ngs overview
DESCRIPTION
BlueSEQ's presentation given at the CHI Digital PCR meeting. This was one half of a "Digital PCR vs Next Gen Sequencing" panel discussion.TRANSCRIPT
Shawn C. Baker, Ph.D.
The Advantages and Future of NGS
NGS is Easy!
Erm…
Help!
Rapidly growing market
130% increase in placed systems in one year
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500
1000
1500
2000
2500
3000
3500
4000
4500
Previous optimization path:Precipitous drop in price/base
$0.01
$0.10
$1.00
$10.00
$100.00
$1,000.00
$10,000.00
Cost per Million Bases SequencedDropped nearly 5 orders of magnitude over
past 11 years2001
2012
Previous optimization path:Increase output/run
Gb/r
un
Solexa 1G - 1Gb
GAIIx - 95Gb
GA - 5Gb
GAIIx - 50GbGAII - 30Gb
HiSeq 2000 - 200Gb
2007 2008 2009 2010 2011
HiSeq 2000 - 600Gb
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
Exome Sequencing
Targeted DNA Sequencing
Small Genome Sequencing
Transcriptome Sequencing
ChIP Sequencing
Metagenome Sequencing
Whole Genome Sequencing
Basic research
Cancer genomics
Unknown genetic cause
Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
Exome Sequencing
Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
Lower cost
Easier analysis
Medical genomics
Targeted DNA Sequencing
Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
Focused research
Gene sets
Much less expensive
Much faster
Requires upfront design
Small Genome Sequencing
Credit: Rocky Mountain Laboratories, NIAID, NIH
Credit: Graham Colm (Wikipedia)
Basic research
Pathogen ID
Transcriptome Sequencing
Functional studies
Drug response
Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
ChIP Sequencing
Credits: Darryl Leja (NHGRI), Ian Dunham (EBI)
Protein-nucleic acid interactions
Genome structure/modifications
Transcription factors
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
Rare variant detection
Haplotyping
Environmental sequencing
Direct detection of base modifications
New applications
Single cell sequencing
Rare variant detection
Haplotyping
Environmental sequencing
Direct detection of base modifications
New applications
Single cell sequencing
Rare variant detection
Haplotyping
Environmental sequencing
Direct detection of base modifications
New applications
Single cell sequencing
Rare variant detection
Haplotyping
Environmental sequencing
Direct detection of base modifications
New applications
Single cell sequencing
Rare variant detection
Haplotyping
Environmental sequencing
Direct detection of base modifications
