Table 2.
Publicly available tumor tissue cohort descriptions
| OMICs | |||||
|---|---|---|---|---|---|
| Publication | DNA methylation | RNA expression/sequencing | Data accession | Analyses | Relevant figures |
| MNG cohorts | |||||
| Gao et al., 2013 | Illumina HumanMethylation450 Beadchip; n = 19 MNG | GSE42882 |
(1) Investigation into MeLB DMP clustering (2) Investigation of d-MeLB signature meningioma specificity. |
(1/2) Figure 1c, e | |
| Capper et al., 2018 | Illumina HumanMethylation450 Beadchip; n = 149 MNG | GSE109381 | |||
| Harmanci et al., 2018 | Illumina HumanMethylation450 Beadchip; n = 57 MNG | GSE85135 | |||
| Bayley et al., 2022 | Illumina Methylation EPIC; n = 110 MNG | GSE189521 |
(1) Independent validation of p-MeLB. (2) Validation of p-MeLB classifications. (3) Independent validation of tissue-based LDA. |
(1) Figure 2b (3) Figure S4b |
|
| Choudhury et al., 2022 | Illumina Methylation EPIC; n = 565 MNG | Illumina HiSeq 4000 (Homo Sapiens): n = 185 MNG | GSE183656 |
(1) Validation of p-MeLB classifications. (2) Downstream correlation of gene transcription and DNA methylation across RR PGPs (tissue- and serum-identified). |
(2) Figure 3d, f, g |
| Non-MNG cohorts | |||||
| Capper et al., 2018 | Illumina HumanMethylation450 Beadchip; n = 1,20 Non-MNG tumors (embryonal, ependymal, etc.) | GSE109381 |
(1) Investigation into MeLB DMP clustering. (2) Investigation of d-MeLB signature meningioma specificity. |
(1/2) Figure 1c, e | |
| Mosella et al., 2021 | Illumina HumanMethylation450 Beadchip; n = 10 Pituitary tumors | Mendeley Data DOI: 10.17632.5pzd2rg5ys.1 | |||
| Kober et al., 2018 | Illumina HumanMethylation450 Beadchip; n = 34 Pituitary tumors | GSE115783 | |||
| Ling et al., 2014 | Illumina HumanMethylation450 Beadchip; n = 23 Pituitary tumors | GSE54415 | |||
| The Cancer Genome Atlas (TCGA) | Illumina HumanMethylation450 Beadchip; n = 516 Gliomas | N/A | |||
| Sloan et al., 2022 | Illumina Methylation EPIC; n = 20 Intracranial Mesenchymal tumors | GSE164994 | (1) Independent validation of tissue-derived linear discriminant analyses. | (1) Figure S4b | |
| N/A | Illumina Methylation EPIC; n = 16 Gliomas | GSE147391 | |||
| Braun et al., 2019 | Illumina Methylation EPIC; n = 21 Epileptic Nontumor brain | GSE111165 |
(1) Tumor-specific dimension reduction (d-MeLB step #1). (2) Independent validation of tissue-derived linear discriminant analysis (LDA). |
(1) Figure S3b (2) Figure S4b |
|
MNG meningioma, LGG low-grade glioma.