Figure 1: Study design for the construction of genome-wide DNA methylation profiles of metastatic brain tumors. | Scientific Data

Figure 1: Study design for the construction of genome-wide DNA methylation profiles of metastatic brain tumors.

From: Brain metastasis DNA methylomes, a novel resource for the identification of biological and clinical features

Figure 1

(a) Patients with metastatic brain tumors from breast cancer, lung cancer or cutaneous melanoma origin were selected for the study. (b) A representative magnetic resonance imaging (MRI) scan of a single metastatic brain tumor lesion used as part of the clinical diagnosis is shown in the scheme. (c) After surgery, resected tumors were routinely stored as formalin-fixed and paraffin-embedded (FFPE) tissue blocks and stained with hematoxylin and eosin (H&E) for anatomic pathology diagnosis. (d) FFPE tissue sections underwent routine immunohistochemistry (IHC) evaluation to confirm the tumor of origin and molecular subtypes of each case. (e) After tumor cell-rich areas were identified, tissue microdissection followed by DNA purification was performed in each case. (f) DNA specimens passing the quality control metrics were converted with sodium bisulfite, enzymatically fragmented, and hybridized in the HM450K BeadChips. Raw intensity data were normalized and corrected β values for each specimen were generated. A representative heat map of the DNA methylation data is shown in the study scheme.

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