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.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Rousseau M,Ferraiuolo MA,Crutchley JL,Wang XQ,Miura H,Blanchette M,Dostie Jdoi
10.1186/gb-2014-15-4-r60subject
Has Abstractpub_date
2014-04-30 00:00:00pages
R60issue
4eissn
1474-7596issn
1474-760Xpii
gb-2014-15-4-r60journal_volume
15pub_type
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