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Series GSE142241 Query DataSets for GSE142241
Status Public on Oct 28, 2020
Title Reliable tumor detection using cerebrospinal fluid cell-free DNA methylomes in pediatric medulloblastoma
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Medulloblastoma (MB) is an embryonal tumor of the cerebellum and a highly malignant childhood brain tumor. Cell-free circulating tumor DNA (ctDNA) from the cerebrospinal fluid (CSF) of patients with brain tumors faithfully represent genomic alterations of brain tumors. Distinct epigenetic signatures among subgroups of MB allow us to detect epigenetic alterations in CSF to aid classify and guide therapy of MB tumors. Here, we evaluate DNA methylation and hydroxymethylation of ctDNA derived from small amount of CSF (200 µL) and matched tumor DNA from 3 MB patients. We find highly concordance of DNA methylation and hydroxymethylation between CSF ctDNA and tumor DNA, especially in CpG islands. Importantly, CSF ctDNA can mostly recapitulate the dynamic changes of DNA methylation and hydroxymehtylation in tumor species compared to healthy cerebellums. Those MB tumor signature CpGs’ DNA methylation status are recovered in CSF ctDNA can clearly distinguish MB subgroups by utilizing public large cohort data. We further identified potential diagnostic and prognostic DNA methylation markers in CSF ctDNA. Our results show that CSF ctNDA methylation and hydroxymethylation can be a minimal invasive method to assess epigenetic alterations of MB, which is complementary to current diagnoses of MB tumors.
 
Overall design We collected matched CSF and tumors samples from three pediatric MB patients; four Non-MB CSF and two normal cerebellum tissues are as control. We performed WGBS and CMS-IP for these samples
 
Contributor(s) Li J, Sun D, Huang Y, Li X
Citation(s) 33067228
Submission date Dec 17, 2019
Last update date Oct 28, 2020
Contact name Jia Li
E-mail(s) jiali@tamu.edu
Organization name Texas A&M U Health Science Center
Department CEDP
Lab Jia Li Lab
Street address 2121 W HOLCOMBE BLVD
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (22)
GSM4223613 normal cerebellum CMS-IP Cerebellum1_CMS
GSM4223614 normal cerebellum CMS-IP Cerebellum2_CMS
GSM4223615 cerebrospnial fluid from pediatric medullablastoma patient CMS-IP MB1_CSF.CMS
Relations
BioProject PRJNA596280
SRA SRP238023

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Supplementary file Size Download File type/resource
GSE142241_RAW.tar 16.9 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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