Les NGS en pratique. Quelques slides sur les NGS et leur utilisation... Laurent (travail avec Marta, toujours en cours...)

Transcription

1 Quelques slides sur les NGS et leur utilisation... LIFL, Université Lille 1 - INRIA Journées au vert 31 mai - 1er juin

2 NEWS FEATURE HUMAN GENOME AT TEN NATURE Vol April 2010 NATURE Vol April April 2010 HUMAN GENOME AT TEN NEWS FEATURE THE SEQUENCE EXPLOSION A t the time of the announcement of the first drafts of the human genome in 2000, there were 8 billion base pairs of sequence in the three main databases for finished sequence: GenBank, run by the US National Center for Biotechnology Information; the DNA Databank of Japan; and the European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database. The databases share their data regularly as part of the International Nucleotide Sequence Database Collaboration (INSDC). In the subsequent first post-genome decade, they have added another 270 billion bases to the collection of finished sequence, doubling the size of the database roughly every 18 months. But this number is dwarfed by the amount of raw sequence that has been created and stored by researchers around the world in the Trace archive and Sequence Read Archive (SRA). See Editorial, page 649, and human genome special at SOURCE: NCBI; GRAPHICS BY N. SPENCER & W. FERNANDES HOW MANY HUMAN GENOMES? The graphic shows all published, fully sequenced human genomes since 2000, including nine from the first quarter of Some are resequencing efforts on the same person and the list does not include unpublished completed genomes. 1. Venter, J. C. et al. Science 291, (2001). 9. Ahn, S.-M. et al. Genome Res. 19, International Human Genome Sequencing (2009). Consortium Nature 409, (2001). 10. Kim, J.-I. et al. Nature 460, (2009). 3. International Human Genome Sequencing 11. Pushkarev, D., Neff, N. F. & Quake, S. R. Nature Consortium Nature 431, (2004). Biotechnol. 27, (2009). 4. Levy, S. et al. PLoS Biol. 5, e254 (2007). 12. Mardis, E. R. et al. N. Engl. J. Med. 10, Wheeler, D. A. et al. Nature 452, (2008). (2009). 6. Ley, T. J. et al. Nature 456, (2008). 13. Drmanac, R. et al. Science 327, (2009). 7. Bentley, D. R. et al. Nature 456, (2008). 14. McKernan, K. J. et al. Genome Res. 19, Wang, J. et al. Nature 456, (2008). (2009). 15. Pleasance, E. D. et al. Nature 463, (2010). 16. Pleasance, E. D. et al. Nature 463, (2010). 17. Clark, M. J. et al. PLoS Genet. 6, e (2010). 18. Rasmussen, M. et al. Nature 463, (2010). 19. Schuster, S. C. et al. Nature 463, (2010). 20. Lupski, J. R. et al. N. Engl. J. Med. doi: / NEJMoa (2010). 21. Roach, J. C. et al. Science doi: / science (2010) Macmillan Publishers Limited. All rights reserved 671 source :

3 Equipement des ménages source :

4 Marché concurrent, nombreuses nouveautés source :

5 nouvelles versions scale down (plus accessibles) -> ->

6 le SMS arrive sur le marché

7 un SMRTbell

8 des nouveautés surprenantes (à suivre donc...) the world s smallest solid-state ph meter. Prix de 50,000$ et coût des réagents faible (puce à changer 500$) source :

9 des nouveautés surprenantes (à suivre donc...) source :

10 des nouveautés surprenantes (à suivre donc...) source :

11 des nouveautés surprenantes (à suivre donc...) source : video :

12 des nouveautés surprenantes (à suivre donc...)

13 des nouveautés surprenantes (à suivre donc...) Life Technologies approach involves tethering a nanocrystal semiconductor called a quantum dot to a DNA polymerase. A laser excites the dot, which then transfers energy to fluorescent dye-tagged bases, but only when the polymerase adds a base to the DNA chain being built from the template being sequenced source :

14 Cas pratiques Neanderthals & Homo sapiens

15 Cas pratiques Neanderthals & Homo sapiens genome comparisons suggest that the two groups mated an estimated 45,000 80,000 years ago in the eastern Mediterranean area. The sequencing study, from a consortium led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, found that the genomes of non- African H. sapiens today contain around 1 4% of sequence inherited from Neanderthals source :

16 Cas pratiques Désamination C -> U (fréquent sur de l ADN ancien)

17 Cas pratiques RNA dark matter or not? Most of these studies used tiling microarray technology, in which thousands of probes are used to assess the presence of RNA transcripts. But this method is known to suffer from limitations some probes can become attached to inappropriate sequences, for example. More recent research, however, in which RNA transcripts are sequenced directly using a technique called RNA-Seq, have hinted that the amount of the mammalian genome transcribed might not be as great as the earlier work suggested.... The team found that whereas the microarrays reported many mysterious transcripts, the RNA-Seq technology found few transcripts other than those linked to genes coding for proteins.... But Philipp Kapranov of Helicos BioSciences... is seeing quite different results. He says that he and his colleagues continue to find a high percentage of a cell s RNA originating from regions between genes. source : article original :

18 Quelques liens pour suivre ceux qui suivent l actualité NGS (blogs): Dan Koboldt: Nick Loman: Luke Jostins: Daniel Macarthur: un papier récent résumant les technos commercialisés: