Human Genome Project

The Human Genome Project (HGP) endeavored to map the human genome down to the nucleotide (or base pair) level and to identify all the genes present in it.

Contents

1 History

2 Goals

3 Benefits

4 References

5 External links

History

The Project was launched in 1986 by Charles DeLisi, who was then Director of the US Department of Energy's Health and Environmental Research Programs. The goals and general strategy of the Project were outlined in a two-page memo to the Assistant Secretary in April 1986, which helped garner support from the DOE, the OMB and Congress, especially Senator Pete Dominici. A series of Scientific Advisory meetings, and complex negotiations with senior Federal officials resulted in a line item for the Project in the 1987 Presidential budget submission to the Congress.

Initiation of the Project was the culmination of several years of work supported by the US Department of Energy, in particular a feasibility workshop in 1986 and a subsequent detailed description of the Human Genome Initiative (http://www.ornl.gov/sci/techresources/Human_Genome/project/herac2.shtml) in a report that led to the formal sanctioning of the initiative by the Department of Energy¹. This 1987 report stated boldly, "The ultimate goal of this initiative is to understand the human genome" and "Knowledge of the human genome is as necessary to the continuing progress of medicine and other health sciences as knowledge of human anatomy has been for the present state of medicine". Candidate technologies were already being considered for the proposed undertaking at least as early as 1985².

The $3 billion project was formally founded in 1990 by the United States Department of Energy and the U.S. National Institutes of Health, and was expected to take 15 years. Due to widespread international cooperation and advances in the field of genomics (especially in sequence analysis), as well as huge advances in computing technology, a rough draft of the genome was finished in 2000 (announced jointly by US president Bill Clinton and British Prime Minister Tony Blair on June 26, 2000), two years earlier than planned.

President Clinton had already awarded the Citizen's medal to DeLisi for his seminal role in the Project, in January 2000, before the completion of the Project was announced.

The consortium comprised:

Eight years after the HGP was begun, an identical quest was initiated separately with private venture capital by a company called Celera Genomics (founded by Craig Venter) while the HGP was still being pursued. Celera Genomics used a newer, albeit riskier technique called whole genome shotgun sequencing and proceeded at a faster pace and at a fraction of the cost of the taxpayer-funded project (approximately $3 billion of taxpayer dollars versus about $300 million of private research funding). Celera had announced from the start its intent to make their genome freely available like that of the publicly-funded HGP, and in line with the "Bermuda Statement" (Feb 1996), made freely available to the public, 24 hours a day. Nonetheless, President Clinton announced that the genome sequence could not be patented. The statement sent Celera's stock plummeting and the Nasdaq, in particular the biotech sector, into a precipitous decline (the biotech sector lost approximiately $50 billion 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 actual details of their drafts. Special issues of Nature (which published the publicly-funded project's scientific paper) and Science (which published Celera's paper) contained descriptions of the methods used to produce the draft sequence, as well as analysis of said sequence. These drafts are hoped to comprise a 'scaffold' of 90% of the genome with gaps to be filled later.

The competition between the rivals proved to be very good for the project, and they agreed to pool their data. Ultimately the pooling agreement fell apart, though, when Celera refused to deposit its data in Genbank, an unrestricted public database. Celera did incorporate the public data into their genome, but the public effort was not permitted to use or merge the Celera data with theirs. On April 14, 2003, a joint press release (http://www.genoscope.cns.fr/externe/CHODE/English/Actualites/Presse/HGP/HGP_press_release-140403.pdf) announced that the project had been successfully completed by both groups, with 99% of the genome sequenced with 99.99% accuracy.

Each draft sequence has been checked at least four to five times to increase 'depth of coverage' or accuracy. Approximately 47% of the draft were high-quality sequences - the final version will have been checked eight to nine times giving an error rate of just 1 in 10,000 bases.

The human genome project is one of a number of international genome projects in biology, each 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, fruitflies, zebrafish, yeast, nematodes and many microbial organisms and parasites.

In October 2004, researchers of the HGP announced a new estimate of 20,000 to 25,000 genes in the human genome. Previously 30,000 to 40,000 had been predicted, while estimates at the start of the project reached up to as high as 100,000.

Goals

The goals of the original HGP were not only to determine all 3 billion base pairs in the human genome with a minimal error rate, but also to identify all the genes in this vast amount of data. This part of the project is still ongoing although a preliminary count indicates about 25,000 genes in the human genome, which is far fewer than predicted by most scientists.

Another goal of the HGP was to develop faster, more efficient methods for DNA sequencing and sequence analysis and the transfer of these technologies to industry.

The sequence of the human DNA is stored in databases available to anyone on the Internet. The U.S. National Center for Biotechnology Information (and sister organizations in Europe and Japan) house the gene sequence in a database known as Genbank, along with sequences of known and hypothetical genes and proteins. Other organizations such as the University of California, Santa Cruz, and ENSEMBL present additional data and annotation and powerful tools for visualizing and searching it. Computer programs have been developed to analyse the data, because the data itself is difficult to interpret without them.

The process of identifying the boundaries between genes and other features in raw DNA sequence is called genome annotation and is the domain of bioinformatics. While expert biologists make the best annotators, their work proceeds slowly, and computer programs are increasingly used to meet the high-throughput demands of genome sequencing projects. The best current technologies for annotation make use of statistical models that take advantage of parallels between DNA sequences and human language, using concepts from computer science such as formal grammars.

All humans have unique gene sequences, therefore the data published by the HGP does not represent the exact sequence of each and every individual's genome. It is the combined genome of a small number of anonymous donors. The HGP genome is a scaffold for future work in identifying differences between individuals. Most of the current effort in identifying differences between individuals involves single nucleotide polymorphisms.

Benefits

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 inexpensive and easy to administer genetic tests that can show predisposition to a variety of illnesses, including breast cancer, blood clotting, cystic fibrosis, liver diseases and many others.

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

The work on interpretation of genome data is still in its initial stages. In the future the knowledge gained by the understanding of the genome will boost the fields of medicine and biotechnology, eventually leading to cures for cancer, Alzheimer's disease and other diseases.

On a more philosophical level, the analysis of similarities between DNA sequences from different organisms is 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.

See also: genetics, bioinformatics

References

Note 1: Barnhart, Benjamin J. (1989). DOE Human Genome Program (http://www.ornl.gov/sci/techresources/Human_Genome/publicat/hgn/v1n1/01doehgp.shtml). Human Genome Quarterly, 1(1). Retrieved 2005-02-03. Note 2: DeLisi, Charles. (2001). Genomes: 15 Years Later A Perspective by Charles DeLisi, HGP Pioneer (http://genome.gsc.riken.go.jp/hgmis/publicat/hgn/v11n3/05delisi.html). Human Genome News, 11(3-4). Retrieved 2005-02-03.

DNA Testing Goes DIY (http://www.wired.com/news/medtech/0,1286,66822,00.html), Associated Press via Wired News, March 07, 2005.

External links

Human Genome News (http://www.ornl.gov/sci/techresources/Human_Genome/publicat/hgn/hgn.shtml). Published from 1989 to 2002 by the US Department of Energy, this newsletter was a major communications method for coordination of the Human Genome Project. Complete online archives are available.
Project Gutenberg hosts e-texts for Human Genome Project, titled Human Genome Project, Chromosome Number # (# denotes 01-22, X and Y). This information is raw sequence, released in November 2002; access to entry pages with download links is available through http://www.gutenberg.org/etext/3501 for Chromosome 1 sequentially to http://www.gutenberg.org/etext/3524 for the Y Chromosome. Note that this sequence might not be considered definitive due to ongoing revisions and refinements. In addition to the chromosome files, there is a supplementary information file (http://www.gutenberg.org/etext/11799) dated March 2004 which contains additional sequence information.
The HGP information pages (http://www.doegenomes.org/)
Ensembl project (http://www.ensembl.org/), an automated annotation system and browser for the human genome
[1] (http://genome.ucsc.edu) UCSC genome browser
Nature magazine's human genome gateway (http://www.nature.com/genomics/human/), including the HGP's paper on the draft genome sequence
Wellcome charitable trust description of HGP (http://www.wellcome.ac.uk/en/genome/) "Your Genes, your health, your future".
Learning about the Human Genome. Part 1: Challenge to Science Educators. ERIC Digest. (http://www.ericdigests.org/2003-2/genome.html)
Learning about the Human Genome. Part 2: Resources for Science Educators. ERIC Digest. (http://www.ericdigests.org/2003-2/genome2.html)
Clinton Tries To Take Credit For Celera's Achievement by David Holcberg (http://www.objectivescience.com/articles/genes_holcberg.htm)
Genome Breakthrough by Ronald Bailey (http://www.nationalreview.com/comment/comment062700a.html)
Prepared Statement of Craig Venter of Celera (http://clinton4.nara.gov/WH/EOP/OSTP/html/00626_4.html) Venter discusses Celera's progress in deciphering the human genome sequence and its relationship to healthcare and to the federally funded Human Genome Project.