next-generation sequencing from 2005 to 2020

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Next-generation sequencing (NGS) 2020 Christian Frech Bioinformatics Core Unit CCRI Retreat Retz April 13, 2015

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Next-generation sequencing (NGS) 2020

Christian FrechBioinformatics Core Unit

CCRI Retreat RetzApril 13, 2015

NGS 2005

454 sequencer

Why “next”-generation sequencing?(by 2005, compared to good ol’ Sanger)

• Massively parallel– Millions of sequencing reactions vs. 96 wells

• Therefore much cheaper– >1 Mio. $ vs. 25 Mio. $ for human genome

• Shorter reads – 100 bp vs. 700 bp

• Higher error rate– 1-2% error rate vs. 0.5%

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

Genome Analyzer II50bp reads, 3 Gb / run

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

2005 20102006 2007 2008 2009

454Solexa GA1

HiSeq 2000PacBio

Complete Genomics

First Illumina human genome +First tumor/normal pair

Helicos single-molecule

454 WatsonGenomeIllumina GA2

Helicos human genome

SOLiD

Status quo 2010

• Illumina starts dominating NGS market due to rapid improvements of their platform– 200 Gb per run, >$10k for human genome

• Roche 454 10x more expensive, but still valued for longer read length (~400 bp)

• Single-molecule sequencing platforms (Helicos, PacBio) niche players

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporebact. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

2010 20152011 2012 2013 2014

HiSeq X Ten

MiSeq Nanoporeeuk. genome

Nanopore early access

Ion Torrent

PGM PacBiohuman genome

BGI acquiresComplete Genomics

Helicosbancrupt

Ion Proton

454 shutdown

Status quo 2015

• Illumina clear market leader– 80-90% market share– 1,500 Gb per run, >$1k for human genome

• Most serious competitor is Ion Proton– Behind schedule with Chip upgrade

• Single-molecule sequencers on the rise– PacBio, Oxford Nanopore

• Routine human WGS in research and clinic– <$500 EUR per sample– Sequencing-as-a-service– Phasing available for little extra money

• Exploding market for liquid biopsies driven by cheap targeted sequencing and “precision medicine” initiatives

• Single-cell sequencing method of choice to study tumor heterogeneity

• RNA-seq with negligible costs for sequencing– <$20/sample; cost for library prep will dominate– Microarrays are dead (…likely not only for gene expression analysis)

• Single-molecule sequencers still in niche– Limited throughput, high error rates– Rapid amplicon sequencing (results within minutes in the lab)

2015 2020

?

Implications for the CCRI• New research opportunities

– WGS to characterize “atypical” tumors– Liquid biopsies for solid tumors, disease monitoring– Single-cell sequencing (RNA, DNA)

• Established assays will be increasingly complemented/challenged by cheap sequencing alternatives– PCR, FISH, MLPA, SNP-arrays– WGS as one-stop solution for mutation/CNA/SV detection

• Data volumes will grow significantly– Efficient computational pipelines utilizing all available hardware– Storage capacity– Cloud computing

Thank you!

SOLiD 2015