Targeted Enrichment
Related: NGS Library Preparation · Whole-Genome Sequencing · Metagenomic NGS · Multiplex PCR
1. Principle
Targeted enrichment concentrates sequences of interest before or during NGS — via hybrid-capture probes or multiplex amplicons — so scarce pathogen genomes can be recovered from host-dominated specimens.
2. Step-by-Step Procedure (conceptual)
Hybrid capture
- Make shotgun library from extract.
- Hybridize to biotinylated probes (viral panels, AMR panels, bacterial bait sets).
- Pull down with streptavidin beads → wash → amplify → sequence.
Amplicon enrichment
- Multiplex PCR tiles the target genome (e.g., SARS-CoV-2 ARTIC-style).
- Pool amplicons → adapters → sequence.
3. Interpretation
- Great on-target rate for known pathogens; blind to off-panel organisms.
- Escape mutations under primer/probe sites → dropout (coverage holes).
- Still needs bioinformatics QC and reference mapping.
4. Clinical Use Cases
- Viral whole-genome surveillance from swabs.
- Resistome panels from mixed samples.
- Culture-negative infections when a candidate pathogen class is suspected.
5. Comparison with Other Methods
| Method | Scope | Sensitivity for known targets |
|---|---|---|
| Targeted enrichment | Panel only | High |
| Metagenomic NGS | Broad | Lower without depletion |
| Multiplex PCR | Small panel | Highest speed |
6. Mnemonic / Visual Aid
Fish with bait (capture) vs photocopy known chapters (amplicons).
Active Recall
- Hybrid capture vs amplicon — which better tolerates primer-site mutations?
- Why can enriched SARS-CoV-2 genomes show amplicon dropouts?
- When choose mNGS over enrichment?