title: 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.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Rousseau
authors.forename: Maria A
authors.initials: MA
authors.lastname: Ferraiuolo
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Crutchley
authors.forename: Xue Qing
authors.initials: XQ
authors.lastname: Wang
authors.forename: Hisashi
authors.initials: H
authors.lastname: Miura
authors.forename: Mathieu
authors.initials: M
authors.lastname: Blanchette
authors.forename: Josée
authors.initials: J
authors.lastname: Dostie
mesh_terms: D045744:Cell Line, Tumor; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D042002:Chromatin Assembly and Disassembly; D018398:Homeodomain Proteins / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D007938:Leukemia / Q000175:diagnosis / Q000235:genetics*
chemical_list: D002843:Chromatin; D018398:Homeodomain Proteins; C088144:HoxA protein