Study
Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures
| Study ID | Alternative Stable ID | Type |
|---|---|---|
| EGAS00001006576 | Other |
Study Description
Cancer genomes harbor a broad spectrum of structural variants (SV) driving tumorigenesis, a relevant subset of which are likely to escape discovery in short reads. We employed Oxford Nanopore Technologies (ONT) sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assemble complex rearrangements and such associated with telomeric sequences, including a 1.55 Megabasepair chromothripsis event. We uncover a complex SV pattern termed "templated insertion thread", characterized by short (mostly less than 1kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50kbp in size. Templated insertion threads occur in 3% of cancers, with a prevalence ranging to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in seven cancer-driver genes. Our ... (Show More)
Study Datasets 6 datasets.
Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data
| Dataset ID | Description | Technology | Samples |
|---|---|---|---|
| EGAD00001009411 |
ONT (PromethION) sequencing of chromothriptic medulloblastoma. Three samples: blood, primary tumor, and relapse tumor. Includes a fourth low-coverage run that multiplexes blood and primary tumor.
|
PromethION | 3 |
| EGAD00001009424 |
Illumina whole genome sequencing of Medulloblastoma Blood, Primary tumor, and Relapse tumor
|
HiSeq X Ten | 1 |
| EGAD00001009425 |
Illumina RNA-sequencing of Medulloblastoma primary and relapse tumor.
|
Illumina HiSeq 2000 | 1 |
| EGAD00001009483 |
Circle-Seq experiment.
|
HiSeq X Ten | 1 |
| EGAD00001009484 |
NA
|
GridION | 1 |
| EGAD00010002370 |
450k methylation arrays of primary and relapse tumor of a single case of sonic hedgehog medulloblastoma with Li-Fraumeni syndrome
|
HumanMethylation450 | 2 |
Who archives the data?
