Before we know more about the human genome project, we must first know what the meaning of the genome. Genome of an organism is a complete set of DNA, including all genes. Each
genome contains all the information needed to build and maintain the organism.
In humans, a copy of the entire genome has more than 3 billion DNA base pairs which are contained in all cells that have nucleus.  In addition, genome is the entire hereditary information of organisms. It is encoded either in the DNA or, for many types of viruses, the RNA. Genome includes both coding and non-coding DNA sequences. 
The Human Genome Project (HGP) is an international scientific research effort to sequence and map all of the genes together known as the genome of members of our species, Homo sapiens. This project was officially started in 1990 and was completed in 2003, whichever is earlier than the expected time. This project was initially headed by James D. Watson at the U.S. National Institutes of Health. In addition, universities in the USA also have an additional role as well as partners from United Kingdom, France, Germany, Japan, and China has contributed to the success of this project. The main purpose of this research is to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. As researchers learn more about the functions of genes and proteins, this knowledge will have a major impact in the fields of medicine, biotechnology, and the life sciences.
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The Goals of Human Genome Project
When we do things, we must know what our purpose to do the same. So, in the Human Genome Project, there is some purpose or goal in doing so in addition to the main goals that I emphasize as above. Among other purposes is done Human Genome Project is to identify the approximate 100,000 genes in human DNA. Before this, we expected that there are about 100,000 genes in human. However, when the scientists have completed the human genome project, there are only about 20,000 genes that we have. Furthermore, the other goal is to determine the sequences of the more 3 billion bases that make up human DNA. When these have been done, it is so benefit in the future researches. Then, all the data of our genes can be stored in databases for further study.
In the mid 1950s, we have had a very rough physical map of the human genome which is distinguished the chromosomes by size and shape. To obtain the physical characteristics that clearly on the chromosome, it requires sophisticated technology that has not existed at that time. A main problem was that the initial goal of obtaining a human genetic map which could act as a platform for building detailed physical map. However this way seemed impossible.
However, in the late 1970s, scientists know that the great majority of the sequence variation in our genome occurred outside of genes and could be assayed. So, the variation had been study but then become focused on protein polymorphisms. Only a few protein markers could be studied because coding DNA is a very small fraction (2%) of the genome. The coding DNA is important because it is highly conserved during evolution. In the other hand, the non coding region of DNA is not well conserved and is very susceptible to changes in DNA sequence. In this year, there are methods which are restriction fragment length polymorphisms (RFLPs) that became available to assay DNA variation for the first time. Finally, the idea of constructing a comprehensive, nonclassical human genetic map becomes a reality.
The history of human genetics discoveries up to the 50th anniversary of the discovery of the DNA helical structure in 1953
Gregor Mendel proposes basic laws of heredity based on pea plants
Walter Fleming (embryologist) discovers tiny threads in the nuclei of cells of salamander larvae that appeared
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to be dividing. These later turn out to be chromosomes.
Francis Galton coins the term eugenics referring to improving the human race
Thomas Morgan's experiments with the fruit fly (Drosophila) reveal some characteristics that are sex-linked: confirms genes reside on chromosomes
US biologist Hermann Muller discovers X-rays cause genetic mutations in fruit flies
Oswald Avery, Colin McLeod & Maclyn McCarthy discover DNA, not protein, is the hereditary material in most living organisms
Francis Crick and James Watson discover double helical nature of DNA
Charles Yanofsky and colleagues prove sequence of nucleotides in DNA correspond exactly to the sequence of amino acids in proteins
First gene in a piece of bacterial DNA isolated. The gene plays a role in the metabolism of sugar
Researchers at the University of Wisconsin synthesis a gene from scratch
First genetic engineering experiment: Insertion of a gene from an African clawed toad into a bacterium
First call for guidelines governing genetic engineering
Maxam, Gilbert and Sanger develop DNA sequencing
First human gene cloned: insulin
Mapping human genome proposed using RFLPs (restriction fragment length polymorphisms)
First genetically engineered drug approved: insulin
Genetic marker for the genetic condition Huntington disease (HD) located on chromosome 4
Kary Mullis develops PCR (polymerase chain reaction) to rapidly reproduce DNA from a very small sample that enables genetic testing for health and other applications
First use of DNA "fingerprinting" in a criminal investigation
First automated sequencer developed
Approval for first genetically engineered vaccine for humans, for hepatitis B
Creation of the National Centre for Human Genome Research (headed by James Watson) which would oversee the Human Genome Project (HGP) to map and sequence the genes in human DNA by 2005
Formal launch of the HGP First human gene therapy experiment performed on a 4 yr old girl with an immune deficiency
Publication of Michael Crichton's novel "Jurassic Park" in which bio-engineered dinosaurs roam a palaentological theme park: the experiment goes awry
First gene involved in inherited predisposition to breast cancer and ovarian cancer (BRCA1) located on chromosome 17
US Army begins collecting blood and tissue from all new recruits as part of a "genetic dog tag" program to give better identification of soldiers killed in combat
First rough map of all 23 chromosomes produced Gene for HD cloned
H. influenzae (virus) sequenced Microarray (CHIP) technology developed
S. cerevisae (yeast) sequenced
Cloning of "Dolly"
C. elegans (worm) sequenced
USA announce a 3 year mouse genome project
First human chromosome sequenced: chromosome 22
Drosophila (fruit fly) genome sequenced
Chromosomes 5, 16 &19 draft sequence
Chromosome 21 sequenced
"Working draft" of human genome sequence announced
Publication of initial working draft of the human genome published in Science & Nature by the two rival private and public groups
Genome of mouse completed
April 25th 2003
Completion of the mapping of the genes in the human genome announced setting the stage for determining
the function of the then estimated 30, 000 or so genes
Method for human genome : Mapping and Sequencing
Mapping is the process where chromosomes are divided into smaller pieces that can be increased and were interpretive with their respective locations on chromosomes. After mapping is completed, the next step is to determine the base sequence of each of the ordered DNA fragments. There are some strategies in the mapping which are:
Genetic Linkage Maps
Genetic linkage map will show the relative locations of specific DNA marker along the chromosome. Therefore, any physical characteristics that can be transmitted person to detect a difference are a potential genetic marker. Markers can be expressed DNA segments or DNA regions (genes) that have no known coding function but its inheritance pattern can be followed. DNA markers that useful are that have DNA sequence differences because it's a lot and easy to characterize rightly. For make the markers useful, it must be polymorphic. Its mean that individuals must have alternative form so that they can be detect among different members in family studies. In addition, polymorphisms are variations in DNA sequence that occur on average once every 300 to 500 bp. For example, if the variations occur in the exon, sequences give the changes that we can see by naked eyes such as eye color, blood type, and disease susceptibility. Meanwhile, if the variation within intron, there are only little effect or no effect to the appearance of the organisms. Furthermore, this will be used as a DNA marker. Then, the examples of these markers are restriction fragment length polymorphisms (RFLPs) and variable number of tandem repeat sequences. The RFLPs is reflect sequence variations in DNA sites that can be cleaved by DNA restriction enzymes meanwhile the tandem repeated sequences are short repeated sequences that vary in the number of repeated units, so its characteristics are easily measured. With observing how frequently two markers are inherited together, we can construct a human genetic linkage map.
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If the two markers are located near each other on the same chromosome, it will tend to be passed together from parent to progeny. For example, when a meiotic recombinant happened between sperm and egg cells, two markers from the same chromosome will separate. So, when the markers are located near each other, the possibilities of the markers separated become less.
Furthermore, in the genetic map, the distances between each marker are measure by centimorgans (cM) unit. This unit comes from the American geneticist Thomas Hunt Morgan. A genetic distance of 1 cM is roughly equal to a physical distance of 1 million bp (1 Mb). When we follow the inheritance of DNA markers that presented in affected person, we actually can determine the value of the genetic map is that an inherited disease can be located on the map. This genetic map also benefit in finding the exact chromosomal location of the diseases gene such as Tay- Sachs disease, cystic fibrosis, fragile X syndrome, sickle cell disease, and myotonic dystrophy.
There are two types of physical mapping which are Low-Resolution Physical Mapping and High- Resolution Physical Mapping. This vary occur because their have different degree of resolution.
Low-Resolution Physical Mapping
Firstly, we must know what is the meaning of the low-resolution physical mapping. So, it is the chromosomal (or cytogenetic) map, which is based on the distinctive banding patterns observed by light microscopy of stained chromosomes. In a chromosomal map, genes or DNA fragments assigned to their chromosomes and their distances measured in base pairs. In addition, these markers can combine with particular bands (identified by cytogenetic staining) by in situ hybridization technique. This technique involves the tagging of DNA marker with observable label. So, when the labeled probe binds to its complementary DNA strand, the location of the labeled probe can be distinguished. The use of chromosomal mapping is to find genetic markers that are determined based on features that can be seen with the naked eye are in an organism. Because the mapping of this chromosome based on estimates of the physical distance, it is also categorized as physical mapping. Furthermore, the numbers of base pairs within a band only can be estimated, not exactly determined the amount.
The other map that include on this low-resolution physical mapping is cDNA map. This map shows the positions of expressed DNA regions (exons) relative to particular chromosomal regions or bands. The way for we synthesize cDNA in the lab is we must use the mRNA as a template. When doing this, we must follow the base-pairing rules. For example, when we use T from mRNA template, we must bind to A in the new strands of the DNA. We can't against the rule because the mismatch template will break the new strands. Then, this cDNA can be mapped to genomic regions.
High- Resolution Physical Mapping
There are two approaches of high- resolution physical mapping which are top- down mapping (macrorestriction map) and bottom- up mapping (contig map). The both maps represent the order set of DNA fragment that produce from the cutting of genomic DNA by restriction enzyme. Then, the fragments are amplified with PCR chain or cloning.
In the top- down mapping, a single chromosome is cute into large pieces by restriction enzyme. Then, the pieces are dividing into smaller pieces for easy to mapping. From the resulting macro-restriction map, we can describe at which order and distance the restriction enzyme cut it. The advantage from this map is the gap between the fragments becomes less and the fragment becomes more continuity. However, the map resolution is lower and can't help in finding particular genes. So, it does not produce long stretches of mapped sites.
Meanwhile in the bottom- up mapping, the chromosome is cutting into small fragment and then each of the fragments is cloned and ordered. The ordered fragments form contiguous DNA blocks (contigs). The advantage of this mapping is this clone is stable and makes researchers can access the clone. Contig construction can be verified by FISH, which localizes cosmids to specific regions within chromosomal bands. Contig maps consist of a linked library of small overlapping clones that show a complete chromosomal segment. contig maps are useful for finding genes localized to a small area (under 2 Mb), its difficult to extend over large stretches of a chromosome because all regions are not clonable. DNA probe techniques can be used to fill in the gaps, but needed much more time.
Types of Genome Maps
In the flow sorting, the flow cytometry is used. This instrument will isolate the chromosome according the size during cell division when the cells are condensed and stable. A chromosome will flow singly past a laser beam and they are differentiate by analyzed the amount of DNA present. After that, the individual chromosomes are go to the specific collection tubes.
Meanwhile in somatic cell hybridization, human cell and tumor cell are fused together and form a hybrid. After that, the human chromosomes are lost from the hybrid cell until remain one or few cell. Those individual hybrid cells are then propagated and maintained as cell lines containing specific human chromosomes.
DNA Amplification: Cloning and Polymerase Chain Reaction
Cloning (in vivo DNA amplification)
Cloning is the use of recombinant DNA technology to spread DNA fragment into other cell (foreign host). The fragments come from isolation of chromosome by restriction enzyme and then it will be combining with a carrier (vector). In the suitable host cells, the fragment will synthesize together with the host cell DNA. For our information, the vector is an other form of storage genetic information that will be found in virus, bacteria and yeast cells. The bacterial vectors such as plasmids and cosmids can place foreign DNA fragments ranging from 12,000 bp meanwhile the yeast vector such as yeast artificial chromosomes can place about 1 Mb.
PCR (in vitro DNA amplification)
Polymerase chain reaction is a process where the new DNA copies of the target in turn serve as template to make more copies still in a chain reaction.  The 4 DNA bases and 2 DNA fragments are mixed together with the target sequence. Then this mixture is heat to separate the double strands of the DNA. After that, its will cool down to allow the primer find their complement strand in the separate strands and bind it. Then, the polymerase will extend the primer to form new strands.
So, when repeating the heating and cooling, it will amplify more DNA strands.
Benefits of the Human Genome Project
There are some benefits in the human genome project. The benefits were in several fields as describe below:
When all of the human genes are sequenced, the disease genes become known. So that, it will be improve diagnosis of disease in human body. In addition, the other benefit is an earlier detection of predispositions to disease. Furthermore, the rational drugs could be design with the detection of the disease. The drugs will be more efficient in action with the disease. The gene therapy and control system can be making. The human genome project also benefit in organ replacement.
Microbial Genome Research
In the field of microbial genome research, human genome project give the benefit in producing new energy sources such as biofuels. In addition, we can monitor environmental to detect pollutants. The benefit is also in protection from biological and chemical warfare. Then, the technology nowadays makes toxic waste clean up become more safe and efficient. So, our environment will safe and maintain healthy.
Meanwhile, the human genome project also benefit in the DNA forensic field. It is because, when the entire human gene had sequenced, we can identify potential suspects at crime scenes. The evident that found at the crime site can be sequence to determine the DNA. Then, the police will arrest the suspect and make a comparison between its DNA and DNA that had found and see it whether it match or not. So, the police can exonerate wrongly accused persons and the innocent person doesn't be punished for what they have not done. In addition, it will be easier to the police to identify crime and catastrophe victims and the right person that do the crime will be punished. In some other cases, we can establish paternity and other family relations. When the chromosomes are known, we can know from which family we come from and is that our family related which our friend's family.
Evolution and Human Migration
In the other hand, human genome project also benefit in the aspect of human evolution and human migration. Scientist use germ line mutations in lineages to study evolution. They study migration of different population groups based on female genetic inheritance. In addition, they also study mutations on the evolutionarily stable Y chromosome to trace lineage and migration. So, when they have study the entire element, they can compare breakpoints in the evolution of mutations with ages of populations and historical events.
Although there are many benefits of the Human Genome Project, but there are still some fear and concern in terms of abuse such as human cloning and eugenically motivated experimentation. So, to avoid all this anxiety and fear of becoming a reality, as much as 3 percent of the budget to do the HGP has been extended to study the issues in terms of ethical, legal and social effects that may occur from this project. Besides, this is the largest study of biology in human history.
In addition, the ethics rise from the aspects of genetics privacy and legislation. On the date of May 21, 2008, the president of the USA, G.W.Bush signed Genetic Information Nondiscrimination Act (GINA) laws. Based on this law, insurance companies and employers are forbidden to discrimination an employee after genetic testing done. For example, if a person is diagnosed with heart disease, an employer can not dismiss him from work while the insurance company will not reduce insurance rates that sick workers. In addition, employers and insurance companies absolutely forbidden to ask someone do the genetic testing. Therefore, it has a right guaranteed by the law despite the existence of this useful technology.
In addition, there are some clinical issues related to the ethical. The clinical issues in education is a doctor, health services provided, patients, the limitations of science, social risk, assessment standards and quality control in a test procedure. However, clinical issues will be more focused on gene testing. test gene or DNA testing is a technique used to test for any genetic disorders, involve direct examination of the DNA molecule itself. This test is the test of the latest and most sophisticated one. There is some use of gene tests are:
preimplantation genetic diagnosis
confirmational diagnosis of a symptomatic individual
prenatal diagnostic testing
presymptomatic testing for predicting adult-onset disorders such as Huntington's disease
presymptomatic testing for estimating the risk of developing adult-onset cancers and Alzheimer's disease
So, the question is why this method has raised ethical issues? For example, by using these gene tests, parents can determine the likelihood of future disease in the face by the lives of their children later. So they can abort it if such things happen. Are this does not contradict the ethics of all human beings are blessed with a love and a sound mind. In addition, this issue also involves a disease that slowly emerged, but passed through generations, such as Alzheimer's and cancer. Someone who had ancestors who had the disease will not necessarily get it 100%. With gene testing, only the probability of the disease will be known. So it's still a question to the scientists themselves because they believe that a disease may also be caused by unknown mutations and environmental influences.
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