ngs overview

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

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/

120

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

www.blueseq.comsbaker@blueseq.com