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| Status |
Public on Sep 30, 2024 |
| Title |
Methylation profiling of plasma cell-free DNA in pediatric brain tumor patients |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Using cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq), we analyzed methylation profiles in 93 plasma samples from 77 pediatric brain tumor patients and 16 non-neoplastic patients. Binomial GLMnet classifiers of tumor and tumor subtypes were built in training sets, and performance was evaluated in test sets. The methylation profiles from plasma cfMeDIP-seq discriminated tumor from non-tumor patients with 0.83 accuracy (precision = 0.93, sensitivity = 0.86, and specificity = 0.67). Among major tumor subtypes vs. nontumors, circumscribed astrocytic glioma showed an accuracy of 0.86 (precision = 0.88, sensitivity = 0.88, and specificity = 0.83), and glioneuronal tumors had an accuracy of 0.83 (precision, sensitivity, and specificity = 0.83). Circumscribed astrocytic glioma and glioneuronal tumors could be discriminated from other tumor subtypes with 0.79 and 0.82 accuracy, respectively.
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| Overall design |
We analyzed methylation profiles in 93 plasma samples from 77 pediatric brain tumor patients and 16 non-neoplastic patients. Binomial GLMnet classifiers of tumor and tumor subtypes were built in training sets, and performance was evaluated in test sets.
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| Contributor(s) |
Horbinski C, An S, McCortney K, Walshon J, Leonard K, McCord M, DeCuypere M |
| Citation missing |
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| Submission date |
Aug 24, 2024 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Shejuan An |
| Organization name |
Northwestern University
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| Street address |
303 East Superior Street
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60302 |
| Country |
USA |
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| Platforms (2) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL34284 |
Illumina NovaSeq X Plus (Homo sapiens) |
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