From DNA to Genomics: The Rise of Bioinformatics - Catherine Abbott

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Outline of Talk:

- Introduce bioinformatics
- Very very basic introduction to:
- DNA-molecular biology
- Genes
- Genomes
- Human Genome Project
- Genomics
- The challenges and the future

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From DNA to Genomics: The Rise of Bioinformatics - Catherine Abbott

  1. 1. From DNA to genomics: the rise of bioinformatics Catherine Abbott Cathy.abbott@flinders.edu.au Monday 2 December BioInfoSummer 2013 NB. Most images in this presentation are via Google images. 1
  2. 2. Outline of talk • Introduce bioinformatics • Very very basic introduction to – DNA-molecular biology – Genes – Genomes • Human Genome Project • Genomics • The challenges and the future 2
  3. 3. What is Bioinformatics? • Bioinformatics is the field of science in which biology informatics: computer science, information technology, mathematics, statistics and other sciences 3
  4. 4. Ouzounis CA.PLoS Comput Biol. 2012;8(4):e1002487. doi: 10.1371/journal.pcbi.1002487. Epub 2012 Apr 26. Rise and demise of bioinformatics? Promise and progress. • The ―Infancy‖ Period: 1996–2001 • The ―Adolescence‖ Period: 2002–2006 • The ―Adulthood‖ Period: 2007–2013
  5. 5. Central paradigm of Molecular Biology DNA Guanine- G Adenine- A Thymine- T Cytosine- C RNA Guanine- G Adenine- A Uracil- U Cytosine- C Protein Phenotype G Glycine Gly P Proline Pro A Alanine Ala V Valine Val 20 amino acids 5
  6. 6. Central paradigm of Molecular Biology 6
  7. 7. What is a gene? • The gene is the basic physical unit of inheritance http://www.bbc.co.uk/schools/gcsebitesize/science/add_aqa_pre_2011/celldivision/celldi vision1.shtml 7
  8. 8. 8
  9. 9. DNA Sequences- three bases and stop codons http://www.genome.gov/EdKit/bio2b.html 9
  10. 10. Reading frames http://www.genome.gov/EdKit/bio2e.html 10
  11. 11. Exons and Introns http://www.genome.gov/EdKit/bio2i.html 11
  12. 12. Further information • http://www.dnai.org/ • http://www.dnalc.org/websites/dnaftb.ht ml
  13. 13. 1977: Sanger Sequencing • used chemically altered "dideoxy" bases to terminate newly synthesized DNA fragments at specific bases (either A, C, T, or G). • Was awarded two nobel prizes 1958 and 1980 (shared with Gilbert and Berg) 13
  14. 14. Evolution of Sequencing Technology 1865 : Mendal shows inheritance in peas 1953 : Watson and Crick structure of DNA 1977 : Era of sequencing begins 1980 : Shotgun sequencing coined 1982 : GenBank founded 1983 : Kary Mullis and colleagues develop PCR 1986 : First commercial ABI sequencer launched 1990 : Blast algorithm developed at NCBI 1991 : EST strategy developed
  15. 15. Evolution of Sequencing Technology 1995 : Cycle Sequencing by Amersham; Applied Biosystems releases capillary electrophoresis system Prism 310; output 5000 bases per day 1997 : MegaBACE 1000 capillaries;output 250,000-500,000 bases per day 1998 : Pyrosequencing developed 2001 : Draft human sequence 2005 : Launch of Genome Sequencer 20 System by 454 Life Sciences based on Pyrosequencing technology; output 20 million bases per run
  16. 16. Fihlo JS Breast Cancer Research 2009
  17. 17. Traditional Sequencing vs 454 Technology 17
  18. 18. Genbank: 18
  19. 19. Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7.
  20. 20. Nucleic Acids Res. 2011 Jan;39(Database issue):D32-7.
  21. 21. What is Genomics? • An organism's complete set of DNA is called its genome • Genomics is the study of the entire genome of an organism • investigations into the structure and function of very large numbers of genes undertaken in a simultaneous fashion. 21
  22. 22. The Race 20th July 1969 26th June 2000 22
  23. 23. President Clinton 26th June 2000 • “We are here to celebrate the completion of the first survey of the entire human genome. Without a doubt, this is the most important, most wondrous map ever produced by humankind.” 23
  24. 24. Prime Minister Blair 26 June 2000 • “……a revolution in medical science whose implications far surpass even the discovery of antibiotics…... And every so often in the history of human endeavor there comes a breakthrough that takes humankind across a frontier and into a new era. ……a breakthrough that opens the way for massive advances in 24
  25. 25. February 2001 $2.7 billion US $300 million US 25
  26. 26. Cost of Private effort-13 years ago • 300 machines running night and day for over a year • $30,000,000 to buy • $2 M a month in electricity • $4 M a month in chemicals • Fits on 5 CDs 26
  27. 27. 27
  28. 28. Human Genome Project • The biggest bioinformatics project of its time • So what have we learned so far – 3.2 billion bases in the human genome – Just over 20,000 protein coding genes – Humans vary 1/1000bp • 3.2 million differences between nonrelatives • Almost as much information as in the entire genome of E.coli (4.6 million bases) 28
  29. 29. Completed Human Genomes Craig Venter 2001-2003 James D Watson 2007 Bishop Desmond Tutu 2010 29
  30. 30. James D. Watson • • • • June 2007 454 Sequencer Took 4 months Cost <$1 Million Richard Carson/Reuters 30
  31. 31. 2005 2009 2008 2007 2010 31
  32. 32. 19 August 2011 • Baylor College of Medicine Human Genome Sequencing Center and the AGRF in Melbourne, Australia. • WGS and Sanger sequencing • 2 x coverage • 5.9 x coverage on ABI SOLID • 2,574 Megabase Renfree et al. Genome Biology 2011, 12:R81 32
  33. 33. Complete Genomes-Nov 2010 • http://www.ncbi.nlm.nih.gov/ Genomes/ • There are now over 1000 complete Prokaryotic Genomes available in Entrez Genome • All three main domains of life - bacteria, archae and eukaroytic- are represented, as well as many viruses and organelles • Humans, mice, rats, worms and flies have been completed 33 http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/org.html
  34. 34. 34
  35. 35. http://www.1000genomes.org/about
  36. 36. http://www.icgc.org/
  37. 37. DIY genomics
  38. 38. Summary and Challenges Ahead • DNA sequencing is becoming faster and cheaper at a pace far outstripping Moore’s law (the rate at which computing gets faster and cheaper). • the ability to determine DNA sequences is starting to outrun the ability of researchers to store, transmit and especially to analyze the data. http://infoproc.blogspot.com/201 1/11/dna-data-deluge.html
  39. 39. Summary and Challenges Ahead • Data handling is now the bottleneck • It costs more to analyze a genome than to sequence a genome. • The cost of sequencing a human genome — all three billion bases of DNA in a set of human chromosomes — plunged to $10,500 last July from $8.9 million in July 2007
  40. 40. Summary and Challenges Ahead • Storage and access to data causes issues – Not all data in Genbank or in a format that can be easily accessed • Demand from non-scientists for tools to visualize, understand and interpret their own genomic data http://www.missionmassimo.com/?page_id=8
  41. 41. Personalized Medicine: the future
  42. 42. Ouzounis CA.PLoS Comput Biol. 2012;8(4):e1002487. doi: 10.1371/journal.pcbi.1002487. Epub 2012 Apr 26. Rise and demise of bioinformatics? Promise and progress. Fig 1. The use of the term ―bioinformatics‖ in Google Trends http://www.indeed.com/joban alytics/jobtrends?q=bioinfor matics&l=
  43. 43. BioInfoSummer 2013 program • Monday-Background to Biology and Statistics • Tuesday- Evolution Biology • Wednesday- Systems Biology • Thursday-Next Generation Sequencing (NGS) • Friday- Programing for Bioinformatics 43
  44. 44. • Thank You! 44

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