Table 1 Summary of the types of technologies used in clonality analysis
Methods | Depth/resolution | CNA | BAF | Variant detection | Subclonal reconstruction | Comment |
|---|---|---|---|---|---|---|
CGH arrays | Low: 5–10 Mb | ✓ | x | x | x | Suitable for clonality analysis in tumours with high SCNA |
Low coverage WGS | Low: <4× | ✓ | x | x | x | |
SNP arrays | 300 K–1 M SNPs | ✓ | ✓ | x | x | Suitable for clonality analysis in tumours with high and low SCNA |
Targeted sequencing panel | High depth (>200×) but only on target regions | ✓ | x | ✓ | ✓ | SCNA called from off-target sequence suited to clonality analysis but BAF may be unreliable with so few genes; phylogenetic analysis is possible with ultra-deep sequencing (>500×) using TRONCO but limited power due to selective genomic markers [9] |
Low coverage WES | 30–60× | ✓ | ✓ | ✓ | x | Read depth might be too low for subclonal analyses but suited to clonality analyses of paired/multi-region samples. Needs matching normal DNA for maximum power. |
High coverage WES | High: >60× | ✓ | ✓ | ✓ | ✓ | Powerful for clonality analyses but needs matching normal DNA. Low purity might interfere with the estimation of subclonal SCNA especially at lower depth. |
WGS | High breakpoint resolution but depth can be low >30× | ✓ | ✓ | ✓ | ✓ | |
Single cell sequencing | Low individual cell resolution | ✓ | ✓ | x | ✓ | Individual cell allele-specific CN for deep subclonal reconstruction [10, 11]; mutation calling still challenging due to allelic dropout at the individual cell level. |