Introduction
Materials and methods
Experimental design
Nanopore whole genome sequencing
Copy number analysis
Methylation analysis
Structural variant detection
Amplicon sequencing
Microarray methylation profiling
Statistics
Data and material availability
Results
ID | Age at diagnosis | Sex | WHO 2016 integrated diagnosis | Nanopore sequencing performed | Nanopore methylation-based classification | Key alterations identified by nanopore sequencing |
---|---|---|---|---|---|---|
3523T | 70 | F | Glioblastoma, IDH-wildtype | WGS, amplicon | Not classifiable | pTERT C228T |
2197T | 58 | F | Glioblastoma, IDH-wildtype | WGS, amplicon | Glioma, IDH-wildtype | TP53 p.S241F, pTERT C228T |
3427T | 72 | F | Glioblastoma, IDH-wildtype | WGS, amplicon | Glioma, IDH-wildtype | pTERT C228T, CDKN2Aloss, EGFRamp
|
2402T | 58 | M | Anaplastic oligodendroglioma, IDH-mutant, and 1p/19q-codeleted | WGS, amplicon | Not classifiable | IDH1 p.R132H, 1p/19q codeletion, pTERT C228T |
2965T | 29 | F | Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted | WGS, amplicon | Glioma, IDH-mutant | IDH1 p.R132H, 1p/19q codeletion, pTERT C228T |
2483T | 51 | F | Anaplastic astrocytoma, IDH-mutant | WGS, amplicon | Glioma, IDH-mutant | IDH1 p.R132C TP53 p.R273C, p.R282Q |
2922T | 44 | M | Diffuse astrocytoma, IDH-mutant | WGS | Glioma, IDH-mutant | N/D |
6228T | 33 | F | Diffuse midline glioma, H3.3 K27M-mutant | WGS, amplicon | Classifiable | PDGFRAamp
|
5337T | 21 | M | Glioma H3.3 G34R | WGS, amplicon | Glioma IDH-wildtype | H3F3A G34R, CDK4amp, PDGFRAamp
|
8347T | 28 | M | Desmoplastic/nodular medulloblastoma, SHH-activated and TP53 wild type | Amplicon | N/D | pTERT C228T |
8372T | 25 | M | Classic medulloblastoma, non-WNT/non-SHH | WGS, amplicon | Medulloblastoma, group 4 | pTERT C228T |
MB683 | 7 | F | Classic medulloblastoma, WNT-activated | WGS, amplicon | Medulloblastoma, WNT-activated | chr6 loss |
8137T | 48 | M | Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted | WGS, amplicon | Glioma, IDH-mutant | IDH2 p.R172 W, 1p/19q codeletion, pTERT C228T |
8146T | N/A | F | Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted | WGS, amplicon | Glioma, IDH-mutant | pTERT C228T |
7382T | 76 | F | Glioblastoma, IDH-wildtype | WGS, amplicon | Glioma, IDH-wildtype | pTERT C228T, PDGFRAamp
TP53 p.V197M |
7455T | 45 | M | Glioblastoma, IDH-wildtype | WGS, amplicon | Glioma, IDH-wildtype | pTERT C228T |
8355T | 56 | M | Glioblastoma, IDH-wildtype | WGS | Not classifiable | N/D |
8356T | 73 | F | Breast adenocarcinoma, GFAP+, S100+ | WGS | Breast cancer | N/D |
8357T | 79 | M | Neuro-endrocrine (prostate adeno) carcinoma, TTF1+ | WGS | Lung cancer | N/D |
8358T | 63 | F | Lung adenocarcinoma | WGS | Lung cancer | N/D |
8359T | 51 | M | Bladder urothelial carcinoma | WGS, amplicon | Not classifiable | TP53 p.R280 K |
8360T | 65 | F | Lung adenocarcinoma | Amplicon | N/D | TP53 p.I195T |
4596T FFPE | 44 | F | Anaplastic oligodendroglioma, IDH-mutant and 1p/19q-codeleted | WGS, amplicon | Not classifiable | pTERT C228T |
5539T FFPE | 28 | M | Anaplastic astrocytoma, IDH-mutant | Amplicon | N/D | pTERT C228T¶
|
3718T | 78 | F | Glioblastoma, IDH-wildtype | WGS | N/D | N/D |
3719T | 74 | M | Glioblastoma, IDH-wildtype | WGS | N/D | N/D |
2211T | 75 | F | Glioblastoma, IDH-wildtype | WGS | N/D | N/D |
3724T | 65 | M | Glioblastoma, IDH-wildtype | WGS | N/D | N/D |