Comprehensive analysis of the (epi)genome of pediatric atypical teratoid/rhabdoid tumours (AT/RTs)

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Dataset ID	Description	Technology	Samples
EGAD00001001444	Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants and young children. Although the prognosis of ATRT patients is poor, some patients respond very well to current treatments, suggesting inter-tumor molecular heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large cohort of ATRTs (n = 170). Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location and type of SMARCB1 alterations, were identified using DNA-methylation or gene expression analyses. Whole genome DNA- and RNA-sequencing found no other recurrent mutations explaining the differences between subgroups. However, whole genome bisulfite-sequencing and H3K27Ac ChIP-sequencing of primary tumors revealed clear differences in methylation patterns and enhancer landscapes, leading to the identification of subgroup-specific regulatory networks.	Illumina HiSeq 2000 Illumina HiSeq 2500	55
EGAD00001002135	ChIPseq data of Atypical teratoid/rhabdoid tumors (ATRT)	Illumina HiSeq 2000 Illumina HiSeq 2500	15
EGAD00001002136	RNA sequencing data of Atypical teratoid/rhabdoid tumors (ATRT)	Illumina HiSeq 2000	25
EGAD00001002137	WGBS data of Atypical teratoid/rhabdoid tumors (ATRT)	Illumina HiSeq 2000 Illumina HiSeq 2500	15
EGAD00001002138	WGS data of Atypical teratoid/rhabdoid tumors (ATRT)	Illumina HiSeq 2000	36
EGAD00001003408	Chip-Seq sequencing data of Atypical teratoid/rhabdoid tumors (ATRT)	Illumina HiSeq 2000	19

Publications	Citations
Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation. Erkek S, Johann PD, Finetti MA, Drosos Y, Chou HC, Zapatka M, Sturm D, Jones DTW, Korshunov A, Rhyzova M, Wolf S, Mallm JP, Beck K, Witt O, Kulozik AE, Frühwald MC, Northcott PA, Korbel JO, Lichter P, Eils R, Gajjar A, Roberts CWM, Williamson D, Hasselblatt M, Chavez L, Pfister SM, Kool M. Cancer Cell 35: 2019 95-110.e8	40
Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration. Chun HE, Johann PD, Milne K, Zapatka M, Buellesbach A, Ishaque N, Iskar M, Erkek S, Wei L, Tessier-Cloutier B, Lever J, Titmuss E, Topham JT, Bowlby R, Chuah E, Mungall KL, Ma Y, Mungall AJ, Moore RA, Taylor MD, Gerhard DS, Jones SJM, Korshunov A, Gessler M, Kerl K, Hasselblatt M, Frühwald MC, Perlman EJ, Nelson BH, Pfister SM, Marra MA, Kool M. Cell Rep 29: 2019 2338-2354.e7	37
Pilocytic astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response. Aichmüller CF, Iskar M, Jones DTW, Korshunov A, Radlwimmer B, Kool M, Ernst A, Pfister SM, Lichter P, Zapatka M. Neuro Oncol 22: 2020 1327-1338	7
Locoregionally administered B7-H3-targeted CAR T cells for treatment of atypical teratoid/rhabdoid tumors. Theruvath J, Sotillo E, Mount CW, Graef CM, Delaidelli A, Heitzeneder S, Labanieh L, Dhingra S, Leruste A, Majzner RG, Xu P, Mueller S, Yecies DW, Finetti MA, Williamson D, Johann PD, Kool M, Pfister S, Hasselblatt M, Frühwald MC, Delattre O, Surdez D, Bourdeaut F, Puget S, Zaidi S, Mitra SS, Cheshier S, Sorensen PH, Monje M, Mackall CL. Nat Med 26: 2020 712-719	143