3D genome topology distinguishes molecular subgroups of medulloblastoma

Medulloblastoma (MB) has four molecular subtypes, but their 3D genome architecture differences are unclear. We used in situ Hi-C on 28 surgical specimens and a patient-derived xenograft to reconstruct the 3D genome architecture of MB subtypes, finding that topologically associating domain (TAD) insulation scores could distinguish MB subtypes.

Type: Epigenetics
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD50000000771	29 Hi-C datasets [8 G3 (MB3667, MB3687, MB3690, MB3692, MB3693, MB4010, MB4037, MB4141), 13 G4 (MB0558, MB3510, MB3670, MB3689, MB3716, MB3760, MB3761, MB3807, MB4079, MB4132, MB4174, MBSF7, SNC_2_5), 7 SHH (MB3612, MB3661, MB3662, MB3695, MB3697, MB3724, MB4143), and 1 WNT (MB4036)]. Fresh tissue samples were obtained from The Hospital for Sick Children (Toronto, ON). In situ Hi-C libraries were generated using approximately 2.5 million dissociated cells as input. All Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).	HiSeq X Ten	29

Publications	Citations
3D genome topology distinguishes molecular subgroups of medulloblastoma. Lee JJY, Johnston MJ, Farooq H, Chen HM, Younes ST, Suarez R, Zwaig M, Juretic N, Weiss WA, Ragoussis J, Jabado N, Taylor MD, Gallo M. Am J Hum Genet 111: 2024 2720-2734	0