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Genome Biol. 2014 Apr 30;15(4):R60. doi: 10.1186/gb-2014-15-4-r60.

Classifying leukemia types with chromatin conformation data.

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.

PMID:
24995990
[PubMed - in process]
PMCID:
PMC4038739
Free PMC Article

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