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Human Genome Project

The Human Genome Project (HGP) endeavoured to map the human genome down to the nucleotide (or base pair) level and to identify all the 20-25,000 genes present in it.

History

The $3 billion project was 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.

The consortium comprised:

On April 14, 2003, a joint press release (http://www.genoscope.cns.fr/externe/English/Actualites/Presse/HGP/HGP_press_release-140403.pdf) announced that the project had been successfully completed, with 99% of the genome sequenced with 99.99% accuracy.

Another reason for the accelerated work was the commercially financed HGP at Celera Genomics, which used a new method called shotgun sequencing, and also that Celera Genomics planned to patent all genes found, unlike the gene sequences found by the original publicly-funded HGP, which are in line with the so called Bermuda Statement (Feb 1996) made freely available to the public, 24 hours a day. This sort of competition proved to be very good for the Project.

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 provide a 'scaffold' of about 90% of the genome upon which gaps can be closed.

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.

Today, the sequence of the human DNA is stored in databases and is available for everyone on the Internet. The U.S. National Center for Bioinformatics (and sister organizations in Europe and Japan) houses the genomic sequence, 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 through it. Computer programs have been developed to analyse that data, as the data itself is next to useless without interpretation.

The process of identifying the boundaries of genes and other features in raw DNA sequence is called annotation and is the domain of bioinformatics. While expert biologists make the best annotators, such annotation 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 genomic sequence, as such, 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

The work on automated interpretation on genome data has just begun. The knowledge gained by the understanding of the genome is hoped to boost the fields of medicine and biotechnology, eventually leading to cures for cancer, Alzheimers disease and other diseases.

For example, a biological researcher investigating a certain form of cancer may have narrowed down their 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.

One particularly exciting technology arising from genomics is the DNA microarray (also called DNA chip), an array of probes for simultaneously measuring the amount of each of the 20,000+ human genes present in a given sample. This has aroused great interest as a potential diagnostic tool for science and medicine. It seems likely that there will be many more downstream technologies as a result of the human genome project.

On a more philosophical level, the analysis of similarities between DNA sequences from different organisms is opening new avenues in the study 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

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