|
| Status |
Public on Feb 27, 2014 |
| Title |
Classifying leukemia types with chromatin conformation data (ChIP-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Background: Although genetic or epigenetic alterations have 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.
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| |
|
| Overall design |
Examination of CTCF and RAD21 binding sites in THP-1 cell.
|
| |
|
| Contributor(s) |
Rousseau M, Ferraiuolo MA, Crutchley JL, Wang XQ, Miura H, Blanchette M, Dostie J |
| Citation(s) |
24995990 |
| |
| Submission date |
Feb 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Josée Dostie |
| E-mail(s) |
josee.dostie@mcgill.ca
|
| Phone |
1-514-398-4975
|
| Organization name |
McGill University
|
| Department |
Biochemistry
|
| Street address |
3655 Promenade Sir-William-Osler
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
Canada |
| |
|
| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (3) |
|
| This SubSeries is part of SuperSeries: |
| GSE55408 |
Classifying leukemia types with chromatin conformation data |
|
| Relations |
| BioProject |
PRJNA239520 |
| SRA |
SRP038996 |
