Brad Langhorst
Product Development Group Leader - New England Biolabs
Recent updates to
primer-monitor.neb.com
Date
Brad Langhorst
Brad Langhorst, Matt Campbell, Caiden Kumar
Talk Plan
- Review primer-monitor.neb.com
- Recent enhancements
- Demostration (Caiden)
- Next steps / Discussion
Why does NEB Care About SARS-CoV-2 Variants?
We want be sure that our LAMP, qPCR and sequencing SARS-CoV2 kits can be updated as new variants arise
They don't like sunlight
Don't get them wet
Don't feed them after midnight!
https://medium.com/@Naturalish/gremlins-three-rules-an-evolutionary-analysis-de4c4fae2785
Other people probably need this too... FDA guidance
What can we do???
Shine some light
Aligned Sequences AY.1
Lineage Variants
Other Variants Matter for Diagnostics
Data, well-organized, is light
Nightly Download
Genome Alignment
Variant Calling
RelationalDatabase
Matt Campbell, Caiden Kumar
https://www.nature.com/articles/d41586-023-01517-9
Visualization - simple
Visualization - multiplex PCR
Challenges
- not interactive enough
- can't fit multiplex PCR (too many primers)
- not auto-updating (manual publishing needed)
- does not visualize geography (map based?)
- dense data (SARS-CoV-2) vs. sparse data (all others)
- variant frequency vs time is not visible
Take it away Caiden
Planned Features
- More geographic detail ✅
- Fully automated intake/update ✅
- Automated visualization updates ✅ (almost)
- Automated notification ✅
- Primer set scores ✅
- View primer set as a whole ✅
- mulitplex PCR visualizations
- Add data sources for RSV, influenza, HPV, ...?
- Variants by time
- Suggestions welcome!
Thanks!
Caiden Kumar
Matt Campbell
NEB Leadership
Discussion/ Questions
Possible Topics:
- Can we achieve good coverage with 1.4 kb amplicons in typical clinical samples? Ct limitations?
- Initial results from collaborators with clinical samples show good performance even at higher Ct (27-32)
Primer Monitor Update - 2023-08
By Brad Langhorst
