Human genome project and DNA profiling

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Human Genome Project

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Human Genome Project

Francis Crick and James Watson, in 1953, made a discovery of the structure of the DNA (Davies 2001, p. 310). Following this discovery, numerous developments have followed that have enabled the computing of DNA sequence with social and financial implications. The term genome refers to an organism’s set of DNA with all information of the genes involved. Each of the genomes in a human body has information that the organism requires for maintenance (Quackenbush 2011, p. 189). There are more than three billion pairs of DNA bases all human cells that have nucleus. Because of the enormous strides made in developing technology, the human genome project was developed. The goal of developing this project was so that the sequence of a human genome could be learned including finding out the genes that are within each human genome.

This Human Genome Project began in 1990 and was completed in 2003. It was an in international scientific project meant to learn the chemical make-up or sequence of chemical base pairs within DNA that make up DNA (Davies 2001, p. 310). The completion of the project was two years before the expected date of completion. The work that researchers did in the genome project was a great stride for science as it allowed the understanding of DNA blueprints. With the enhancement of this knowledge, scientists have learned more about the workings and functions of proteins and genes (Quackenbush 2011, p. 189). Consequently, the field of medicine has a major boost especially in areas dealing with protein-based diseases such as cancer. Life sciences, biotechnology and other fields of science have benefitted from the developments of the human genome project.

The genome project was developed with certain specific goals in mind. One of the main goals was to facilitate the knowledge of the three billion pairs of DNA bases in that theirs sequences are known. Linked to this was the goal of finding all the sequences that are present in human genes. That meant finding approximately 25,000 genes (Davies 2001, p. 310). Developing an accurate sequence of the DNA base pairs is critically instrumental in the field of medicine. On the same breath, yet another goal is that the project wanted to sequence the genomes of other organism that are important and instrumental in medical research (Cooper 1994, p. 360). These organisms include the fruit fly and mouse. The project also sought to establish tools that would be instrumental in analyzing and obtaining DNA information as well as making the information available to other interested parties. The human genome project was correctly predicted to have an effect on the society in terms of social, ethical and ethical aspects. As such, the project also aimed to explore the social, ethical and legal implications of the genome project (Gert et al. 1996, p. 242).

At the conclusion of the genome project in 2003, the researchers had managed to complete a first-rate sequence of the whole human genome. This is just one of the achievements that the human genome project managed. From this knowledge, other achievements developed. The working draft of the genome established in 2001 was finished (Davies 2001, p. 310). The exact locations of certain human genes were pinpointed as well as their organizations and structures. Tools for the analysis of the human genome were put on the internet for general use. The project also managed to sequence the genomes of other organisms of medical significance. These organisms include the roundworm and brewers’ yeast among others. Human genes are different and studying these differences and similarities has enabled researchers to identify some of the genes that are vital for life (Oliver & McGuire 2011, p. 38-40).

Because it is such an important part of life, the Human Genome Project had certain social, ethical and legal implications. These effects affect individuals, families and the society as a whole and they are abbreviated as ELSI (Oliver & McGuire 2011, p. 38-40). These implications include the consequences of the genome research in the society including fairness and privacy in the utilization of the genetic information obtained. There is a potential for the discrimination of genetics, especially in their insurance and employment (Gert et al 1996, p. 242). In addition, fairness in the integration of updated genetic technologies in clinical research and medicine. Other than that, there are ethical issues that need consideration in the conducting and designing of genetic research with human subjects. This includes the processes involved in obtaining informed consent from the subjects. An additional social implication is the education of policy makers, the public, students and healthcare professionals on the complexity of issues that are associated with genetic research. Other implications apply to areas of genetic testing, discrimination, genetic counseling and genetics and reproduction.

In the process of accomplishing the Human Genome Project, certain techniques for DNA sequencing were developed. Sanger and Coulson developed the ‘plus and minus’ technique that involves the use of the bacteriophage T4 DNA polymase and the polymerase I Escherichia coli in combination with different restrictive nucleoside triphosphates (Quackenbush 2011, p. 189). Acrylamide gels with ionophoresis resolve products of the polymerase. This method was later modified and was known as chaintermination or dideoxynucleotide method (Cooper 1994, p. 360). In this method, DNA fragments are polymerized by a catalyzed enzymatic reaction. These two techniques are enzymatic. There are chemical techniques of DNA sequencing including that developed by Maxam and Gilbert. Their methods uses chemical degradation and, one of the DNA fragments is taken through random cleavage at thymine, cytosine, adenine and guanine positions with the aid of specific chemicals (Quackenbush 2011, p. 189). This process involves there macro steps. The first step is to modify the base of the DNA. After the base has been modified, it is separated from its sugar. Following this, the DNA is broken into strands at the sugar position.

Another sequencing technique involves a process known as pryosequencing. This refers to the sequencing of DNA in a real time situation through detecting PPi released from the DNA. When the DNA is undergoing the polymermization reaction, the release of PPi is detected (Quackenbush 2011, p. 189). The fast sequencing of DNA is enabled by the use of a technique known as single-molecule sequencing with exonuclease. Individual florescent nucleotides are detected. The florescent bases in each fragment are first labeled. After this, the fragment that was labeled is attached to a microsphere. The fragment moves to a flowing buffer stream where it is digested by an exonuclease (Quackenbush 2011, p. 189).

Four of the best techniques of sequencing DNA are the Maxam and Gilbert method, the Sanger method, the single-molecule sequencing with exonuclease and pyrosequencing. Newer ways of DNA sequencing are bound to develop as technology advances further. The human genome project represents one of the major strides in DNA research (Quackenbush 2011, p. 189). Some of the findings of the genome project are posted on the Genome database where other researchers can access and expound on them, as they prefer.

List of References

Cooper, NG 1994, The Human Genome Project: Deciphering the Blueprint of Heredity ed, University Science Books, Mill Valley, CA. p. 360.

This collection focuses on the scientific concepts involved in constructing gene maps: the classification structure for DNA sequences, the construction of copy DNAs (cDNAs), polymerase chain reactions (PCRs) and sequence-tagged sites, and single-molecule spectroscopy (used for rapid DNA sequencing). Also included are discussions of the history of genetic research, the future of genomics, and electronic publishing of sequence data

Davies, K 2001, Cracking the Genome: Inside the Race to Unlock Human DNA, Free Press, New York. p .310.

Davies, the editor of Nature Genetics, closely followed the ongoing Human Genome Project for 10 years. He details the finances, the scientific developments, and the key players involved in mapping the human genome.

Gert, B, Berger, E M, Cahill, G F, Clouser, K D, Culver, C M, Moeschler, J B & Singer, G H S 1996, Morality and the New Genetics: A Guide for Students and Health Care Providers, Jones and Bartlett Publishers, Sudbury, MA. p. 242.

This textbook is the product of a three-year collaboration by ethicists, scientists, and medical professionals at Dartmouth. It includes an historical overview of genome research, a critique of principlism in the ethical analysis of genetic issues, and a discussion of the psychosocial aspects of «genetic malady».

Quackenbush, J 2011, The Human Genome: The Book of Essential Knowledge, Imagine, New York. p.189.

After providing a brief history of the Human Genome Project (HGP), the author traces the history of molecular biology from Mendel‘s experiments to the sequencing of the fruit fly. He synopsizes population genetics, personalized medicine, systems biology, and stem cell research, and discusses the future of genomic medicine.

Oliver, JM & McGuire, AL 2011, “Exploring the ELSI Universe: Critical Issues in the Evolution of Human Genomic Research,” Genome Medicine vol. 3, no. 6, p.38-40

The authors report on the National Human Genome Research Institute (NHGRI) Ethical, Legal, and Social Implications Research Program 2011 Congress, Exploring the ELSI Universe, held in Chapel Hill, North Carolina (USA) on April 12-14, 2011. ELSI researchers reported on projects addressing privacy issues with biobanks, and on the potential impact of genomic research on health care disparities

DNA PROFILING

Forensic scientists employ certain processes and procedures in an effort to identify people using their DNA. This technique is known as DNA profiling. Apart from monozygotic twins, every human being has unique DNA making it their profile. By matching certain DNA to particular people, forensic scientists practice DNA profiling, DNA typing, genetic fingerprinting or DNA testing. With enough DNA, one person can be distinguished from another using their DNA profile (set of numbers that are a representation of a person’s DNA). Repetitive sequences are utilized in DNA profiling. Each and every cell in a person’s body contains a chemical code. This is the DNA that makes up that individual. Its unique quality is what makes it a good tool in criminal forensics (Trivedi et al. 2002, p. 150-155).

Researchers have long been seeking a way to match biological evidence from crime scenes from specific individuals with 100% accuracy. The advent of DNA profiling allows this to happen to a certain degree. Over the years, there have been vast development and, as a result, a vast number of diverse DNA has been discovered. Consequently, various techniques of analyzing these variations have been developed (Australian institute of criminology 1990, p. 3). The vast developments in molecular biology in combination with different applications of population genetic principles give forensic scientists the ability to arrive to exclusion of a convincing degree of individuals from a particular DNA profile (Australian institute of criminology 1990, p. 3). When it comes to the assurance from DNA profiling, it is easier to get differences from DNA of people with non familial connection than in those who do.

The process of DNA profiling starts with the obtaining of a reference sample. The reference sample is the individual’s DNA that is going to be profiled. Once the sample has been obtained, it is analyzed so that a profile of the individual’s DNA is obtained. Once this has happened, the profile can be compared against others that were collected before, or those in databases such as the combined DNA Index System (CODIS database) (Australian institute of criminology 1990, p. 3). DNA profiling has come a long way to include various techniques like RFLP (restriction fragment length polymorphism) analysis, PCR (polymerase chain reaction) analysis, STR (Short tandem repeats) analysis, AmpFLP (Amplified fragment length polymorphism) analysis, DNA family relationship analysis, Y-chromosome analysis and mitochondrial analysis (Balloux & Lugon-Moulin 2002, p. 155– 165).

The molecules in DNA demonstrate varying type of polymorphisms that are categorized in different classes (Trivedi et al. 2002, p. 150-155). There are polymorphisms in the coding regions and polymorphisms in the non-coding regions. Those in the non-coding regions comprise of variable number of tandem repeats, which are the microsatellites and minisatellites (Trivedi et al. 2002, p. 150-155). They also comprise single nucleotide polymorphisms.

DNA is present in most cells in the body meaning that it can be found in white blood cells, hair roots, semen and body tissue. Little traces of DNA can be found in sweat and perspiration. Ancestry can be traced through the extraction of mitochondrial DNA from the bones or hair of an individual. One of the types of DNA profiling is called the restriction fragment length polymorphism (RFLP) (Kashyap et al. 2004, p. 11-30). In this procedure, DNA that is double stranded is extracted from the blood. A sequence specific enzyme is then used to cut the DNA into small pieces. Through electrophoresis, the fragments are disconnected or separated (Trivedi et al. 2002, p. 150-155). The sample that has already gone through electrophoresis is put in a substance called agarose gel into which a voltage is applied. Once this happens, the fragments move to the other end of the gel (Kashyap et al 2004, 11-30). Smaller fragments move faster than the larger ones. The separation, thus, happens based on molecular weight.

The gel and fragments are then exposed to 0.25M of HCl for purposes of nicking the sugar phosphate backbone as well as depurinating the DNA. These processes both ultimately assist in the transfer of fragments (Kashyap et al 2004, 11-30). Cleaving takes place when the fragments are washed in NaCl/NaOH. This process denatures the DNA, which is then moved to a nylon membrane. This enables the examination of the variable minisatellite region of the DNA. Probes are used for this examination (Kashyap et al 2004, 11-30). The probes are made up of 32P- radiolabelled single stranded short DNA. The probe binds to the complementary sequence present on the membrane. When exposed to film, the radiolabelled membrane creates an autoradiograph (Balloux & Lugon-Moulin 2002, p. 155– 165).

The techniques of DNA profiling all look to identify certain markers that will show molecular variation. Among these markers are microsatellites, which are regions in the DNA that have variable numbers (Balloux & Lugon-Moulin 2002, p. 155– 165). These are numbers of short tandem repeats that have been flanked by a certain unique sequence. In essence, these short sequences belong to nucleotides that have been tandemly repeated (Balloux & Lugon-Moulin 2002, p. 155– 165). Alleles belonging to microsatellites have different repeats that characterize them. There are short tandem repeats (STRs), simple sequence repeats (SSRs) found in Microsatellites loci, simple sequence tandem repeats (SSTRs), variable number tandem repeats (VNTRs), sequence tagged microsatellites (STMS), simple sequence length polymorphisms (SSLP) and simple sequence repeats (SSR). These repeats can be amplified using the polymerase chain reaction (PCR) (Trivedi et al. 2002, p. 150-155). This is an advantage because it enables specific allele references in population surveys based on the DNA sequence. This procedure also allows for the resolution of other alleles giving the researcher the ability to carry out genome sequencing and disease diagnosis. However, the amplification of VNTRs through PCR yields large products making them an unsuitable choice in general applications.

DNA profiling is evolving as technology keeps evolving. One of the greatest advantages of the techniques of DNA sampling is that researchers and scientists have the ability to analyze smaller DNA samples with greater accuracy (Australian institute of criminology 1990, p. 3). In addition, the processes involved in DNA profiling are faster than they were a decade ago (Australian institute of criminology 1990, p. 3). Technology and more in-depth knowledge into DNA profiling allows for greater automation of the processes in DNA profiling. However, there remains a disadvantage because of the inability to give completely accurate results, especially when it comes to the profiling of DNA of twins (Murphy 2009, p. 291-348). This is a great disadvantage because the greatest application of DNA profiling is in criminal forensics where two individuals need to be distinguished from each other (Murphy 2009, p. 291-348). The resolution of these issues will result in greater discrimination of results in presentation of results in court.

List of References

Australian institute of criminology 1990,
The Forensic Use of DNA Profiling, vol. 26, viewed 10 February 2012, <http://www.aic.gov.au/documents/1/2/8/%7B12877982-624A-4136-80D4-ACF694FD1144%7Dti26.pdf>.

The authors discuss different methods of DNA profiling including RFLP and the impact of changing technology on these methods. They also raise a number of issues that limit the use of profiling in forensic investigations, and stress the importance of the establishment of national standard techniques and the establishment of population frequency databases that reflect Australia’s particular ethnic composition

Balloux, F & Lugon-Moulin, N 2002, “The estimation of population differentiation with microsatellite markers,” Molecular Ecology, vol. 11, pp. 155 – 165.

The authors discuss how DNA techniques have opened a new frontier in forensic analysis. The authors also discuss how the way to a new course of events was first paved by the introduction of minisatellites using multilocus probes (MLPs), providing incomparably higher discriminatory power.

Kashyap, VK, Sitalaximi, T, Chattopadhyay, P & Trivedi, R 2004, “DNA profiling technologies in forensic analysis,” International journal of human genetics, vol. 4, no. 1, pp. 11-30.

The authors show the enormous strides that DNA technologies have made in the fields of medicine, medical diagnosis, human identification and understanding evolution. They also show the overview of current technologies used in forensic genetics, their evolution and the emerging trends

Murphy, E E 2009, “Relative Doubt: Familial Searches of DNA Databases,” Michigan Law Review, vol. 109, pp. 291-348.

This article talks about the application of DNA profiling in the criminal justice system with specific reference to the issues surrounding errors in DNA profiling. The forensic Use of DNA Profiling is acknowledged as a major contribution to the debate on law reform.

Trivedi, R, Chattopadhyay, P, Maity, B & Kashyap ,VK 2002, “Genetic polymorphism at nine microsatellite loci in four high altitude Himalayan desert human populations,” Forensic Science International, vol. 127, pp. 150-155.

DNA profiling has been described as a powerful breakthrough in forensic science with the advent of the polymerase chain reaction (PCR) as the turning point in the crucial issue of analytical efficiency of the DNA variants in the genome. The authors highlight that since then the field of molecular identification seems to have acquired a virtual unlimited power of analysis allowing experts to address even the most inaccessible sources of DNA