|
| Status |
Public on Nov 05, 2011 |
| Title |
Methylation profiling of enchondromas with and without IDH1 mutations |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
Ollier disease and Maffucci syndrome are non-hereditary skeletal disorderscharacterized by multiple enchondromas (Ollier disease) combined with spindle cellhemangiomas (Maffucci syndrome). Somatic heterozygous IDH1 (R132C and R132H) orIDH2 (R172S) mutations were found in 87% of enchondromas, benign cartilage tumors,as well as in 70% of spindle cell hemangiomas, benign vascular lesions. In total, 35 of 43(81%) patients with Ollier disease and 10 of 13 (77%) patients with Maffucci syndromecarried IDH1 (98%) or rarely IDH2 (2%) mutations in their tumors. Fourteen patientswith multiple tumors at different anatomic locations displayed identical mutations inseparate lesions. Since in other tumor types the presence of an IDH1 mutation is strongly associated withhypermethylation 26, 27, we assessed whether there was a difference in methylation patternof enchondromas with (n = 8) and without (n = 4) IDH1 mutations detactable at Sangersequencing. Methylation and expressionprofiling showed that IDH1 mutations in cartilage tumors are associated withhypermethylation and downregulation of the expression of several genes.
|
| |
|
| Overall design |
Total 12 samples which includes 8 enchondromas with IDH1 mutation (4 Ollier enchondromas, 2 Maffucci enchondromas and 2 solitary enchondromas) and 4 enchondromas (1 Ollier enchondroma, 3 solitary enchondromas) without IDH1 or IDH2 mutations were used. Of these 4 enchondromas without IDH1 mutation, one had R132G IDH1 mutated cells present in the subpopulation, below the threshold level of Sanger sequencing. Bisulfite treatment was performed using EZ DNA Methylation™ Kit (ZymoResearch, Orange, CA). Bisulphite converted DNA was then hybridized to IlluminaHumanMethylation27 BeadChip (Illumina Inc., San Diego, CA) by followingmanufacturer’s instructions. Infinium Unsupervised clustering analysis was performed 25 using the Ward’s clustering algorithm based on Euclidian distance. The 2000 most variable CpG sites (excluding those on the X and Y chromosomes) were used in the clustering analysis.
|
| |
|
| Contributor(s) |
Pansuriya TC, Bovée Jv, d’ Adamo P |
| Citation(s) |
22057234 |
| Submission date |
Aug 11, 2011 |
| Last update date |
Jan 02, 2015 |
| Contact name |
Twinkal Chandubhai Pansuriya |
| E-mail(s) |
t.c.pansuriya@lumc.nl
|
| Phone |
0031715266528
|
| Organization name |
LUMC
|
| Department |
Pathology
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| State/province |
Zuid-Holland |
| ZIP/Postal code |
2333ZA |
| Country |
Netherlands |
| |
|
| Platforms (1) |
| GPL8490 |
Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) |
|
| Samples (12)
|
|
| This SubSeries is part of SuperSeries: |
| GSE30844 |
Somatic mosaic IDH1 and IDH2 mutations are associated with enchondroma and spindle cell haemangioma in Ollier disease and Maffucci syndrome |
|
| Relations |
| BioProject |
PRJNA154167 |
Less...
More...