1. The Human Genome Race

2. Collins vs. Venter Collins Venter

3. Collins Francis Collins, a physician, is director of the National Human Genome Research Institute. His research laboratory was responsible for identifying the genes responsible for Cystic Fibrosis, Neurofibromatosis, and Huntington's disease.

4. http://gen.lib.rus.ec/

5. Collins: Goals of NHGRI “At the beginning, the goals of the genome project were to focus on building maps. You can think of those as mile markers along the chromosomes to sort of get you oriented. Not the precise single letter code of A, C, G, and T, but the mile markers. …

6. Collins: Goals of NHGRI They are various types of maps; they are genetic maps and physical maps. Those were achieved about a year and a half ahead of schedule in 1994 and 1996, so we were able to get those markers in place to begin to roll up our sleeves and go after the hard part of reading out the precise script.”

7. Venter Venter founded the nonprofit Institute for Genomic Research in 1992. Before that he was section chief and a laboratory chief at the National Institutes of Neurological Disorders and the National Institutes of Health. Celera Genomics is part of the PE Corporation.

8. Venter Celera is a for-profit organization whose motto is “Discovery Can’t Wait”

9. Venter: Goals of Celera “Well, our goal over the first few years is to get some basic information on several genomes, including the human genome, so we're trying to decipher the complete genetic code of the human genome, the mouse genome, an insect and the rice genome.

10. Venter: Goals of Celera And those genomes will provide the foundation for the future of agriculture and human medicine, so we're creating giant databases of information.

11. Venter: Goals of Celera We're an information company, and our goal is to provide that information to the medical, scientific, and pharmaceutical communities, and to individuals to understand their own individual variation and possible propensity and prevention of disease.”

12. Intro to Sequencing

13. To read the DNA, the chromosomes are cut into tiny pieces, each of which is read individually. When all the segments have been read they are assembled in the correct order. Link these fragments to self-replicating forms of DNA = vectors.

14. Intro to Sequencing Two approaches have been used to sequence the genome. They differ in the methods they use to cut up the DNA, assemble it in the correct order, and whether they map the chromosomes before decoding the sequence.

15. Intro to Sequencing First approach was the “BAC to BAC” approach. A second, newer method is called “whole genome shotgun sequencing.”

16. Intro to Sequencing: BAC to BAC The BAC-to-BAC method: the first to be employed in human genome studies slow but sure also called the “map based method”

17. Intro to Sequencing: Whole Genome Shotgun Whole Genome Shotgun Method brings speed into the picture, enabling researchers to do the job in months to a year. Developed by Celera president Craig Venter in 1996 when he was at the Institute for Genomic Research.

18. BAC to BAC - 1 I. First create a rough physical map of the whole genome before sequencing the DNA I.requires cutting the chromosomes into large pieces and then figuring out the order of these big chunks of DNA before taking a closer look and sequencing all the fragments.

19. BAC to BAC - 2 II. Several copies of the genome are randomly cut into pieces that are about 150,000 base pairs (bp) long.

20. BAC to BAC - 2

21. BAC to BAC - 3 III. Each of these 150,000 bp fragments is inserted into a BAC I. A BAC is a man made piece of DNA that can replicate inside a bacterial cell. II. The collection of BACs containing the entire human genome is called a BAC library.

22. BAC to BAC - 3

23. BAC to BAC - 4 IV. These pieces are fingerprinted to give each piece a unique identification tag that determines the order of the fragments. I. cutting each BAC fragment with a single enzyme and finding common sequence landmarks in overlapping fragments that determine the location of each BAC along the chromosome.

24. BAC to BAC - 4 IV. … II. Then overlapping BACs with markers every 100,000 bp form a map of each chromosome

25. BAC to BAC - 4

26. BAC to BAC - 5 V. Each BAC is then broken randomly into 1,500 bp pieces and placed in another artificial piece of DNA called M13. This collection is known as an M13 library.

27. BAC to BAC - 5

28. BAC to BAC - 6 VI. All the M13 libraries are sequenced. I. 500 bp from one end of the fragment are sequenced generating millions of sequences

29. BAC to BAC - 6

30. BAC to BAC - 7 VII. These sequences are fed into a computer program called PHRAP that looks for common sequences that join two fragments together.

31. BAC to BAC - 7

32. Whole Genome Shotgun Sequencing Method

33. Whole Genome Shotgun - 1 I. The shotgun sequencing method goes straight to the job of decoding, bypassing the need for a physical map.

34. Whole Genome Shotgun - 2 II. Multiple copies of the genome are randomly shredded into pieces that are 2,000 bp long by squeezing the DNA through a pressurized syringe. This is done a second time to generate pieces that are 10,000 bp long.

35. Whole Genome Shotgun - 2

36. Whole Genome Shotgun - 3 III. Each 2,000 and 10,000 bp fragment is inserted into a plasmid, which is a piece of DNA that can replicate in bacteria. I. The two collections of plasmids containing 2,000 and 10,000 bp chunks of human DNA are known as plasmid libraries.

37. Whole Genome Shotgun - 3

38. Whole Genome Shotgun - 4 IV. Both plasmid libraries are sequenced. I. 500 bp from each end of each fragment are decoded generating millions of sequences. II. Sequencing both ends of each insert is critical for the assembling the entire chromosome.

39. Whole Genome Shotgun - 4

40. Whole Genome Shotgun - 5 V. Computer algorithms assemble the millions of sequenced fragments into a continuous stretch resembling each chromosome.

41. Whole Genome Shotgun - 5

42. What does the draft human genome sequence tell us? By the Numbers The human genome contains 3 billion chemical nucleotide bases (A, C, T, and G). The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin (muscle protein) at 2.4 million bases. The total number of genes is estimated at around 30,000--much lower than previous estimates of 80,000 to 140,000. Almost all (99.9%) nucleotide bases are exactly the same in all people. The functions are unknown for over 50% of discovered genes. U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

43. What does the draft human genome sequence tell us? The Wheat from the Chaff Less than 2% of the genome codes for proteins. Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome. Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, creating entirely new genes, and modifying and reshuffling existing genes. The human genome has a much greater portion (50%) of repeat sequences than the mustard weed (11%), the worm (7%), and the fly (3%). U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 http://doegenomes.org

44. Anticipated Benefits of Genome Research Molecular Medicine improve diagnosis of disease detect genetic predispositions to disease create drugs based on molecular information use gene therapy and control systems as drugs design “custom drugs” (pharmacogenomics) based on individual genetic profiles Microbial Genomics rapidly detect and treat pathogens (disease-causing microbes) in clinical practice develop new energy sources (biofuels) monitor environments to detect pollutants protect citizenry from biological and chemical warfare clean up toxic waste safely and efficiently U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003

45. Anticipated Benefits of Genome Research Molecular Medicine improve diagnosis of disease detect genetic predispositions to disease create drugs based on molecular information use gene therapy and control systems as drugs design “custom drugs” (pharmacogenomics) based on individual genetic profiles Microbial Genomics rapidly detect and treat pathogens (disease-causing microbes) in clinical practice develop new energy sources (biofuels) monitor environments to detect pollutants protect citizenry from biological and chemical warfare clean up toxic waste safely and efficiently U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003

46. DNA Identification (Forensics) identify potential suspects whose DNA may match evidence left at crime scenes exonerate persons wrongly accused of crimes identify crime and catastrophe victims establish paternity and other family relationships identify endangered and protected species as an aid to wildlife officials (could be used for prosecuting poachers) detect bacteria and other organisms that may pollute air, water, soil, and food match organ donors with recipients in transplant programs determine pedigree for seed or livestock breeds authenticate consumables such as caviar and wine U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 Anticipated Benefits of Genome Research-cont. http://doegenomes.org

47. DNA Identification (Forensics) identify potential suspects whose DNA may match evidence left at crime scenes exonerate persons wrongly accused of crimes identify crime and catastrophe victims establish paternity and other family relationships identify endangered and protected species as an aid to wildlife officials (could be used for prosecuting poachers) detect bacteria and other organisms that may pollute air, water, soil, and food match organ donors with recipients in transplant programs determine pedigree for seed or livestock breeds authenticate consumables such as caviar and wine U.S. Department of Energy Genome Programs, Genomics and Its Impact on Science and Society, 2003 Anticipated Benefits of Genome Research-cont. http://doegenomes.org

48. CSIRO. INI Meeting July 2010 - Tutorial - Applications Plant Genomes – Haploid Size Human Arabidopsi s Rice Potato Sugarcane Cotton Barley Wheat Diameter proportional to genome haploid genome size

49. CSIRO. INI Meeting July 2010 - Tutorial - Applications Plant Genomes – Total Size Human Cotton Barley Sugarcane Wheat