The human genome Project
Completed in 2003, The Human genome project (HGP) was a thirteen year project with the main goal of determining the sequence of chemical base pairs which make up DNA and to identify and map the approximately 20,000 to 25,000 genes of the human genome from both a physical and functional standpoint. Some benefits of the HGP are to predict and prevent diseases, to develop new and improved medicines, to ensure the accuracy of diagnosis, and to improve forensic science. The HGP was coordinated by the U.S. department of Energy and the National Institutes of Health. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner, additional contributions came from Canada, New Zealand, Japan, France, Germany, China, and other countries.
What is a Genome?
All the DNA in an organism, including its genes, is known as its genome. Genes carry information for making all the proteins required by all organisms and these proteins determine, for example, how the organism looks, how well it metabolizes food, and fights infections. DNA is made up of four different chemicals known as bases; adenine (A), thymine (T), cytosine (C), and guanine (G).
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These four bases are repeated millions or billions of times throughout a genome. The specific order of these bases is extremely important for it dictates the proteins formed in an organism. Every species has its own unique genome. In the human genome there are 23 pairs of chromosomes that are up to over 2 million base pairs in length. (The figure to the right depicts a normal human male karyotype).
Since all organisms are related through similarities in DNA sequences, information gained from nonhuman genomes, such as gorillas, often lead to new knowledge about human biology.
Methods for Sequencing
There are many different methods of gene sequencing which were used in the human genome project but the following are the most prominent.
The primary method used by the HGP to produce the finished version of the genetic information Testing">human genetic code is BAC-based sequencing. BAC is the acronym for “bacterial artificial chromosome.” Human DNA is fragmented into pieces that are relatively large but still manageable in size (between 150,000 and 200,000 base pairs).
The fragments are cloned in bacteria, which store and replicate the human DNA so that it can be prepared in quantities large enough for sequencing. If carefully chosen to minimize overlap, it takes about 20,000 different BAC clones to contain the 3 billion pairs of bases of the human genome.
In the BAC-based method, each BAC clone is “mapped” to determine where the DNA in BAC clones comes from in the human genome. Using this approach ensures that scientists know both the precise location of the DNA letters that are sequenced from each clone and their spatial relation to sequenced human DNA in other BAC clones.
For sequencing, each BAC clone is cut into still smaller fragments that are about 2,000 bases in length. These pieces are called “subclones.” A sequencing reaction is carried out on these subclones. The products of the sequencing reaction are then loaded into the sequencing machine (sequencer).
The sequencer generates about 500 to 800 base pairs of A, T, C and G from each sequencing reaction, so that each base is sequenced about 10 times. A computer then assembles these short sequences into contiguous stretches of sequence representing the human DNA in the BAC clone.
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Another method that was used was known as the Dideoxy Sanger Method. This method uses DNA polymerase, the same enzyme used in DNA replication, to produce DNA sequence information. DNA polymerase binds to a single-stranded DNA template and adds DNA bases to the 3′ end of the complementary DNA strand it synthesizes. DNA polymerase requires an existing primer with a free 3′ end to which it adds new DNA bases in a 5′ to 3′ manner, and it moves along the template strand in a 3′ to 5′ direction.
Researchers combined the DNA template they were interested in sequencing with DNA polymerase, a single-stranded DNA primer, free deoxynucleotide bases (dATP, dCTP, dGTP, and dTTP), and a sparse mixture of fluorescently labeled dideoxynucleotide bases (ddATP, ddCTP, ddGTP, and ddTTP) that were each labeled with a different color and would terminate new DNA strand synthesis once incorporated into the end of a growing DNA strand due to the missing alcohol group on the third carbon. The mixture was first heated to denature the template DNA strand and then this is followed by a cooling step to allow the DNA primer to anneal. Following primer annealing, the polymerase synthesized a complementary DNA strand. The template would grow in length until a dideoxynucleotide base (ddNTP) was incorporated; the conditions were such that this occurred at random along the length of the newly synthesized DNA strands. In the end, the researchers were left with a mixture of newly synthesized DNA strands that differed in length by a single nucleotide, and that were labeled at their 3′ end with the color of the ddNTP-associated dye molecule.
In order to determine the sequence of the newly synthesized, color-coded DNA strands, researchers needed a way to separate them based on their size, which differed by only one DNA nucleotide so they used gel electrophoresis. To accomplish this, they electrophoresed the DNA through a gel matrix that permitted single-base differences in size to be easily distinguished. Small fragments run more quickly through the gel, and larger fragments run more slowly. By putting the entire mixture into a single well of the gel, a laser can be used to scan the DNA bands as they move through the gel and determine their color; this data can be used to generate a sequence trace showing the color and signal intensity of each DNA band that passes through the gel. The color of each band represents the final 3′ base incorporated at that position, and by reading from the bottom to the top of the gel, one can determine the sequence of the newly synthesized DNA strand from the 5′ to the 3′ end.
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Benefits of the Human Genome Project
The benefits of the Human Genome Project will more than likely be felt throughout the world. The expenditures on genomics research in U.S. industry are projected to be 45 billion dollars by 2009. This projected dollar amount is through the sales of DNA based products and technologies in the biotechnology industry.
One of the potential benefits is in the field of molecular medicine. The benefits in this field could include better diagnosis of diseases, early detection of certain diseases, and gene therapy and control systems for medications. In the future there should be new treatments in molecular medicine that don’t just treat the symptoms but look more at the major causes of the problem at hand. Another field that may reap the benefits of the HGP is the field of microbial genomics. This field may be able to find new energy sources, through the sequencing of a bacterial genome. This could lead to discoveries that are useful in energy production, toxic waste reduction, and industrial processing. The HGP can also be very useful for the understanding of human evolution and human migration. It may help lead scientists to find out how humans have evolved and how humans are evolving today. It will also help to understand the common biology that we share with all life on earth. Comparing our genome with others may help to lead to associations of diseases with certain traits. One last field that will undoubtedly receive monumental benefits from the HGP is the field of agriculture and livestock breeding. This technology could help to develop disease, insect, and drought resistant crops thus being able to produce more for the world. It would also help to produce healthier, more productive, and possibly disease resistant animals to be sent to market.
Ethical, Legal, and Social Concerns Related to the Human Genome Project
The general public and people in the HGP have shown a lot of concern over the ethical issues involved with the Human Genome Project. Because of this concern the Department of Energy and the National Institutes of Health have put 3% to 5% of their annual budget for the HGP to studying the ethical, legal, and social issues involved in the project. The use of sequencing will make a profound impact on genetic screening of individuals. Medical professionals will be able to look at a person’s genome and be able to tell many things about that person. This new technology will bring a number of issues, such as the fairness in the use of genetic information. This issue brings the questions; who should have access to genetic records and how can they be used. Some of those targeted are insurers, employers, courts, schools, and the military. If this information is used by some of these agencies there could be discrimination based on genetic disorders such as hereditary diseases and mental disorders.
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The privacy and confidentiality of genetic information could also lead to problems. For certain reasons, many people would want for no one to see what their genetic makeup is. There would also be concerns of psychological problems associated with knowing your own genetic makeup. If someone were to find out they have a good chance of developing a rare disease it would most likely drastically change their thinking on life. For reproduction, there could be compatibility problems of two individuals to have normal children. This would cause stress in a large number of people’s lives.
Another issue that has risen is the use of gene therapy to treat disease. In gene therapy a faulty or infected gene is replaced with a normal gene, so the individual does not display the trait that they were naturally born with. Many people feel that this is wrong because we are more or less taking over the course of nature, and they feel that this is not the natural way.
The HGP will also cause concerns over commercialization of the technology. If there are only a few agencies that are working on the project, who will get the rights to the technology? The major concerns will most likely be over the patients and copyrights of the technology.
There are also critics of the HGP that contend that the high cost of the project is not justified. Some critics also say that the ability to diagnose a genetic disorder before any treatment is available causes more harm than good, because it will create anxiety and frustration among individuals that may lead to depression. When and where will the use of genetic material be allowed in society now that the HGP is finished?
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The Human Genome Project was created in 1990 with the goal of sequencing the three billion base pairs in the human genome. Various methods, such as BAC-based sequencing and dideoxy Sanger method, were used. The benefits that were to be attained from the HGP were to better the diagnosis and treatment of genetic disorders and to improve forensic science. Many ethical issues are presented about the HGP related to the use and ownership of the information and technologies. In my opinion, the human genome project is something that will benefit the masses because it helps in the diagnosis of diseases, better medicines can be created, and certain disorders can be prevented.
When diagnosing diseases there is always room for error due to the limited amount of information that can be collected from blood, urine, etc. samples. With the information that can be collected from the new technologies and information provided by the HGP, there is less room for error making treatment or cures easier to administer or provide.
From all that doctors and scientists have learned from the human genome project many new medications and forms of treatment can be created, ones that are perhaps more efficient. When the human genome is mapped and one can see what the real problem is then the most effective treatment can be provided by the best means possible.
The human genome project has made gene therapy much easier to use and understand. Many genetic disorders can be prevented or removed. Many may say that this is unethical because it is too great an interference in the course of nature, but it must also be taken into consideration that many of today’s medical procedure do the same thing and help keep people alive for longer. Also, it is important to understand that gene therapy is not something that can be used lightly but is necessary for certain people with hereditary disorders that they could pass on to their offspring.