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6. Out of the shadows - the future of bioinformatics


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This is the sixth presentation at Eagle Genomics second symposium 29th March 2012. Presented by Mick Watson who is Director of ARK-Genomics, The Roslin Institute. …

This is the sixth presentation at Eagle Genomics second symposium 29th March 2012. Presented by Mick Watson who is Director of ARK-Genomics, The Roslin Institute.
With bench scientists increasingly incapable of handling the volumes and types of sequence data, bioinformatics is now the most important aspect of genomics. It is impossible to carry out genomics research without sophisticated tools and intelligent, driven bioinformaticians. Often, bioinformaticians are best placed to design experiments and to advise on how to get the best results from genomics projects. BBSRC describe the current period of research as "The Age of Bioscience" when perhaps it should be "The Age of Bioinformatics". It is now time for bioinformatics to mature as a science, to increase the emphasis on "bio" as well as "informatics", and for bioinformaticians to lead the new wave of genomics research. Rather than a single genome per species, we must now recognise that every individual consists of a collection of genomes that are structurally variant; in addition to which, we can now measure epigenetic effects, such as methylation, at single-base accuracy. The paradigm is one individual, many genomes, many epigenomes. In addition to microbial metagenomics and the challenges faced therein, we are rapidly approaching large, eukaryotic metagenomics. All of these, combined with modern ways for communicating scientific research, combine to demand a new paradign for genomics research and an increased emphasis on the importance of bioinformatics.

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  • 1. Out of the shadows – the future of bioinformatics (The next ten years of genome content management) Mick Watson Director of ARK-Genomics The Roslin Institute
  • 2. Structure• Genomics and global challenges• Roslin; ARK-Genomics• Current Research• Genome Content Management• Future of Bioinformatics
  • 4. Challenges in food security• The World’s food system doesn’t work: – 1.5bn overweight, 500m obese1 – 925m experience hunger, +1bn “hidden hunger”2• Moving forward, there are a number of key pressures: 1. WHO [] 2. Foresight report “The Future of Food and Farming: Challenges and choices for global sustainability”
  • 5. Should we be worried? • Yes and no! Humans have been improving food for many centuries • Note: no information for beef cattle and sheep
  • 7. Personalised medicine in the UK
  • 8. Basic recommendations• Diagnosis of disease (esp. heritable)• Analysis of clinically relevant data• Development of biomedical informatics• Development of evidence base• Genomic screening
  • 9. The missing link? Genome Variation ? SNP Disease
  • 10. Success – Nicholas Volker •Mayer AN, Dimmock DP, Arca MJ, Bick DP, Verbsky JW, Worthey EA, Jacob HJ,Margolis DA. A timely arrival for genomic medicine. Genet Med. 2011 13(3):195-6. •Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, Basehore MJ, Broeckel U, Tomita-Mitchell A, Arca MJ, Casper JT, Margolis DA, Bick DP, Hessner MJ, Routes JM, Verbsky JW, Jacob HJ, Dimmock DP. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011 13(3):255-62.• Six year old boy, sever case of inflammatory bowel disease• Doctors unable to diagnose• Underwent exome sequencing -> 16124 variants• Found one, XIAP gene, indicating bone marrow transplant• Significant recovery after treatment
  • 12. The Roslin Institute LIVESTOCK GENETICS Bioscience underpinning health ANIMAL HEALTH BIOTECH HUMAN HEALTH Food security
  • 13. The Roslin Institute: Aims Enhance animal health and welfare through knowledge animal genetics Enhance sustainability and productivity of livestock systems Enhance food safety by understanding host-pathogen interactions Enhance human health through an understanding of disease Identify new and emerging zoonoses Enhance quality of life for farmed animalsHighlights Wilmut at al (1997) Viable offspring derived from fetal and adult mammalian cells. Nature 385(6619):810-3 C. McKenzie Zhao et al (2010) Somatic sex identity is cell autonomous in the chicken. Nature 464(7286):237-242 Lyall et al (2011) Suppression of avian influenza transmission in genetically modified chickens. Science 331(6014):223-6 Baillie JK et al (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature. 479(7374):534-7.
  • 14. • ARK-Genomics – High-throughput facility focusing on the genetics and genomics of animals – Based at the Roslin Institute, University of Edinburgh – Offering research, collaborations and service provision – Investing in the latest genomics technologies • Sequencing • Genotyping • Transcriptomics • Comparative Genomics • Bioinformatics
  • 16. Current Research• Virus discovery• Pathogen genomics• Host genomics – Re-sequence: Chicken – New: e.g. Falcon, Elephant• Host-pathogen interactions• Metagenomics• Industrial Biotechnology
  • 18. What is a genome?• Paradigm so far: species-level reference (+ variants)• For hereditary disease, we need to know individual-level genome• For cancer, we need to know the tissue- or cell-type- specific genome and epigenome• Genomes within an individual vary: retrotransposons, SV etc• Methylation states can be static or dynamic Future Paradigm One individual -> many genomes -> many epigenomes
  • 19. The future of genome content management We will each own, and manage, our own + Personalised medicine
  • 21. DNA sequencing isrevolutionizing biology and medicine
  • 22. Bioinformatics is now themost crucial step in DNA sequencing
  • 23. Bioinformaticians shouldbe designing and leading genomics projects
  • 24. What is Bioinformatics?• Dayhoff, M. O. and R. S. Ledley (1962). Comprotein: A Computer Program to Aid Primary Protein Structure Determination. In Proceedings of the Fall Joint Computer Conference, 1962, 262-274.• J. M. Bennett and J. C. Kendrew (1952). The computation of Fourier synthesis with a digital electronic calculating machine. Acta Cryst. 5, 109-116• Fisher, R. A. (1950) Gene frequencies in a cline determined by selection and diffusion. Biometrics 6: 353–361.• Types of bioinformatician? 1) The software developer 2) The statistician 3) The data miner/analyst 4) The database developer• Is a bioinformatician “all of the above” plus knowledge of biology?• How do you teach that?
  • 25. Bioinformatics research (the “Watson Square”) Holy Grail Less Memory Quicker Technology No improvement More functional information Better assembly Initial bioinformatics tool Biology
  • 26. Future Technologies• Third-generation sequencing (TGS)• Single molecule sequencing The Promise The current reality Billions of reads ~80,000 reads 10,000 – 50,000 read length up to 2.5kb High accuracy 15% error rate• Challenges – Each observation relates to zero, one or more realities – Technology-aware software Branton et al (2008) Nat. Biotech. 26(10):1146 Schadt et al (2010) Hum. Mol. Gen. 19(R2):R227
  • 27. Future technologies• There are no “game changers” yet – Helicos – Pacific Biosciences• There’s a complex IP landscape• What will we do when we no longer have to assemble things? – Functional, statistical – Closer to function
  • 28. Will the future happen in 2012?• Single molecule sequencing• Reads 100Kb+• What will this enable? – Easier assembly – Analysis of structural variation – Analysis of within individual variation – Faster diagnosis
  • 29. Q: What will we do when we no longer need to assemble genomes?A1: (technical) With the flood of data from individual genomics, we will need software and tools to manage itA2: (biological) We will also need people to interpret it Both are within the domain of bioinformatics
  • 30. SUMMARY
  • 31. Summary• There are serious, global challenges ahead• Genomics (and genetics) can and will help• We are rapidly approaching individual genomics• Bioinformatics remains a key skill – Technology development – Biological interpretation• Bioinformaticians can (and do) lead genomics projects