Table 1 Comparison between somatic mutation discovery methods
Feature | Bulk sequencing | Duplex sequencing | Clonal expansion | Single-cell WGA (PTA) | LCM clones |
|---|---|---|---|---|---|
Applicability to any tissue | Yes | Yes | No | Yes | No |
Mutation types discovered | All | SNVs and indels | All | All | All |
Applicability to long read | Yes | Yes | Yes | Inefficient | Inefficient |
Fraction of genome sampled (%) | 100 | 30–100, depending on fragmentation method | 100 | Approximately 90 per cell; 100 across cells | 100 |
Detection of early and clonally expanded mutations | Most | Minority | Depending on clone number | Depending on cell number | Depending on clone number |
Overall mutation spectrum | No | Yes | Yes | Yes | Yes |
Likely amount of artefacts | Small (10−4) | Very small (less than 10−8) | Small (10−4) | Some | Small (10−4) |
Information on cell lineages | No | No | Yes | Yes | Yes |
Advantages | Sensitive detection of high-frequency mutations of all types | Obtaining overall mutation spectrum even at low (0.5–2×) duplex coverage | Accurate mutation discovery at a single-cell level | Mutation discovery at a single-cell level in any tissue | Accurate mutation discovery at a single-cell level |
Limitations | Need for high coverage; missing low-frequency mutations | Only SNVs and indels; missing high-frequency mutations at low (0.5–2×) coverage | Applicable to culturable or reprogrammable cells | Less than 50% sensitivity because of dropout and amplification artefacts | Applicable to tissues with visible clonal substructures |
