Sample interview questions: How do you handle the challenges of working with degraded DNA or RNA samples in genomics analysis?
Sample answer:
Challenges in Working with Degraded DNA/RNA Samples
- Fragmentation: Degraded samples yield smaller DNA/RNA fragments, limiting sequencing read lengths and assembly accuracy.
- Base modifications: Chemical modifications induced by degradation can introduce sequencing errors and ambiguity in base calling.
- Low yield: Degraded samples often have low DNA/RNA concentrations, requiring highly sensitive amplification methods.
Strategies to Handle Degraded Samples
Sample Preparation:
- Optimize extraction methods: Use specific kits designed for degraded samples, which minimize shearing and chemical modifications.
- Assess sample quality: Quantify DNA/RNA concentration and assess fragmentation using gel electrophoresis or automated assays.
- Optimize amplification: Employ techniques like PCR with proofreading polymerases and optimize amplification cycles to minimize errors.
Sequencing:
- Select appropriate sequencing platforms: Utilize platforms like Nanopore sequencing, which can sequence long and damaged DNA/RNA fragments.
- Optimize library preparation:… Read full answer