Human Genome Project (HGP) is an international research effort to determine the DNA sequence of the entire human genome. Genome is the whole genetic information of an organism. The idea of human genome project started in December 1984, when the U.S. Department of Energy (DOE), National Institutes of Health (NIH) and international groups had sponsored meeting to consider the feasibility and usefulness of mapping and sequencing the human genome. The aim of DOE is to make human genome as a way of aiding the detection of mutations that nuclear reaction might cause. While the aim of NIH and Wellcome Trust from Britain is to make advancement in medicine.
Human Genome Initiative is proposed by DOE to the U.S. Congress in 1987 and at the same time NIH had started funding grants for genome project. In 1988, National Research Council recommended a concerted program to map and sequence the human genome and in 1989, the U.S. Congress agreed with the idea. NIH and DOE joined Human Genome Project. In 1990, Human Genome Project began. DOE and NIH published plan for the first five years programme. Human Genome Project was projected to be a 15-year project. The goals of this phase are mapping human genome, determine the sequence of all 3.2 billion letters, mapping and sequencing the genome of other organisms which is important for studying biology, developing technology for analysing DNA and study the ethical, legal and social implication of genome research.
Human Genome Project made progress efficiently and it worked faster than schedule so on October 1993 second Human Genome Project five-year plan was published with new goals which are creating detailed genetic and physical maps, developing efficient strategies for sequencing and encouraging technology research. In 1998, third Human Genome Project five-year plan was published with the goals of completing human genome sequencing, studying human genome sequence variation and mouse genome. In 1999, full-scale of human genome sequencing began. In 2003, Human Genome Project completed and the finish sequence covers 99% of human genome and is accurate to 99.99%. In 2004, analysis of human genome sequence is refined.
The analysis reduced the estimate number of genes from 35000 to only 20000 to 25000. The finished sequence contains 2.85 billion nucleotides interrupted by only 341 gaps which cover 99% of genome with accuracy of 1 error per 100000 bases. Other than that, the existence of 19599 protein-coding genes is confirmed by the researcher and 2188 of other DNA segment that thought to be protein coding genes is identified.
DNA Sequencing in Human Genome Project
The method use for sequencing whole human genome preferred by Human Genome Project researcher is by using hierarchical shotgun sequencing method. The advantage of this approach is sequencers are less likely to make mistakes when assembling the shotgun fragments into contigs (which is the overlapping DNA sequence and to overlapping physical segments (fragments) contained in clones) depending on the context as long as full chromosomes.
Firstly, the researcher need to identified thousands of DNA sequence marks which will help them to understand the map of the chromosomes. This map also helps the geneticists to discover disease genes. Then the scientists try to create libraries of clones. Each clone contains a small fragment of human DNA and it is stored in bacteria, E. Coli. The DNA sequence marks will tell the scientist about the part of each human DNA fragment come from. This clone-by-clone approach is used to double check the location of each DNA sequence.
In clone libraries, the DNA fragments are stored in E. Coli (bacteria that live in human intestines). Each E. Coli cell stores a single segment of human DNA. Clone libraries help scientists to track and copy human DNA fragment easily.
Clone libraries are prepared by using bacterial artificial chromosomes (BAC). By using BAC, 100,000 to 200,000 bases of DNA sequence can be stored. Large BAC clones are used to establish the order of the DNA sequences while small BAC clones are used to sequence the DNA. Large BAC clones are cut into smaller fragments of about 2,000 bases. These smaller fragments are stored in viruses called phage. Phage can infect E. Coli cells.
E. Coli to Store and Copy DNA
E. Coli cells which containing fragments of human DNA can be stored in freezers. E. Coli is revived by bringing them back up to 37??C. The E. Coli cells act as copiers and they produce many copies of the human DNA sequence that stored inside them. The clone cells are put into a rich, warm broth. The cells are shaken vigorously for providing them with air and then causing them to divide rapidly. After incubating for a night, the broth will contain large number of E. Coli cells so large numbers of copies of the particular fragment of human DNA are produced.
Preparing DNA for Sequencing Reactions
The E. coli cells are broken for releasing their DNA. The human DNA is separated from the cell debris and it is cleaned.
A DNA sequencing reaction needs template of DNA copied by the E. coli, free bases, the building blocks of DNA that consist of primers and DNA polymerase. A DNA strand can be replicated only from its 3' end.
Products of Sequencing Reactions
A completed DNA sequencing reaction contains coloured DNA fragments. The shortest fragments correspond to the length of the primer plus one dye-coloured base while the longest fragments are between 500 and 800 bases long. The products of sequencing reactions are put into an automatic sequencing machine. Automatic sequencers can run more samples, process the samples more quickly, and are easier to operate. The primer sequence will bind to the template of DNA and continue with free bases. Some of the free bases in the solution have a fluorescent dye which attached to them which a different coloured dye is attached to each of the four kinds of bases. When a dye-bearing base attaches to the growing strand, the strand will stop from replicating any further.
Separating the Sequencing Products
Sequencing products are separated from each other by electrophoresis. DNA molecules are negatively charged so when the sequencing machine sets up an electric field, all the DNA molecules moves through a porous gel toward the positive electrode. Shorter DNA fragments move quickly through the holes of the gel while larger DNA fragments is vice versa.
Reading the Sequencing Products
As the DNA fragment reaches the end of the gel, a laser will excite the fluorescent dye attached to the base. Then, camera will detect the colour of the emitted light and the information is interpreted by computer. The colours of the DNA fragments are recorded one by one by the machine.
Assembling the Results
Computer program will integrate the data and it will spot the overlapping DNA fragments and assemble them as their real arrangement in the chromosome. Every base pair of DNA are sequenced an average of nine times.
Working Draft Sequence
The assembled of 2,000 or more bases is placed into public databases within 24 hours. The public (especially other researcher) can see and analyse the sequence data.
Hap Map: Catalogue of human genetic variation
DNA sequences are analysed from different populations and a catalogue of human genetic variation called the Hap Map is produced. It completed in 2005. Single nucleotide polymorphisms (SNP) are used by the Hap Map for identifying haplotypes (large blocks of DNA sequence) that have probability to be inherited. The researchers compare haplotypes between people with and without a disease. Haplotypes shared by people with the same disease are examined for looking it associated genes. Hap Map play important role in identifying disease genes.
Bioinformatics is the attainment, storage and analysis of the information found in nucleic acid and protein sequence data. Half of the genes identified by the Human Genome Project have no known function so by using bioinformatics researchers can identify genes, discover their functions and develop gene-based strategies for preventing, diagnosing, and treating disease. A DNA sequencing reaction will produce a sequence that is hundred bases long but gene sequences usually consist of thousands of bases. Scientists will assemble long DNA sequences from series of shorter overlapping sequences and then placed their assembled sequences into genetic databases so that other scientists may use the data. By computer program, scientists can use sequence data to look for genes, get clues to gene functions, examine genetic variation and explore evolutionary relationships.
Ethical, legal and social issues (ELSI)
Coverage and Reimbursement of Genetic Tests
Genomic medicine has the capacity to revolutionize clinical practice, but if insurance companies and Medicare are unwilling to pay for genetic testing, this important progress will be stalled. The mapping of the human genome has created new opportunities for genetic tests to predict, prevent and treat disease. Reimbursement decisions about genetic testing are complicated by a lack of extensive data evaluating the economics of genetic testing, and by the cost of evaluating new technologies. Several government agencies are working towards the development of regulatory standards for genetic testing laboratories and comprehensive integration of genetic testing into routine medical care. The Centres for Medicare and Medicaid Services (CMS) administers Medicare, the largest health insurance program in the United States. CMS also manages the Clinical Laboratory Improvement Amendments (CLIA) program, which inspects and regulates clinical laboratories, including those doing genetic testing. The Centres for Disease Control has an advisory group specifically focused on the CLIA regulations and projects studying validation of genetic tests and the integration of genetic tests into clinical practice. The Secretary's Advisory Committee on Genetics, Health, and Society (SACGHS) issued a comprehensive coverage report summarizing the issues surrounding reimbursement of genetic tests.
The Ethical, Legal and Social Implications (ELSI) Research Program
Ethical, Legal and Social Implications (ELSI) Research Program was established in 1990 as an integral part of the Human Genome Project (HGP) to foster basic and applied research on the ethical, legal and social implications of genetic and genomic research for individuals, families and communities. The ELSI Research Program funds and manages studies, and supports workshops, research consortia and policy conferences related to these topics. NHGRI's strategic plan published for the future of human genome research called Charting a course for genomic medicine from base pairs to bedside. The NHGRI has developed the following broad research priorities which are genomic research, genomic health care, broader societal issues and legal, regulatory and public policy issues.
Genomic research is the issues that arise in the design and conduct of genomic research, particularly as it increasingly involves the production, analysis and broad sharing of individual genomic information that is frequently coupled with detailed health information. Genomic health care is how rapid advances in genomic technologies and the availability of increasing amounts of genomic information influence how health care is provided and how it affects the health of individuals, families and communities. Broader societal issues are the normative underpinnings of beliefs, practices and policies regarding genomic information and technologies, as well as the implications of genomics for how we conceptualize and understand such issues as health, disease, and individual responsibility. Legal, regulatory and public policy issues are the effects of existing genomic research, health and public policies and regulations and the development of new policies and regulatory approaches.
Many Americans fear that participating in research or undergoing genetic testing will lead to them being discriminated against based on their genetics. Such fears may dissuade patients from volunteering to participate in the research necessary for the development of new tests, therapies and cures, or refusing genomics-based clinical tests. To address this, in 2008 the Genetic Information Nondiscrimination Act (GINA) was passed into law, prohibiting discrimination in the workplace and by health insurance issuers.
Regulation of Genetic Tests
As the science of genomics advances, genetic testing is becoming more commonplace in the clinic. Genetic tests are used as a health care tool to detect gene variants associated with a specific disease or condition, as well as for non-clinical uses such as paternity testing and forensics. Yet most genetic tests are not regulated, meaning that they go to market without any independent analysis to verify the claims of the seller. The Food and Drug Administration (FDA) has the authority to regulate genetic tests, but it has to date only regulated the relatively small number of genetic tests sold to laboratories as kits. Whereas the Centres for Medicare and Medicaid Services (CMS) does regulate clinical laboratories, it does not examine whether the tests performed are clinically meaningful. FDA in 2010 announced plans to expand its regulation to all genetic tests. Federal agencies that play role in the regulation of genetic tests: Medicare and Medicaid Services (CMS), Food and Drug Administration (FDA) and the Federal Trade Commission (FTC) which regulates false and misleading advertisement.
Health Issues in Genetics
Genetic research is designed to advance our understanding of the human genome and the role of individual genes or groups of genes in human health. However, beyond the hoped-for improvements in the medical profession's ability to treat and cure diseases, genetic research raises questions concerning how the information and technologies it yields will affect standards of patient care. Genetic testing and counselling, as well as gene therapy, raise difficult questions. Should physicians and health counsellors, for example, tell patients that they might be at high risk for developing an illness because of their genetic makeup when there is no effective treatment or cure for that disease now? Should health care practitioners perform genetic testing of an unborn foetus when the results might lead its parents to abort the pregnancy? Does the nature of genetic information create a need to revisit issues of informed consent and other ethical questions in the use of human subjects in genetics research? And how can the biomedical community use genetic information to improve standards of patient care?
The National Human Genome Research Institute (NHGRI) supports highly technical genetic research that is rapidly advancing our understanding of the human genome. This new information, although potentially beneficial to the health of human being (especially American), can also be misused. The insights gained through the Ethical, Legal and Social Implications (ELSI) Research Program inform the development of federal guidelines, regulations and legislation to guard against misuse of genetic information.
Informed Consent for Genomics Research
Informed consent involves two fundamental components: a document and a process. The informed consent document provides a summary of the research project (including the study's purpose, research procedures, potential risks and benefits, etc.) and explains the individual's rights as a research participant. This document is part of an informed consent process, which consists of conversations between the research team and the participant and may include other supporting material such as study brochures. The informed consent process provides research participants with on-going explanations that will help them make informed decisions about whether to begin or continue participating in the research project. Thus, informed consent is an on-going, interactive process, rather than a one-time information session. Given the complexity of the scientific and ethical issues that arise when conducting genomics research in the collaborative research setting that includes activities such as deposition of individual-level data into controlled-access databases for broad sharing, evolving IT technology, and the prospect of changing attitudes about privacy, this material is by nature dynamic and not meant to provide definitive answers. Instead, it is meant to be a first iteration of an evolving discussion that serves as a useful resource for scientific investigators as they work with their collaborators, IRBs, research participants, and communities to develop appropriate informed consent materials for genomic studies.
Intellectual Property and Genomics
Whether or not genes can be patented has been debated since the inception of the Human Genome Project. At the heart of the debate have been questions about whether discovery of a gene is sufficient to claim an invention and whether gene patents encourage or stifle research and the clinical use of genomics. In a landmark decision in June 2013, the Supreme Court determined that DNA in its natural form cannot be patented.
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