This document outlines the structure and aims of a series of lectures on the human genome. It discusses the public and private projects to sequence the human genome. The public project was a large collaboration that mapped chromosomes and cloned overlapping fragments to sequence. The private project took a "whole genome shotgun" approach, randomly cloning the genome and assembling it de novo with new sequencing technologies and powerful computers. Both projects faced limitations from technology, data storage, coverage depth, and assembly of repetitive regions.

1. The Human Genome
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Dr. Hasan Alhaddad
Guest lecturer: Molecular Basis of Human Diseases
October 12th, 14th, 16th 2014
Room 244 (1 PM)

2. Lectures structure
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• 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. 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.
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4. Why sequencing the human genome?
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1. Understand the basis of human diseases
a. Mendelian genetic diseases
b. Complex genetic diseases
c. Risk factors
d. Cancer

5. Why sequencing the human genome?
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1. Understand the basis of human diseases
Genetic testing of human diseases

6. Why sequencing the human genome?
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Cancer!!!

7. Why sequencing the human genome?
2. Understanding the basis for the human phenotypic
diversity (hair color, skin color, etc.).
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8. Why sequencing the human genome?
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3. Understanding the human evolutionary history.

9. Why sequencing the human genome?
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4. Understanding the human history (Eugenics).

10. Why sequencing the human genome?
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5. Understanding the genetic basis for human’s
morality and cognitive abilities (such as language)

11. Why sequencing the human genome?
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6. Understanding human variation to apply findings
for forensic and judicial applications.

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.
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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. Review
What are the requirements to sequence any fragment of
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DNA?
1) Enough copies of the DNA fragment
2) Primers corresponding to known locations

15. Review
How do we get enough copies of DNA to start
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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. Cloning vectors
Vectors contain an origin of replication, selection gene, and a
cloning site.
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17. Molecular cloning
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18. Molecular cloning revisited
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What are the benefits of molecular cloning to
sequencing projects?
1) Provides enough DNA copies to carryout sequencing
reactions.

19. Molecular cloning revisited
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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.
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21. Molecular cloning revisited
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What are the benefits of molecular cloning to
sequencing projects?
3) Allows coping DNA fragments of different sizes.

22. Molecular cloning revisited
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What are the benefits of molecular cloning to
sequencing projects?
4) Provides information about the size of the unknown
fragment.

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).
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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.
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25. The public human genome project
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James Watson

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.
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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.
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28. The public human genome project
The plans of the public project were:
4) Each lab constructs physical and genetic maps of the clones.
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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.
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30. Paired-end sequencing
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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
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32. The public human genome project
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33. The Private human genome project
Craig Venter: Working for genome research in NIH.
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34. The Private human genome project
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35. The Private human genome project
Eugene Myers: Computer science and bioinformatics
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36. The Private human genome project
Hamilton Smith: Restriction enzymes and clone libraries.
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37. The Private human genome project
Best sequencing technology and a lot of machines
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38. The Private human genome project
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Best supercomputer

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?
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40. The Private human genome project
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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.
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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.
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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.
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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.
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45. Celera Successes
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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.
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