Classifying leukemia types with chromatin conformation data
Mathieu Rousseau12†, Maria A Ferraiuolo1†, Jennifer L Crutchley1†,
Xue Qing David Wang1, Hisashi Miura1, Mathieu Blanchette2* and
* Corresponding authors: Mathieu Blanchette firstname.lastname@example.org –
Josée Dostie email@example.com
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.