Whole Chromosome View of Segmented CNV data
You can now use Xena to see segmented copy number variation on part or all of a chromosome.
Co-deletions in Lower Grade Glioma
Above you can see a subset of samples from TCGA Lower Grade Glioma. For each of the three subtypes in column A, you can see corresponding deletions in chromosome 1 (column B) and chromosome 19 (column C). Column D shows a close up of the deletion in the p-arm of chromosome 1.
Deletions and Amplifications in Gliomas
Looking more broadly at Glioblastoma Multiforme (GBM) and Lower Grade Glioma (LGG) in TCGA (column A), we can see the same arm-level co-deletions in chr1p (column B) and chr19q (column C) primarily in LGG tumors. Columns D and E show us an amplification in EGFR and a deletion in PTEN, both of which are associated with GBM rather than LGG tumors.
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