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The Human Genome Project - Part II

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Part II

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The Human Genome Project - Part II

  1. 1. The Human Genome HAGenetics.org Dr. Hasan Alhaddad Guest lecturer: Molecular Basis of Human Diseases October 12th, 14th, 16th 2014 Room 244 (1 PM)
  2. 2. Lectures structure HAGenetics.org • Part I (Sunday Oct 12th): • The book of life (Matt Ridely’s analogy with modifications). • Introduction to the technologies at the time. • Part II (Tuesday Oct 14th): • Why sequencing genomes/the human genome? • Genome war (public and private projects). • Sequencing the genome. • Genome assembly. • Part III (Thursday Oct 16th): • Genome annotation. • Genome outcome. • The Genomic era.
  3. 3. AIMS (part II) • Learn the importance of sequencing the human genome. • Understand some of the advantages of sequencing any genome. • Learn the strategies adopted by the public human genome project group. • Learn the strategies adopted by the private human genome project group. • Understand the limitations and the concerns of both groups. HAGenetics.org
  4. 4. Why sequencing the human genome? HAGenetics.org 1. Understand the basis of human diseases a. Mendelian genetic diseases b. Complex genetic diseases c. Risk factors d. Cancer
  5. 5. Why sequencing the human genome? HAGenetics.org 1. Understand the basis of human diseases Genetic testing of human diseases
  6. 6. Why sequencing the human genome? HAGenetics.org Cancer!!!
  7. 7. Why sequencing the human genome? 2. Understanding the basis for the human phenotypic diversity (hair color, skin color, etc.). HAGenetics.org
  8. 8. Why sequencing the human genome? HAGenetics.org 3. Understanding the human evolutionary history.
  9. 9. Why sequencing the human genome? HAGenetics.org 4. Understanding the human history (Eugenics).
  10. 10. Why sequencing the human genome? HAGenetics.org 5. Understanding the genetic basis for human’s morality and cognitive abilities (such as language)
  11. 11. Why sequencing the human genome? HAGenetics.org 6. Understanding human variation to apply findings for forensic and judicial applications.
  12. 12. Why sequencing the human genome? 7. For romantic reasons and philosophical ones such as pure knowledge. We are the only species that can study other species and study itself. HAGenetics.org
  13. 13. HAGenetics.org Why sequencing any genome? 1) Gain better understanding of the biology. 2) Sequence one organisms’s genome helps to complete and better annotate other organisms’ genomes. 3) Gain knowledge of mutations and phenotypes that can serve as models for human phenotypes. 4) Knowing the genome of some organisms allows conducting advanced experiments (knockout genes in mice). 5) Allows the comparisons between taxa and understand evolution.
  14. 14. Review What are the requirements to sequence any fragment of HAGenetics.org DNA? 1) Enough copies of the DNA fragment 2) Primers corresponding to known locations
  15. 15. Review How do we get enough copies of DNA to start HAGenetics.org sequencing? Now: 1) Performing PCR using primers of known sequences. 2) Adding synthetic adapters of known sequence to act as primers At the time: cloning the DNA fragment to vectors (plasmids or Bacterial Artificial Chromosomes (BAC)).
  16. 16. Cloning vectors Vectors contain an origin of replication, selection gene, and a cloning site. HAGenetics.org
  17. 17. Molecular cloning HAGenetics.org
  18. 18. Molecular cloning revisited HAGenetics.org What are the benefits of molecular cloning to sequencing projects? 1) Provides enough DNA copies to carryout sequencing reactions.
  19. 19. Molecular cloning revisited HAGenetics.org
  20. 20. Molecular cloning revisited What are the benefits of molecular cloning to sequencing projects? 2) The cloning site of the vector is of known sequence, which can be used as primers for the sequencing reactions. HAGenetics.org
  21. 21. Molecular cloning revisited HAGenetics.org What are the benefits of molecular cloning to sequencing projects? 3) Allows coping DNA fragments of different sizes.
  22. 22. Molecular cloning revisited HAGenetics.org What are the benefits of molecular cloning to sequencing projects? 4) Provides information about the size of the unknown fragment.
  23. 23. Molecular cloning revisited What are the benefits of molecular cloning to sequencing projects? 5) Allows the mapping of the unknown fragments to specific locations of the chromosome. This can greatly affect the genome assembly (later). HAGenetics.org
  24. 24. The human genome project • The human genome project was initially originated by the collaborations of the US, Europe, and japan and China (~ 20 labs) in the late 1980s. • It is a government funded project (3 Billion $). • One of the people advocating for sequencing the human genome is James Watson. • The project was to take approximately 10 years. • Huge project with specific plans and goals. • I will refer to this human project as the public human genome project. HAGenetics.org
  25. 25. The public human genome project HAGenetics.org James Watson
  26. 26. The public human genome project The plans of the public project were: 1) Divide the genome into chromosomes. 2) Individual labs are responsible for specific chromosomes. HAGenetics.org
  27. 27. The public human genome project The plans of the public project were: 3) Each lab constructs AN OVERLAPPING BAC clone library for their corresponding chromosome. HAGenetics.org
  28. 28. The public human genome project The plans of the public project were: 4) Each lab constructs physical and genetic maps of the clones. HAGenetics.org
  29. 29. The public human genome project The plans of the public project were: 5) Each lab shotgun each clone and sequence sequence it using Sanger method. HAGenetics.org
  30. 30. Paired-end sequencing HAGenetics.org
  31. 31. The public human genome project The plans of the public project were: 6) Sequence the Euchromatic regions of each chromosomes (why?) 7) Sequences must be deposited within 24 hours of sequencing to a public domain where they can be accessed freely by everybody. 8) Draft sequence and check for errors and correct them HAGenetics.org
  32. 32. The public human genome project HAGenetics.org
  33. 33. The Private human genome project Craig Venter: Working for genome research in NIH. HAGenetics.org
  34. 34. The Private human genome project HAGenetics.org
  35. 35. The Private human genome project Eugene Myers: Computer science and bioinformatics HAGenetics.org
  36. 36. The Private human genome project Hamilton Smith: Restriction enzymes and clone libraries. HAGenetics.org
  37. 37. The Private human genome project Best sequencing technology and a lot of machines HAGenetics.org
  38. 38. The Private human genome project HAGenetics.org Best supercomputer
  39. 39. The Private human genome project • A number of investors in the US wanted to get involved in the new trend in biology. • Perkin Elemers is a company developing technologies for research and commercial applications of biological findings. • A new company was formed called Celera. • Celera means fast. • It is the american way to show the power of the private sector (capitalism). • The intension is to sequence the human genome fast and cheap. • Why the human genome? Where is the money? HAGenetics.org
  40. 40. The Private human genome project HAGenetics.org
  41. 41. The private human genome project The plans of the private project were: 1) Shotgun the entire genome (whole-genome shotgun) and make random clones. HAGenetics.org
  42. 42. The private human genome project The plans of the private project were: 1) Shotgun the entire genome (whole-genome shotgun) and make random clones. HAGenetics.org
  43. 43. The private human genome project The plans of the private project were: 2) Assemble the genome De Novo with out any reference. 3) Use mathematical models and computer programs to assemble the genome. HAGenetics.org
  44. 44. The private human genome project The plans of the private project were: 4) use the sequencing technologies developed by Perkin Elmer before anybody. 5) Privatize and patent genes and make a lot of money in the way. 6) Illustrate that the private sector is better faster than the universities that uses the tax money unwisely. HAGenetics.org
  45. 45. Celera Successes HAGenetics.org
  46. 46. Limitations in both camps 1) Technology: need a better automated system 2) Data depository: need a super computer 3) Coverage: how many times to sequence a fragment to ensure accuracy. 4) Incomplete genome: some regions of the genome are not clone-able sequence-able 5) Genome assembly difficulties for regions with repeats 6) Ethical problems: Which individuals represent the human species. HAGenetics.org

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