The human genome project (HGP) is the international project to sequence the DNA of the human genome. The sequencing work is conducted in many laboratories around the world, but the majority of the work is being done by five institutions: the Whitehead Institute for Medical Research in Massachusetts (WIMR), the Baylor College of Medicine in Texas, the University of Washington, the Joint Genome Institute in California and The Sanger Centre near Cambridge in the United Kingdom. Most of the Funding for these centers is provided by the United States National Institute of Health and Department of Energy, and the Wellcome Trust, a charitable foundation in the UK.
Completely sequencing the human genome was first suggested at a conference in Alta, Utah in 1984. The conference was convened by the US Department of Energy, which was concerned with measuring the mutation rate of human DNA when exposed to low-level radiation, similar to conditions after an attack by nuclear weapons. The technology to make such measurements did not exist at the time, and the sequence of the genome was one step required for this aim to become possible. The genome was estimated to be 3000Mb long, however, and sequencing it seemed and arduous task, especially using the sequencing technology of the time. If most of the DNA was "junk" (not coding for genes), then scientists assumed that they could spped the process along by targeting specific genes for sequencing. This could be done by sequencing complementary DNAs (cDNA) which are derived from mRNAs used to code for proteins in the cell. Despite several advocates for this method, it was decided that the whole genome would be sequenced, with a year-2005 target completion date. The Human Genome Project quickly became the world's premier science project for biology, involving large factory-like laboratories rather than small laboratories of independent geneticists.
The strategy employed by the HGP involved three stages, and is termed hierarchical shotgun sequencing. The first stage involved generating physical and genetic maps of the human genome. The second stage was placing clones from a genomic library on to these maps. The third stage was fragmenting these genomic clones into smaller overlapping clones (shotgun cloning), which were a more suitable size for sequencing. Then, the complete sequence of each chromosome could be reconstructed by assembling the fragments of sequence that overlapped with each other to generate the sequence of the genomic clone. The sequence of each genomic clone could then be fitted together using the assembly (contig) of genomic clones on the genetic and physical map.
Although the ultimate aim was high-quality sequence of the human genome, it was recognized that the genetic and physical maps generated by the first stage of the HGP would be by themselves very useful for genetic research. The first generation physical map was constructed by screening a yeast artificial chromosome (YAC) genomic library to isolate YACs, and overlaps were identified by restriction enzyme digest "fingerprints" and STS content mapping. These STSs were sequence around the highly polymorphic CA-repeat markers (microsatellites) that were used to generate the genetic map. Genetic maps were also constructed. These use recombination between markers in families to deduce the distance separating and order of these markers. The first human genetic map used restriction fragment length polymorphisms (RFLPs) as markers, which only have two alleles per marker, but common microsatellites were used to create a high resolution genetic map.
The second stage of human genome sequencing was made simpler by the development of bacterial artificial chromosomes (BACs), cloning vectors that could carry up to 150kb of DNA. Before then, it was assumed that a contig of YACs and cosmids, carrying up to 2Mb and 40kb of DNA respectively, would be assembled. These two types of genomic clone were found to be liable to rearrangement; the DNA in the vector could be in chunks that were not necessarily in the same order as in the genome. The BAC vector did not rearrange DNA, and could carry more DNA than many other types of genomic clone.
The third stage was made easier by development of high-throughput DNA sequencing and affordable computing power to enable reassembly of the sequence fragments. It was these developments that led to the idea of whole genome shotgun sequencing of the human genome. In contrast to the HGP plan involving the use of genetic contigs and physical maps as a framework for genomic clones and sequence, scientists suggested that the whole genome could be fragmented into small chunks for sequencing, and then reassembled using overlap between fragment sequences (whole genome shotgun sequencing). This required large amounts of computing power to generate the correct assembly, but was considerably faster than the HGP approach. Many scientists did not believe that this method would assemble the genome properly, and suggested that overlap between small fragments could not be the only guide to assembly, because the genome contained many repeated DNA sequences. However, American biochemist J.Craig Venter believed the method could work, and formed Celera, a private company that would sequence the human genome before the HGP. Celera demonstrated that the whole genome shotgun method would work by sequencing the genome of a model organism, the fruitfly Drosophila melanogaster. Despite the successful sequencing of the fly, many people were still skeptical that the method would be successful for the bigger human genome.The publicly funded HGP, in face of Celera's competition, decided to concentrate, like Celera, on a draft of the human genome sequence (3x coverage-- that is each nucleotide has been sequenced an average of three times), before generating a more accurate map of 8x coverage. Celera had an advantage, because the HGP had agreed to release all its data as it was generated on to a freely accessible database, as part of the Bermuda rules (named after the location of a series of meetings during the early stages of the HGP). This allowed Celera to use HGP data to link its sequence fragments with the BAC contigs and genetic/physical maps.
The human genome draft sequence of both groups were published in February 2001 by Celera and the HGP consortium in the journals Science and Nature, respectively. Celera had imposed restrictions on access to its genomic data, and this was a source of disagreement between the private company and the HGP. Celera scientists argue that their methods are cheaper and quicker than the HGP framework method, but HGP scientists, in turn, argue that Celera's assembly would not have been possible without the HGP data.
For human geneticists in general, and medical researchers in particular, the genome sequence is abundantly useful. Even in its draft form--the complete version is due in 2003--the ability to identify genes, single nucleotide polymorphisms from a database search speeds up research. Previously, mapping and finding ('positionally cloning') a gene would take several years of research, a task which now takes several minutes. The investment in the sequencing centers will continue to be of use, with a mouse sequencing project underway, and many genomes of pathogenic bacteria sequenced. This study of genomes and parts of genomes has been called genomics. The medical benefits of genomics were emphasized throughout the project partly to ensure continuing government support. These benefits are not likely to be immediate nor direct, but the genome sequence will have the greatest effect on pharmocogenetics, which studies how genetic variants can affect how well a drug can treat a disease. The impact on non--scientists has been substantial, with the HGP suggested to be the ultimate in self knowledge. Although the mapping of the human genome by the HGP is an important scientific achievement, WIMR director Eric Lander offered a humbling perspective regarding the amount of information yet to be discovered by future generations of scientists. In a speech at the White House, Lander said, "We've called the human genome the blueprint, the Holy Grail, all sorts of things. It's a parts list. If I gave you the parts list for the Boeing 777, and it has 100,000 parts, I don't think you could screw it together, and you certainly wouldn't understand why it flew."
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