Table 1 Current status of genomic and related information
From: Integrating cancer genomic data into electronic health records
Technologies | Applications | Challenges |
|---|---|---|
IHC | Measuring gene overexpression | Expensive |
Flow cytometry | Cell surface protein tagging by fluorophores, detects co-expression and loss of expression | Limited spectral frequencies of fluorophores |
FISH | Copy number and rearrangement detection | Only works on known targets, cannot detect novel aberrations |
Polymerase chain reaction | Confirmatory test and detection of minimal residual disease | May only be scaled to a limited number of variants |
Gene expression panels | Production of a single score based on gene expression panel | Commercially available products are based on older datasets |
NGS panels | Detection of somatic variants using mostly full-exon sequencing. NGS panels may vary greatly in size (25–500+ genes) | Removing spurious results, identifying VUS, presenting results to clinicians |
WES/WGS | Sequencing of coding/all DNA, respectively | High cost, computational complexity, handling VUS, handling incidental findings |
Circulating cell-free tumor DNA | Monitoring solid tumor heterogeneity, surveying difficult-to-reach tumors | Not yet widely accepted, no consensus on technical approach, slow turnaround, high cost |
Washable IHC | Measuring protein expression with limited tissue sampling | Expensive technique, still experimental |
Mass cytometry | Protein tagging by metal ion tags, detects co-expression and loss of expression | Only applicable in cases with known targets, expensive, still experimental |
Methylation panels | Determines methylation patterns, which correlate with hypomethylating agent efficacy | Slow adoption of these panels |