NGS overview
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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.

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 NGS overview Presentation Transcript

  • The Advantages and Future of NGS Shawn C. Baker, Ph.D.
  • NGS is Easy!
  • Erm…
  • Help!
  • 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
  • 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
  • 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
  • Result
  • Current optimization path:Decrease instrument cost $500k-$800k $50k-$125k
  • Current optimization path:Decrease runtime
  • Current optimization path:Decrease cost per run
  • Current optimization path: Increase ease of use Touchscreen operation Higher level of automation Cartridge-based reagent system Connected to cloud-based analysis tools
  • NGS Strengths
  • NGS Strengths Hypothesis-free design
  • NGS Strengths Versatile
  • NGS Strengths Counting
  • NGS Weaknesses
  • NGS Weaknesses Too much info
  • NGS Weaknesses No absolute quantitation – everything is relative
  • Diverse set of applications Whole Genome Sequencing Small Genome Sequencing Targeted DNA Sequencing Exome Sequencing Transcriptome Sequencing ChIP Sequencing Metagenome Sequencing
  • Whole Genome Sequencing  Basic research  Cancer genomics  Unknown genetic causeCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  • Exome Sequencing  Lower cost  Easier analysis  Medical genomicsCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  • Targeted DNA Sequencing  Focused research  Gene sets  Much less expensive  Much faster  Requires upfront designCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  • Small Genome Sequencing  Basic research  Pathogen IDCredit: Rocky Mountain Laboratories, NIAID, NIH Credit: Graham Colm (Wikipedia)
  • Transcriptome Sequencing  Functional studies  Drug responseCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  • ChIP Sequencing  Protein-nucleic acid interactions  Genome structure/modific ations  Transcription factorsCredits: Darryl Leja (NHGRI), Ian Dunham (EBI)
  • Metagenome Sequencing  Microbe communities  Enzyme/gene discovery  Human health
  • So what happens next? New Platforms promise: • Cheaper • Quicker • Longer
  • Sequencing by hybridization
  • Nanopore sequencing
  • New applications Single cell sequencing Rare variant detection Haplotyping Environmental sequencing Direct detection of base modifications
  • New applications Single cell sequencing
  • New applications Rare variant detection
  • New applications Haplotyping
  • New applications Environmental sequencing
  • New applications Direct detection of base modifications
  • www.blueseq.comsbaker@blueseq.com