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Classifying leukemia types with chromatin conformation data.

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

SUBMITTER: Rousseau M

PROVIDER: S-EPMC4038739 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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Classifying leukemia types with chromatin conformation data.

Rousseau Mathieu M Ferraiuolo Maria A MA Crutchley Jennifer L JL Wang Xue Qing XQ Miura Hisashi H Blanchette Mathieu M Dostie Josée J

Genome biology 20140430 4

<h4>Background</h4>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.<h4>Results</h4>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 tes ...[more]

PMID: 24995990

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