ct-DNA Liquid Biopsy Methods, Their Pros and Cons, and the Applications in Liquid Biopsy for H3K27M Altered DMG
| Ct-DNA Liquid Biopsy Method . | Pros . | Cons . | Best Suited for . |
|---|---|---|---|
| Sanger Sequencing | Affordable, rapid, sequencing-based | Cannot detect lower than ~15% VAF | Generally not suitable for liquid biopsy |
| ddPCR | Affordable, rapid, precise, can detect VAFs down to ~0.05% | Generally limited to single allele assays; assay design and validation are arduous | Frequent monitoring of known hotspot mutations |
| Targeted NGS sequencing | Can survey a wide variety of mutations. Panel design is relatively low-effort | Expensive, long turnaround times | Disease screening, initial diagnostics, and tumor evolution monitoring |
| Targeted nanopore sequencing | Affordable assays and equipment costs. Rapid turn-around times | Requires concatemeric assays for error correction to increase sensitivity for low VAF samples | Frequent monitoring of a panel of genes or known resistance markers |
| NGS WES/WGS sequencing | Characterization of the entire tumor genome/exome. Unparalleled breadth of diagnostic information | Expensive, long turnaround times, lower depth per locus limiting sensitivity for low VAF samples | Limited utility due to current feasibility |
| Ct-DNA Liquid Biopsy Method . | Pros . | Cons . | Best Suited for . |
|---|---|---|---|
| Sanger Sequencing | Affordable, rapid, sequencing-based | Cannot detect lower than ~15% VAF | Generally not suitable for liquid biopsy |
| ddPCR | Affordable, rapid, precise, can detect VAFs down to ~0.05% | Generally limited to single allele assays; assay design and validation are arduous | Frequent monitoring of known hotspot mutations |
| Targeted NGS sequencing | Can survey a wide variety of mutations. Panel design is relatively low-effort | Expensive, long turnaround times | Disease screening, initial diagnostics, and tumor evolution monitoring |
| Targeted nanopore sequencing | Affordable assays and equipment costs. Rapid turn-around times | Requires concatemeric assays for error correction to increase sensitivity for low VAF samples | Frequent monitoring of a panel of genes or known resistance markers |
| NGS WES/WGS sequencing | Characterization of the entire tumor genome/exome. Unparalleled breadth of diagnostic information | Expensive, long turnaround times, lower depth per locus limiting sensitivity for low VAF samples | Limited utility due to current feasibility |
Abbreviations: CapEx = capital expenditure/equipment cost; ddPCR = droplet digital PCR; DMG= diffuse midline glioma; NGS = next generation sequencing; VAF = variant allele fraction; WES = whole exome sequencing; WGS = whole genome sequencing.
ct-DNA Liquid Biopsy Methods, Their Pros and Cons, and the Applications in Liquid Biopsy for H3K27M Altered DMG
| Ct-DNA Liquid Biopsy Method . | Pros . | Cons . | Best Suited for . |
|---|---|---|---|
| Sanger Sequencing | Affordable, rapid, sequencing-based | Cannot detect lower than ~15% VAF | Generally not suitable for liquid biopsy |
| ddPCR | Affordable, rapid, precise, can detect VAFs down to ~0.05% | Generally limited to single allele assays; assay design and validation are arduous | Frequent monitoring of known hotspot mutations |
| Targeted NGS sequencing | Can survey a wide variety of mutations. Panel design is relatively low-effort | Expensive, long turnaround times | Disease screening, initial diagnostics, and tumor evolution monitoring |
| Targeted nanopore sequencing | Affordable assays and equipment costs. Rapid turn-around times | Requires concatemeric assays for error correction to increase sensitivity for low VAF samples | Frequent monitoring of a panel of genes or known resistance markers |
| NGS WES/WGS sequencing | Characterization of the entire tumor genome/exome. Unparalleled breadth of diagnostic information | Expensive, long turnaround times, lower depth per locus limiting sensitivity for low VAF samples | Limited utility due to current feasibility |
| Ct-DNA Liquid Biopsy Method . | Pros . | Cons . | Best Suited for . |
|---|---|---|---|
| Sanger Sequencing | Affordable, rapid, sequencing-based | Cannot detect lower than ~15% VAF | Generally not suitable for liquid biopsy |
| ddPCR | Affordable, rapid, precise, can detect VAFs down to ~0.05% | Generally limited to single allele assays; assay design and validation are arduous | Frequent monitoring of known hotspot mutations |
| Targeted NGS sequencing | Can survey a wide variety of mutations. Panel design is relatively low-effort | Expensive, long turnaround times | Disease screening, initial diagnostics, and tumor evolution monitoring |
| Targeted nanopore sequencing | Affordable assays and equipment costs. Rapid turn-around times | Requires concatemeric assays for error correction to increase sensitivity for low VAF samples | Frequent monitoring of a panel of genes or known resistance markers |
| NGS WES/WGS sequencing | Characterization of the entire tumor genome/exome. Unparalleled breadth of diagnostic information | Expensive, long turnaround times, lower depth per locus limiting sensitivity for low VAF samples | Limited utility due to current feasibility |
Abbreviations: CapEx = capital expenditure/equipment cost; ddPCR = droplet digital PCR; DMG= diffuse midline glioma; NGS = next generation sequencing; VAF = variant allele fraction; WES = whole exome sequencing; WGS = whole genome sequencing.
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