

2 McGill Centre for Bioinformatics and School of Computer Science, McGill University, Montréal, Québec H3G 0B1, Canada

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Genome Biology 2014, 15:R60  doi:10.1186/gb-2014-15-4-r60

Published: 30 April 2014

Abstract

Background

Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed.

Results

Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data.

Conclusions

Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes.