sequencing at the speed of life. simple is beautiful
TRANSCRIPT
Simple is beautiful
Feel the chemistry
Overall Performance
Field Guide to next-generation DNA Sequencers, Glenn (2011)
Costs and Error Rate
Field Guide to next-generation DNA Sequencers, Glenn (2011)
Technological Summary
• Low costs• Performance limited by the
chip– Moore’s law
• Rapid advancement
http://upload.wikimedia.org/wikipedia/commons/c/c5/PPTMooresLawai.jpg
Advantages
Disadvantages
• Relatively low throughput• Error-prone at homopolymers• Washing can lead to errors
Competitors
• Nov, 2011: Roche plans to migrate 454 optical sequencing to electrochemical detection with help from DNA electronics
• “[The new technology will] build on 454 Life Sciences’ current pyrosequencing-based sequencing platforms by enabling a seamless evolution from optical detection to inexpensive, highly scalable electrochemical detection."
Everything is relative
“In general, all of the massively parallel platforms havesome pain that purchasers and users will feel. This paincan be expressed in many forms, including reagent costs,wait time, instrument failure, failed library preparations,suboptimal numbers of reads or read length, or difficultyin analyses. The trick is to find systems for which the paindelivered best matches your tolerance, problem solvingand coping skills.”
- Field Guide to next-generation DNA Sequencers, Glenn (2011)
Ion Torrrent: ApplicationOpen-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4
After receipt of sample:
3 libraries generated7 sequencing runs79 Mb of sequencing data of 101 (mean) bp reads
Crowd-sourced initial assembly within 24 hours
Sample TY2482 (new) has close similarity to strain 01-09591 (Germany, 2001) based on sequence of 5 house-keeping genes
Single-base difference in adk gene
Difference in homopolymeric run in recA gene
Current Problems
Presently, only 20-40% of sensors give mappable reads
• Incomplete loading of the chip• Insufficient amplification on the bead• Lack of clonality of the template
Future Developments
• Improvement of loading and template preparation• Average read length• Read accuracy
Jonathan M. Rothberg
• 1999: founded 454 Life Sciences
• 2007: founded Ion Torrent