NGS overview
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The document discusses the advantages and future of next-generation sequencing (NGS). It notes that the NGS market has grown rapidly, with costs and runtimes decreasing significantly over time. Current optimization aims to further lower costs and runtimes while increasing ease-of-use. NGS allows for hypothesis-free and versatile experimental design. A diverse set of applications are discussed, including whole genome sequencing, exome sequencing, and metagenome sequencing. The document predicts that new platforms will offer cheaper, quicker, and longer sequencing. Future applications may include single-cell sequencing and direct detection of base modifications.
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NGS overview
- 1. The Advantages and Future of NGS Shawn C. Baker, Ph.D.
- 2. NGS is Easy!
- 3. Erm…
- 4. Help!
- 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. 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. Previous optimization path: Increase output/run HiSeq 2000 - 600Gb HiSeq 2000 - 200Gb GAIIx - 95Gb Gb/run GAIIx - 50Gb GAII - 30Gb GA - 5Gb Solexa 1G - 1Gb 2007 2008 2009 2010 2011
- 8. Result
- 9. Current optimization path: Decrease instrument cost $500k-$800k $50k-$125k
- 10. Current optimization path: Decrease runtime
- 11. Current optimization path: Decrease cost per run
- 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. NGS Strengths
- 14. NGS Strengths Hypothesis-free design
- 17. NGS Weaknesses
- 18. NGS Weaknesses Too much info
- 19. NGS Weaknesses No absolute quantitation – everything is relative
- 20. Diverse set of applications Whole Genome Sequencing Small Genome Sequencing Targeted DNA Sequencing Exome Sequencing Transcriptome Sequencing ChIP Sequencing Metagenome Sequencing
- 21. Whole Genome Sequencing Basic research Cancer genomics Unknown genetic cause Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
- 22. Exome Sequencing Lower cost Easier analysis Medical genomics Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
- 23. Targeted DNA Sequencing Focused research Gene sets Much less expensive Much faster Requires upfront design Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
- 24. Small Genome Sequencing Basic research Pathogen ID Credit: Rocky Mountain Laboratories, NIAID, NIH Credit: Graham Colm (Wikipedia)
- 25. Transcriptome Sequencing Functional studies Drug response Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
- 26. ChIP Sequencing Protein-nucleic acid interactions Genome structure/modific ations Transcription factors Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
- 27. Metagenome Sequencing Microbe communities Enzyme/gene discovery Human health
- 28. So what happens next? New Platforms promise: • Cheaper • Quicker • Longer
- 31. New applications Single cell sequencing Rare variant detection Haplotyping Environmental sequencing Direct detection of base modifications
- 32. New applications Single cell sequencing
- 33. New applications Rare variant detection
- 35. New applications Environmental sequencing
- 36. New applications Direct detection of base modifications