Next-generation sequencing (NGS) 2020
Christian FrechBioinformatics Core Unit
CCRI Retreat RetzApril 13, 2015
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