Table 1.
Important Techniques in Brain Cancer Research and Optimal Sample Types
| Technology/Methodology | Compromised by formalin fixation? | Concordance % FFPE and FF data | Optimal sample | Study model |
|---|---|---|---|---|
| NGS—variant level78 | Minimal | >94% | Fresh Frozen | Colorectal cancer |
| NGS—gene level78 | Yes | >73% | Fresh Frozen | Colorectal cancer |
| miRNA LNA-based arrays81 | No | ~96% | Best Available | Mouse liver |
| miRNA oligo-array81 | Yes | ~56% | Fresh Frozen | |
| mRNA oligo-array81 | Yes | <56% | Fresh Frozen | |
| DNA Methylation analysis (NGS)82,83 | No | >99% | Best Available | Colorectal cancer |
| DNA Methylation analysis (NGS—threshold analysis)82,83 | Yes | 43-49% | Fresh Frozen | Colorectal cancer |
| RT-qPCR—gene expression84 | Yes | ~33% | Fresh Frozen | Breast cancer |
| Proteomics/phosphoproteomics—Mass spectroscopy85–87 | Yes | 70-90% | Fresh Frozen | Ovarian, breast cancer, canine tissue, glioblastoma |
| ctDNA—PCR88 | NA | NA | Liquid biopsies | Glioblastoma |
| Exome studies—fusion detection89 | Minimal | 95-99% | Best Available | Multiple malignancies incl glioblastoma |
| Exome studies—molecular subtype classification89 | Yes | 50-80% | Fresh Frozen | |
| Single-cell RNA sequencing90 | NA | NA | Fresh tissues or frozen cell suspension | Glioblastoma |
| Single-cell DNA sequencing91 | NA | NA | Fresh tissues or frozen cell suspension | Glioblastoma |
| Spatial assays/spatial transcriptomics92 | No | Greater preservation in FFPE | FFPE | Amyotrophic lateral sclerosis |
| Cell culture93 | NA | NA | Fresh tissues | Diffuse intrinsic pontine glioma |
| Patient-derived xenografts (PDX)94 | NA | NA | Fresh tissues | Pediatric midline glioma |
| Organoids95 | NA | NA | Fresh tissues/ established cell lines | Glioblastoma |