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Sequencing at the speed of life

Sequencing at the speed of life. Simple is beautiful. 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.

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Sequencing at the speed of life

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  1. Sequencing at the speed of life

  2. Simple is beautiful

  3. Simple is beautiful

  4. Feel the chemistry

  5. Overall Performance Field Guide to next-generation DNA Sequencers, Glenn (2011)

  6. Costs and Error Rate Field Guide to next-generation DNA Sequencers, Glenn (2011)

  7. Technological Summary Advantages • Low costs • Performance limited by the chip • Moore’s law • Rapid advancement Disadvantages • Relatively low throughput • Error-prone at homopolymers • Washing can lead to errors http://upload.wikimedia.org/wikipedia/commons/c/c5/PPTMooresLawai.jpg

  8. 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."

  9. Everything is relative “In general, all of the massively parallel platforms have some pain that purchasers and users will feel. This pain can be expressed in many forms, including reagent costs, wait time, instrument failure, failed library preparations, suboptimal numbers of reads or read length, or difficulty in analyses. The trick is to find systems for which the pain delivered best matches your tolerance, problem solving and coping skills.” - Field Guide to next-generation DNA Sequencers, Glenn (2011)

  10. Ion Torrrent: Application Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

  11. 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 After receipt of sample: 3 libraries generated 7 sequencing runs 79 Mb of sequencing data of 101 (mean) bp reads Crowd-sourced initial assembly within 24 hours

  12. 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

  13. Jonathan M. Rothberg • 1999: founded 454 Life Sciences • 2007: founded Ion Torrent

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