Human Genome Project

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The Human Genome Project (HGP) is a project to de-code (i.e. sequence) more than three billion nucleotides contained in a haploid reference human genome and to identify all the genes present in it. The reference human genome sequence was considered pragmatically 'complete' at 92% in 2005 in publications by an international public HGP and somewhat independently by a private company Celera Genomics. Recently, several groups have announced efforts to extend this to diploid human genomes including the International HapMap Project, Applied Biosystems, Perlegen, Illumina, JCVI, Personal Genome Project, and Roche-454. The "genome" of any given individual (except for identical twins and cloned animals) is unique; mapping "the human genome" involves sequencing multiple variations of each gene. The project did not study all of the DNA found in human cells; some heterochromatic areas (about 8% of the total) remain unsequenced.

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[edit] Celera Genomics HGP

In 1998, an identical, privately funded quest was launched by the American researcher Craig Venter and his firm Celera Genomics. The $300 million Celera effort was intended to proceed at a faster pace and at a fraction of the cost of the roughly $3 thousand million publicly funded project.

Celera used a newer, riskier technique called whole genome shotgun sequencing, which had been used to sequence bacterial genomes of up to six million base pairs in length, but not for anything nearly as large as the three thousand million base pair human genome.

Celera initially announced that it would seek patent protection on "only 200-300" genes, but later amended this to seeking "intellectual property protection" on "fully-characterized important structures" amounting to 100-300 targets. The firm eventually filed preliminary ("place-holder") patent applications on 6,500 whole or partial genes. Celera also promised to publish their findings in accordance with the terms of the 1996 "Bermuda Statement," by releasing new data quarterly (the HGP released its new data daily), although, unlike the publicly funded project, they would not permit free redistribution or commercial use of the data.

In March 2000, President Clinton announced that the genome sequence could not be patented, and should be made freely available to all researchers. The statement sent Celera's stock plummeting and dragged down the biotechnology-heavy Nasdaq. The biotech sector lost about $50 thousand million in market capitalization in two days.

Although the working draft was announced in June 2000, it was not until February 2001 that Celera and the HGP scientists published details of their drafts. Special issues of Nature (which published the publicly funded project's scientific paper) and Science (which published Celera's paper) described the methods used to produce the draft sequence and offered analysis of the sequence. These drafts covered about 90% of the genome, with much of the remaining 10% filled in later. In February 2001, at the time of the joint publications, press releases announced that the project had been completed by both groups. Improved drafts were announced in 2003 and again in 2005, filling in roughly 8% of the remaining sequence.

The competition proved to be very good for the project, spurring the public groups to modify their strategy in order to accelerate progress. The rivals initially agreed to pool their data, but the agreement fell apart when Celera refused to deposit its data in the unrestricted public database GenBank. Celera had incorporated the public data into their genome, but forbade the public effort to use Celera data.

HGP is the most well known of many international genome projects aimed at sequencing the DNA of a specific organism. While the human DNA sequence offers the most tangible benefits, important developments in biology and medicine are predicted as a result of the sequencing of model organisms, including mice, fruit flies, zebrafish, yeast, nematodes, plants, and many microbial organisms and parasites.

In 2005, researchers from the International Human Genome Sequencing Consortium (IHGSC) of the HGP announced a new estimate of 20,000 to 25,000 genes in the human genome[1]. Previously 30,000 to 40,000 had been predicted, while estimates at the start of the project reached up to as high as 2,000,000. The number continues to fluctuate and it is now expected that it will take many years to agree on a precise value for the number of genes in the human genome.

[edit] History

In 1976, the genome of the virus Bacteriophage MS2 was the first complete genome to be determined, by Walter Fiers and his team at the University of Ghent (Ghent, Belgium)[2][3]. The idea for the shotgun technique came from the use of an algorithm that combined sequence information from many small fragments of DNA to reconstruct a genome. This technique was pioneered by Frederick Sanger to sequence the genome of the Phage Φ-X174, a tiny virus called a bacteriophage that was the first fully sequenced genome (DNA-sequence) in 1977[4]. The technique was called shotgun sequencing because the genome was broken into millions of pieces as if it had been blasted with a shotgun. In order to scale up the method, both the sequencing and genome assembly had to be automated, as they were in the 1980s.

The modern technique came into its own with the sequencing of the first free-living organism, the 1.8 million base pair genome of the bacterium Haemophilus influenzae in 1995. It involved the use of automated sequencers, longer individual sequences using approximately 500 base pairs at that time. Paired sequences separated by a fixed distance of around 2000 base pairs which were critical elements enabling the development of the first genome assembly programs for reconstruction of this bacterial genome.

Three years later, in 1998, the announcement by the newly-formed Celera Genomics that it would scale up the shotgun sequencing method to the human genome was greeted with much skepticism in some circles. The success of both the public and privately funded effort hinged upon a new, more highly automated capillary DNA sequencing machine, called the Applied Biosystems 3700, that ran the DNA sequences through an extremely fine capillary tube rather than a flat gel. Even more critical was the development of a new, larger-scale genome assembly program, which could handle the 30-50 million sequences that would be required to sequence the entire human genome with this method. At the time, such a program did not exist. One of the first major projects at Celera Genomics was the development of this assembler, which was written in parallel with the construction of a large, highly automated genome sequencing factory. The first version of this assembler was demonstrated in 2000, when the Celera team joined forces with Professor Gerald Rubin to sequence the fruit fly Drosophila melanogaster using the whole-genome shotgun method. At 130 million base pairs, it was at least 10 times larger than any genome previously assembled. One year later, the Celera team published their assembly of the three thousand million base pair human genome.

[edit] How it was accomplished

The Celera group used the technique denoted as the “whole-genome shotgun” technique. The shotgun technique breaks the DNA into fragments of various sizes, ranging from 2,000 to 300,000 base pairs in length, forming what is called a DNA "library". Using an automated DNA sequencer the DNA is read in 800bp lengths from both ends of each fragment. This method became a standard approach to the sequencing and assembly of bacterial genomes beginning in 1995, when the first bacterial genome, Haemophilus influenzae, was sequenced. Using a complex genome assembly algorithm and a supercomputer, the pieces are combined and the genome can be reconstructed from the millions of short, 800 base pair fragments.

[edit] Whose genome was sequenced?

In the international public-sector Human Genome Project (HGP), researchers collected blood (female) or sperm (male) samples from a large number of donors. Only a few of many collected samples were processed as DNA resources. Thus the donor identities were protected so neither donors nor scientists could know whose DNA was sequenced. DNA clones from many different libraries were used in the overall project, with most of those libraries being created by Dr. Pieter J. de Jong. It has been informally reported, and is well known in the genomics community, that much of the DNA for the public HGP came from a single anonymous male donor from Buffalo, New York (code name RP11). [5].

HGP scientists used white cells from the blood of 2 male and 2 female donors (randomly selected from 20 of each) -- each donor yielding a separate DNA library. One of these libraries (RP11) was used considerably more than others, due to quality considerations. One minor technical issue is that male samples contain only half as much DNA from the X and Y chromosomes as from the other 22 chromosomes (the autosomes); this happens because each male cell contains only one X or one Y chromosome, but not both. (This is true for nearly all male cells not just sperm cells).

Although the main sequencing phase of the HGP has been completed, studies of DNA variation continue in the International HapMap Project, whose goal is to identify patterns of single nucleotide polymorphism (SNP) groups (called haplotypes, or “haps”). The DNA samples for the HapMap came from a total of 270 individuals: Yoruba people in Ibadan, Nigeria; Japanese people in Tokyo; Han Chinese in Beijing; and the French Centre d’Etude du Polymorphisme Humain (CEPH) resource, which consisted of residents of the United States having ancestry from Western and Northern Europe.

In the Celera Genomics private-sector project, DNA from five different individuals were used for sequencing. The lead scientist of Celera Genomics at that time, Craig Venter, later acknowledged (in a public letter to the journal Science) that his DNA was one of those in the pool.

[edit] Benefits

The work on interpretation of genome data is still in its initial stages. It is anticipated that detailed knowledge of the human genome will provide new avenues for advances in medicine and biotechnology. Clear practical results of the project emerged even before the work was finished. For example, a number of companies, such as Myriad Genetics started offering easy ways to administer genetic tests that can show predisposition to a variety of illnesses, including breast cancer, disorders of hemostasis, cystic fibrosis, liver diseases and many others. Also, the etiologies for cancers, Alzheimer's disease and other areas of clinical interest are considered likely to benefit from genome information and possibly may lead in the long term to significant advances in their management.

There are also many tangible benefits for biological scientists. For example, a researcher investigating a certain form of cancer may have narrowed down his/her search to a particular gene. By visiting the human genome database on the worldwide web, this researcher can examine what other scientists have written about this gene, including (potentially) the three-dimensional structure of its product, its function(s), its evolutionary relationships to other human genes, or to genes in mice or yeast or fruit flies, possible detrimental mutations, interactions with other genes, body tissues in which this gene is activated, diseases associated with this gene or other datatypes.

Further, deeper understanding of the disease processes at the level of molecular biology may determine new therapeutic procedures. Given the established importance of DNA in molecular biology and its central role in determining the fundamental operation of cellular processes, it is likely that expanded knowledge in this area will facilitate medical advances in numerous areas of clinical interest that may not have been possible without them.

The analysis of similarities between DNA sequences from different organisms is also opening new avenues in the study of the theory of evolution. In many cases, evolutionary questions can now be framed in terms of molecular biology; indeed, many major evolutionary milestones (the emergence of the ribosome and organelles, the development of embryos with body plans, the vertebrate immune system) can be related to the molecular level. Many questions about the similarities and differences between humans and our closest relatives (the primates, and indeed the other mammals) are expected to be illuminated by the data from this project.

The Human Genome Diversity Project, spinoff research aimed at mapping the DNA that varies between human ethnic groups, which was rumored to have been halted, actually did continue and to date has yielded new conclusions. In the future, HGDP could possibly expose new data in disease surveillance, human development and anthropology. HGDP could unlock secrets behind and create new strategies for managing the vulnerability of ethnic groups to certain diseases (see race in biomedicine). It could also show how human populations have adapted to these vulnerabilities.

[edit] Criticisms and Controversies

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The U.S. Department of Energy and the National Institute of Health spent 3% to 5% of the Human Genome Project annual budget on studying ethical, legal, and social issues surrounding the Human Genome Project. This allocation made the U.S. bioethics program the largest one around the world, setting an example to other genetic researchers. The issues raised not only concerns the Human Genome Project, but are often discussed alongside with any biotech reforms. Several issues need to be considered:

1. The high cost and money is unjustified. Some people argued that spending research funding on such large-scale research project such as the Human Genome Project takes up scarce resources from researchers who studies special area of interests more efficiently. However, others argue that large-scale projects reduce possible duplicity of research and thus minimize waste of funding. There is also the question of whether we, as a society, should spend the time on finding the differences or teaching to accept these differences. For example, if homosexuality is found to be determined genetically, does it mean society should be more accepting of it? Why not be more accepting of it anyway even if it is purely a lifestyle choice?

2. The ability to diagnose a genetic disease only creates anxiety and frustration since there will be no treatment for the disease. The current method only allows us to predict a person’s chances of getting a genetic disease. Researchers might eventually develop some therapeutic treatments to genetic diseases, but until then, this criticism remains important.

3. Social and political mechanism to regulate the outcome of the research is insufficient. Due to genetic variation, there is not a definite gene sequence that defines normal. It will be hard to discuss public policy. Also, we do not know what it will do to the minority community and how it will change people’s perspective towards them.

4. Controlling the manipulation of the genetic material and information concerns the critics. Who should own and safeguard the genetic information is a unknown.

5. Ethical questions such as whether having the ability equals having to take action need to be considered. Should the scientist do this science just because they can? Some critics brought up the creation of atomic bomb, which caused more harm than good.

6. Fairness in the use of the genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others raises questions. We do not know who should have access to personal information and how it will be used.

The items listed above are only some of the major issues revolving the Human Genome Project or the subject of New Genetics in general. There are many more issues such as the adequacy of physicians and healthcare providers and helpfulness to the public regarding general genetic information. Also, how and where the government should regulate is also very important. The U.S. government, on one hand, is very encouraging of biotech research, but on the other hand, needs to figure out a way to mitigate the problems.

[edit] References

  1. ^ IHGSH (2004). "Finishing the euchromatic sequence of the human genome.". Nature 431: 931-945. 
  2. ^ Fiers W, Contreras R, De Wachter R, Percival J, Haegeman G, Merregaert J, Jou WM, Vandenberghe A., Recent progress in the sequence determination of bacteriophage MS2 RNA, Biochimie. 1971;53(4):495-506
  3. ^ Fiers W, Contreres R, Duerinck F, Haegeman G, Iserentant D, Merregaert J, Min Jou W, Molemans F, Raeymaekers A, Van den Berghe A, Volckaert G, Ysebaert M. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene, Nature. 1976 Apr 8;260(5551):500-7.
  4. ^ Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M., Nucleotide sequence of bacteriophage phi X174 DNA, Nature. 1977 Feb 24;265(5596):687-95
  5. ^ Osoegawa, Kazutoyo (2001). "A Bacterial Artificial Chromosome Library for Sequencing the Complete Human Genome". Genome Research 11: 483-496. 

Access Excellence at the National Health Museum http://www.accessexcellence.org/RC/AB/IE/Ethical_Issues_of_the_HGP.html Human Genome Project Information at U.S. Department of Energy Office of Science http://www.ornl.gov/sci/techresources/Human_Genome/elsi/elsi.shtml


[edit] See also

[edit] External links

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