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| Status |
Public on Jun 02, 2021 |
| Title |
Genome-wide DNA methylation profiling of SCCOHT and SMARCB1-mutated rhabdoid tumours |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
Third-party reanalysis
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| Summary |
Extracranial rhabdoid tumours (ECRT) are an aggressive malignancy of infancy and early childhood. The vast majority of cases demonstrate inactivation of SMARCB1 (ECRT_SMARCB1) but, rarely, ECRT can harbour the alternative inactivation of SMARCA4 (ECRT_SMARCA4) instead of SMARCB1. To explore the place of ECRTSMARCA4 in the "rhabdoid tumour" spectrum, we generated and collected from previous studies genome-wide DNA methylation array data (n = 85) from Atypical/Teratoid Rhabdoid Tumours (ATRT), ECRT_SMARCB1, ECRT_SMARCA4 and small cell carcinomas of the ovary, hypercalcaemic type (SCCOHT) tumours. Using dimensionality reduction and unsupervised clustering approaches, our results demonstrate that ECRT_SMARCA4 display an intermediate DNA methylation profile between SCCOHT and ECRT_SMARCB1.
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| Overall design |
Eighty five tumour samples were profiled using illumina Infinium Human EPIC Beadchip including 54 ATRTs (24 re-analyzed samples from Leruste et al., 2019), 13 ECRT_SMARCB1 (12 re-analyzed samples from Leruste et al., 2019), 9 ECRT_SMARCA4 (4 re-analyzed from Leruste et al., 2019; 5 re-analyzed from GSE161692: GSM4912763, GSM4912765, GSM4912764, GSM4912767, GSM4912768) and 9 SCCOHT samples.
All previously published data included in our study (listed in the 'published_re-analyzed_data.xlsx') have been directly provided by the authors as IDAT files, and only 5 samples have the corresponding GEO records as indicated above.
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| Contributor(s) |
Andrianteranagna M, Cyrta J, Servant N, Bourdeaut F |
| Citation(s) |
33999421 |
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| Submission date |
Jun 01, 2021 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
Nicolas.Servant@curie.fr
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| Organization name |
Institut Curie
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| Street address |
26 rue d'ulm
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| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
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| Platforms (1) |
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| Samples (40)
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| GSM5350833 |
SCCOHT, UGS653 |
| GSM5350834 |
ATRT, INI256 |
| GSM5350835 |
ATRT, INI255 |
| GSM5350836 |
ATRT, INI251 |
| GSM5350837 |
ATRT, INI228 |
| GSM5350838 |
ATRT, INI254 |
| GSM5350839 |
ATRT, INI235 |
| GSM5350840 |
ATRT, INI153 |
| GSM5350841 |
ATRT, INI240 |
| GSM5350842 |
ATRT, INI226 |
| GSM5350843 |
ATRT, INI227 |
| GSM5350844 |
ATRT, INI286 |
| GSM5350845 |
ATRT, INI267 |
| GSM5350846 |
ATRT, INI266 |
| GSM5350847 |
ECRT-SMARCB1, INI289 |
| GSM5350848 |
SCCOHT, UGS663 |
| GSM5350849 |
ATRT, INI104 |
| GSM5350850 |
ATRT, INI159 |
| GSM5350851 |
ATRT, INI206 |
| GSM5350852 |
ATRT, INI258 |
| GSM5350853 |
ATRT, INI292 |
| GSM5350854 |
ATRT, INI293 |
| GSM5350855 |
ATRT, INI295 |
| GSM5350856 |
ATRT, INI296 |
| GSM5350857 |
ATRT, INI301 |
| GSM5350858 |
ATRT, INI246 |
| GSM5350859 |
ATRT, INI232 |
| GSM5350860 |
ATRT, INI239 |
| GSM5350861 |
ATRT, INI147 |
| GSM5350862 |
ATRT, INI158 |
| GSM5350863 |
ATRT, INI162 |
| GSM5350864 |
ATRT, INI165 |
| GSM5350865 |
ATRT, INI287 |
| GSM5350866 |
SCCOHT, UGS666 |
| GSM5350867 |
SCCOHT, UGS667 |
| GSM5350868 |
SCCOHT, UGS668 |
| GSM5350869 |
SCCOHT, UGS669 |
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| This SubSeries is part of SuperSeries: |
| GSE175893 |
SMARCA4-deficient rhabdoid tumours show intermediate molecular features between SMARCB1-deficient rhabdoid tumours and small cell carcinomas of the ovary, hypercalcaemic type. |
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| Relations |
| Reanalysis of |
GSM4912763 |
| Reanalysis of |
GSM4912764 |
| Reanalysis of |
GSM4912765 |
| Reanalysis of |
GSM4912767 |
| Reanalysis of |
GSM4912768 |
| BioProject |
PRJNA734267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE175892_DNA_methylation_EPICarray_betaValue_matrix_updated.txt.gz |
544.4 Mb |
(ftp)(http) |
TXT |
| GSE175892_RAW.tar |
725.0 Mb |
(http)(custom) |
TAR (of IDAT) |
| GSE175892_published_re-analyzed_data.xlsx |
15.5 Kb |
(ftp)(http) |
XLSX |
| Processed data are available on Series record |
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