Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression data from ATRT tumor samples


ABSTRACT: Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants. Although the prognosis of ATRT patients is poor, some patients respond favorably to current treatments, suggesting molecular inter-tumor heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large series of human ATRTs. Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location, and type of SMARCB1 alterations, were identified. Whole-genome DNA and RNA sequencing found no recurrent mutations in addition to SMARCB1 that would explain the differences between subgroups. Whole-genome bisulfite sequencing and H3K27Ac chromatin-immunoprecipitation sequencing of primary tumors, however, revealed clear differences, leading to the identification of subgroup-specific regulatory networks and potential therapeutic targets. 49 ATRT samples were selected for RNA extraction and hybridization on Affymetrix Affymetrix Human Genome U133 Plus 2.0 Arrays. ---------------------------------------- This submission consists of the expression data for 49 of 170 samples only

ORGANISM(S): Homo sapiens

SUBMITTER: Marcel Kool 

PROVIDER: E-GEOD-70678 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes.

Johann Pascal D PD   Erkek Serap S   Zapatka Marc M   Kerl Kornelius K   Buchhalter Ivo I   Hovestadt Volker V   Jones David T W DTW   Sturm Dominik D   Hermann Carl C   Segura Wang Maia M   Korshunov Andrey A   Rhyzova Marina M   Gröbner Susanne S   Brabetz Sebastian S   Chavez Lukas L   Bens Susanne S   Gröschel Stefan S   Kratochwil Fabian F   Wittmann Andrea A   Sieber Laura L   Geörg Christina C   Wolf Stefan S   Beck Katja K   Oyen Florian F   Capper David D   van Sluis Peter P   Volckmann Richard R   Koster Jan J   Versteeg Rogier R   von Deimling Andreas A   Milde Till T   Witt Olaf O   Kulozik Andreas E AE   Ebinger Martin M   Shalaby Tarek T   Grotzer Michael M   Sumerauer David D   Zamecnik Josef J   Mora Jaume J   Jabado Nada N   Taylor Michael D MD   Huang Annie A   Aronica Eleonora E   Bertoni Anna A   Radlwimmer Bernhard B   Pietsch Torsten T   Schüller Ulrich U   Schneppenheim Reinhard R   Northcott Paul A PA   Korbel Jan O JO   Siebert Reiner R   Frühwald Michael C MC   Lichter Peter P   Eils Roland R   Gajjar Amar A   Hasselblatt Martin M   Pfister Stefan M SM   Kool Marcel M  

Cancer cell 20160225 3


Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants. Although the prognosis of ATRT patients is poor, some patients respond favorably to current treatments, suggesting molecular inter-tumor heterogeneity. To investigate this further, we genetically and epigenetically analyzed 192 ATRTs. Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location, and type of SMARCB1 alterations, were identified. Whole-genome DNA a  ...[more]

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