FBW               25-09-2012Wim Van Criekinge
What is Bioinformatics ?                   • Application of information technology to the                     storage, man...
Promises of genomics and bioinformatics• Medicine (Pharma)   – Genome analysis allows the targeting of genetic     disease...
Bioinformatics: What’s in a name ?           • Begin 1990’s           • “Bio-informatics”:  Computing Power  Genbank  (Log...
Bioinformatics: What’s in a name ?   • Begin 1990’s   • “Bio-informatics”:       – convergence of explosive growth in     ...
Time (years)
Happy Birthday …
PCR + dye termination  Suddenly, a flash of insight caused him to pull the car    off the road and stop. He awakened his f...
Bioinformatics, a scientific discipline …                                               Math       Computer Science       ...
Bioinformatics, a scientific discipline …                                               Math                              ...
Bioinformatics, a scientific discipline …                                            Math                                 ...
Doel van de cursus                     • Meer dan een inleiding tot ... het is de                       bedoeling van de c...
Inhoud Lessen: Bioinformatica
Examen         • Theorie           – Deel rond een zelf te kiezen publicatie die in verband             staat met de cursu...
Cursus         • 25 Euro           – Syllabus           – Hand-outs van Les/Practicum 1           – V|Podcasts           –...
• Timelin: Magaret  Dayhoff …
Nexus > FAQ > Bioinformatics Milestones
• http://www.sciencemag.org/cgi/content/fu  ll/291/5507/1195• Printed version in cursus
Setting the stage …                      nature                           the                           Human             ...
Genome Meters • Genomes Online Database (GOLD 1.0)     – http://geta.life.uiuc.edu/~nikos/genomes.html     – http://www.eb...
Genome Size              E. coli = 4.2 x 106              Yeast = 18 x 106              Arabidopsis = 80 x 106            ...
Biological Research                      Adapted from John McPherson, OICR
And this is just the beginning ….Next Generation Sequencing is here
Basics of the “old” technology• Clone the DNA.• Generate a ladder of labeled (colored) molecules  that are different by 1 ...
Basics of the “new” technology• Get DNA.• Attach it to something.• Extend and amplify signal with some color  scheme.• Det...
Next Generation Technologies• 454   –Emulsion PCR   –Polymerase   –Natural Nucleotides• 20-100Mb for 5-15k   –1% error rat...
One additional insight ...
Read Length is Not As Important For Resequencing                                                  100%               % of ...
Two Short Read Techologies• Illumina GA• ABI SOLID
Technology Overview: Solexa/Illumina Sequencing
ABI Solid            Dressman 2003
ABI SOLID
ABI SOLID
Paired End Reads are Important!                                 Known Distance                           Read 1          R...
Adapted from: Barak Cohen, Washington University, Bio5488   http://tinyurl.com/6zttuq http://tinyurl.com/6k26nh           ...
IntroducingNXT GNT DXSNext Generation Diagnostics                              18th september 2009                        ...
develop in shortest time frame best assay for most relevant      clinical application
NXT GNT DXS              • GNT                – Dedicated Team & Network                – Operational: Location           ...
Next next generation sequencing Third generation sequencing       Now sequencing
Complete genomics
Complete genomics
Pacific Biosciences: A Third Generation Sequencing Technology                                                          Eid...
Pacific Biosciences: A Third Generation Sequencing Technology
Nanopore Sequencing
NCBI (educational resources)
Weblems          • What ?            – Web-based problemes (over de huidige les              en/of voorbereiding op volgen...
Weblems          W1.1: To which phyla do the following species belong (a)           starfish (b) ginko tree (c) scorpion  ...
Bioinformatica t1-bioinformatics
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Bioinformatica t1-bioinformatics

  1. 1. FBW 25-09-2012Wim Van Criekinge
  2. 2. What is Bioinformatics ? • Application of information technology to the storage, management and analysis of biological information (Facilitated by the use of computers) – Sequence analysis? – Molecular modeling (HTX) ? – Phylogeny/evolution? – Ecology and population studies? – Medical informatics? – Image Analysis ? – Statistics ? AI ? – Sterkstroom of zwakstroom ?
  3. 3. Promises of genomics and bioinformatics• Medicine (Pharma) – Genome analysis allows the targeting of genetic diseases – The effect of a disease or of a therapeutic on RNA and protein levels can be elucidated – Knowledge of protein structure facilitates drug design – Understanding of genomic variation allows the tailoring of medical treatment to the individual’s genetic make- up• The same techniques can be applied to crop (Agro) and livestock improvement (Animal Health)
  4. 4. Bioinformatics: What’s in a name ? • Begin 1990’s • “Bio-informatics”: Computing Power Genbank (Log) Time (years)
  5. 5. Bioinformatics: What’s in a name ? • Begin 1990’s • “Bio-informatics”: – convergence of explosive growth in biotechnology, paralled by the explosive growth in information technology • Not new: > 30 years that people use “computers” in biology • In silico biology, database biology, ...
  6. 6. Time (years)
  7. 7. Happy Birthday …
  8. 8. PCR + dye termination Suddenly, a flash of insight caused him to pull the car off the road and stop. He awakened his friend dozing in the passenger seat and excitedly explained to her that he had hit upon a solution - not to his original problem, but to one of even greater significance. Kary Mullis had just conceived of a simple method for producing virtually unlimited copies of a specific DNA sequence in a test tube - the polymerase chain reaction (PCR)
  9. 9. Bioinformatics, a scientific discipline … Math Computer Science Theoretical Biology Bioinformatics (Molecular) Informatics Biology Computational Biology
  10. 10. Bioinformatics, a scientific discipline … Math Algorithm Development Computer Science Theoretical Biology NP AI, Image Analysis Datamining structure prediction (HTX) Bioinformatics Interface Design Expert Annotation Sequence Analysis (Molecular) Informatics Biology Computational Biology
  11. 11. Bioinformatics, a scientific discipline … Math Algorithm Development Computer Science Theoretical Biology NP AI, Image Analysis Datamining structure prediction (HTX) Bioinformatics Discovery Informatics – Computational Genomics Interface Design Expert Annotation Sequence Analysis (Molecular) Informatics Biology Computational Biology
  12. 12. Doel van de cursus • Meer dan een inleiding tot ... het is de bedoeling van de cursus een onderliggend inzicht te verschaffen achter de verschillende technieken. • Naast het gebruik van recepten, wat terug te vinden is in delen van de syllabus laat een inzicht in – de werking van databanken – en de achterliggende algoritmen • toe – om wisselende interfaces op nieuwe problemen toe te passen.
  13. 13. Inhoud Lessen: Bioinformatica
  14. 14. Examen • Theorie – Deel rond een zelf te kiezen publicatie die in verband staat met de cursus • Bv Bioinformatics of Computational Biology – Drie inzichtsvragen over de cursus (inclusief  !!) • Practicum (“open-book”) – Viertal oefeningen die meestal het schrijven van een programma veronderstellen • Puntenverdeling 50/50
  15. 15. Cursus • 25 Euro – Syllabus – Hand-outs van Les/Practicum 1 – V|Podcasts – Weblems – Screencasts – Flash Drive • Image to be installed
  16. 16. • Timelin: Magaret Dayhoff …
  17. 17. Nexus > FAQ > Bioinformatics Milestones
  18. 18. • http://www.sciencemag.org/cgi/content/fu ll/291/5507/1195• Printed version in cursus
  19. 19. Setting the stage … nature the Human genome
  20. 20. Genome Meters • Genomes Online Database (GOLD 1.0) – http://geta.life.uiuc.edu/~nikos/genomes.html – http://www.ebi.ac.uk/research/cgg/genomes.html • NCBI – http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.h tml • INFOBIOGEN – http://www.infobiogen.fr/doc/data/complete_genome. html
  21. 21. Genome Size E. coli = 4.2 x 106 Yeast = 18 x 106 Arabidopsis = 80 x 106 C.elegans = 100 x 106 Drosophila = 180 x 106 Human/Rat/Mouse = 3000 x 106 Lily = 300 000 x 106 With ... : 99.9 % To primates: 99% DOGS: Database Of Genome Sizes
  22. 22. Biological Research Adapted from John McPherson, OICR
  23. 23. And this is just the beginning ….Next Generation Sequencing is here
  24. 24. Basics of the “old” technology• Clone the DNA.• Generate a ladder of labeled (colored) molecules that are different by 1 nucleotide.• Separate mixture on some matrix.• Detect fluorochrome by laser.• Interpret peaks as string of DNA.• Strings are 500 to 1,000 letters long• 1 machine generates 57,000 nucleotides/run• Assemble all strings into a genome.
  25. 25. Basics of the “new” technology• Get DNA.• Attach it to something.• Extend and amplify signal with some color scheme.• Detect fluorochrome by microscopy.• Interpret series of spots as short strings of DNA.• Strings are 30-300 letters long• Multiple images are interpreted as 0.4 to 1.2 GB/run (1,200,000,000 letters/day).• Map or align strings to one or many genome.
  26. 26. Next Generation Technologies• 454 –Emulsion PCR –Polymerase –Natural Nucleotides• 20-100Mb for 5-15k –1% error rate –Homopolymers
  27. 27. One additional insight ...
  28. 28. Read Length is Not As Important For Resequencing 100% % of Paired K-mers with Uniquely 90% Assignable Location 80% 70% 60% E.COLI 50% HUMAN 40% 30% 20% 10% 0% 8 10 12 14 16 18 20 Length of K-mer Reads (bp)Jay Shendure
  29. 29. Two Short Read Techologies• Illumina GA• ABI SOLID
  30. 30. Technology Overview: Solexa/Illumina Sequencing
  31. 31. ABI Solid Dressman 2003
  32. 32. ABI SOLID
  33. 33. ABI SOLID
  34. 34. Paired End Reads are Important! Known Distance Read 1 Read 2 Repetitive DNA Unique DNA Paired read maps uniquely Single read maps to multiple positions
  35. 35. Adapted from: Barak Cohen, Washington University, Bio5488 http://tinyurl.com/6zttuq http://tinyurl.com/6k26nh Single Molecule SequencingMicroscope slide * * *Single DNAmolecule Super-cooled primer TIRF microscope dNTP-Cy3 * Helicos Biosciences Corp.
  36. 36. IntroducingNXT GNT DXSNext Generation Diagnostics 18th september 2009 Wim Van Criekinge
  37. 37. develop in shortest time frame best assay for most relevant clinical application
  38. 38. NXT GNT DXS • GNT – Dedicated Team & Network – Operational: Location – Professionalized • DXS – Content engine – Product 1 established – Pipeline for n+1 • NXT – Workflow management – Bioinformatics – Epigenetics
  39. 39. Next next generation sequencing Third generation sequencing Now sequencing
  40. 40. Complete genomics
  41. 41. Complete genomics
  42. 42. Pacific Biosciences: A Third Generation Sequencing Technology Eid et al 2008
  43. 43. Pacific Biosciences: A Third Generation Sequencing Technology
  44. 44. Nanopore Sequencing
  45. 45. NCBI (educational resources)
  46. 46. Weblems • What ? – Web-based problemes (over de huidige les en/of voorbereiding op volgende les) • When ? – Einde van elke les • How ? – Oplossingen online via screencasts – Practicum – Voorbedereiding op het practicum examen ... Niet alle problemen vereisen noodzakelijk programmacode ...
  47. 47. Weblems W1.1: To which phyla do the following species belong (a) starfish (b) ginko tree (c) scorpion W1.2: What are the common names for the following species (a) Orycterophus afer (b) Beta vulagaris (c) macrocystis pyrifera W1.3: What species has the smallest known genome ? And is genome size related to number of genes ? W1.4: What are the 5 latest genomes published ? How complete is “coverage” ? W1.5: For approximately 10% of europeans, the painkiller codeine is ineffective because the patients lack the enzyme that converts codeine into the active molecule, morphine. What is the most common mutation that causes this condition ?
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