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NGS overview

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BlueSEQ's presentation given at the CHI Digital PCR meeting. This was one half of a "Digital PCR vs Next Gen Sequencing" panel discussion.

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NGS overview

  1. 1. The Advantages and Future of NGS Shawn C. Baker, Ph.D.
  2. 2. NGS is Easy!
  3. 3. Erm…
  4. 4. Help!
  5. 5. Rapidly growing market 130% increase in placed systems in one year 4500 4000 3500 3000 2500 2000 1500 1000 500 0 9/1/11 10/1/11 11/1/11 12/1/11 1/1/12 2/1/12 3/1/12 4/1/12 5/1/12 6/1/12 7/1/12 8/1/12
  6. 6. Previous optimization path:Precipitous drop in price/base Cost per Million Bases Sequenced Dropped nearly 5 orders of magnitude over past 11 years $10,000.00 2001 $1,000.00 $100.00 $10.00 $1.00 $0.10 2012 $0.01
  7. 7. Previous optimization path:Increase output/run HiSeq 2000 - 600Gb HiSeq 2000 - 200Gb GAIIx - 95GbGb/run GAIIx - 50Gb GAII - 30Gb GA - 5Gb Solexa 1G - 1Gb 2007 2008 2009 2010 2011
  8. 8. Result
  9. 9. Current optimization path:Decrease instrument cost $500k-$800k $50k-$125k
  10. 10. Current optimization path:Decrease runtime
  11. 11. Current optimization path:Decrease cost per run
  12. 12. Current optimization path: Increase ease of use Touchscreen operation Higher level of automation Cartridge-based reagent system Connected to cloud-based analysis tools
  13. 13. NGS Strengths
  14. 14. NGS Strengths Hypothesis-free design
  15. 15. NGS Strengths Versatile
  16. 16. NGS Strengths Counting
  17. 17. NGS Weaknesses
  18. 18. NGS Weaknesses Too much info
  19. 19. NGS Weaknesses No absolute quantitation – everything is relative
  20. 20. Diverse set of applications Whole Genome Sequencing Small Genome Sequencing Targeted DNA Sequencing Exome Sequencing Transcriptome Sequencing ChIP Sequencing Metagenome Sequencing
  21. 21. Whole Genome Sequencing  Basic research  Cancer genomics  Unknown genetic causeCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  22. 22. Exome Sequencing  Lower cost  Easier analysis  Medical genomicsCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  23. 23. Targeted DNA Sequencing  Focused research  Gene sets  Much less expensive  Much faster  Requires upfront designCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  24. 24. Small Genome Sequencing  Basic research  Pathogen IDCredit: Rocky Mountain Laboratories, NIAID, NIH Credit: Graham Colm (Wikipedia)
  25. 25. Transcriptome Sequencing  Functional studies  Drug responseCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  26. 26. ChIP Sequencing  Protein-nucleic acid interactions  Genome structure/modific ations  Transcription factorsCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  27. 27. Metagenome Sequencing  Microbe communities  Enzyme/gene discovery  Human health
  28. 28. So what happens next? New Platforms promise: • Cheaper • Quicker • Longer
  29. 29. Sequencing by hybridization
  30. 30. Nanopore sequencing
  31. 31. New applications Single cell sequencing Rare variant detection Haplotyping Environmental sequencing Direct detection of base modifications
  32. 32. New applications Single cell sequencing
  33. 33. New applications Rare variant detection
  34. 34. New applications Haplotyping
  35. 35. New applications Environmental sequencing
  36. 36. New applications Direct detection of base modifications
  37. 37. www.blueseq.comsbaker@blueseq.com

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