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Next-generation sequencing from 2005 to 2020

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Recap of the development of next-generation sequencing (NGS) platforms from 2005 to 2015 followed by a brief outlook into the year 2020.

Published in: Science
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Next-generation sequencing from 2005 to 2020

  1. 1. Next-generation sequencing (NGS) 2020 Christian Frech Bioinformatics Core Unit CCRI Retreat Retz April 13, 2015
  2. 2. NGS 2005 454 sequencer
  3. 3. 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%
  4. 4. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  5. 5. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  6. 6. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  7. 7. Genome Analyzer II 50bp reads, 3 Gb / run 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  8. 8. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  9. 9. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  10. 10. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  11. 11. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  12. 12. 2005 20102006 2007 2008 2009 454 Solexa GA1 HiSeq 2000 PacBio Complete Genomics First Illumina human genome + First tumor/normal pair Helicos single-molecule 454 Watson Genome Illumina GA2 Helicos human genome SOLiD
  13. 13. 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
  14. 14. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  15. 15. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  16. 16. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  17. 17. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  18. 18. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  19. 19. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  20. 20. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  21. 21. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  22. 22. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore bact. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  23. 23. 2010 20152011 2012 2013 2014 HiSeq X Ten MiSeq Nanopore euk. genome Nanopore early access Ion Torrent PGM PacBio human genome BGI acquires Complete Genomics Helicos bancrupt Ion Proton 454 shutdown
  24. 24. 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
  25. 25. • 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 ?
  26. 26. 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
  27. 27. Thank you!
  28. 28. SOLiD 2015

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