Using Microsatellites and SNPs as Tools in Medical Genetic Diagnostics and Research
The field of genetics is considered one of the most interesting fields of science, which has been stirring the curiosity and concern of many scientists and researchers in different expertise. In today’s generation, different applications of genetics can be distinguished and enumerated, including its application in the development of genetic engineering and cloning technology, in teaching and education, in research and studies of different biological phenomena, and in the field of medicine. In this regard, this paper aims to discuss the specific application of genetics in the field of medicine through the emphasis on the use of microsatellites and SNPs in medical genetic diagnostics and research. The subject would be discussed by briefly discussing the use of genetics in the medical field, and by emphasizing on the two important terms. Afterwards, the principle, implications, and actual research examples would be. At the end of the paper, a conclusion would be provided to emphasize on the important points made by the discussion.
Medical Genetics: Brief History and Development
It has been reported that the theories and studies in human genetics have a long history. Observations on the inheritance of physical traits in humans were first accounted by the Greeks, who stressed such observations in their ancient literatures. The 18th and 19th century scientists, who published on the inheritance of numerous diseases, including empirical rules on modes of inheritance, followed further studies and observations of the Greeks. A very important step in the development of human genetics and its application of a Mendelian mode of inheritance in alcaptonuria and other inborn errors of metabolism. It was then followed by Pauling’s elucidation of sickle cell anemia as a molecular disease, the discovery of genetic enzyme defects as the causes of metabolic disease, the determination that there are 46 chromosomes in humans, the development of prenatal diagnosis by amniocentesis, and the large-scale introduction of molecular methods ( 1996). In this regard, human genetics was further related and developed to be related to medical genetics, emphasizing on the use of molecular genetics and DNA technology to practical problems on medical concerns. Such applications include the use of DNA variants as genetic markers in the detection of closely linked genes that are suspected to cause manifestations of diseases and abnormalities. Such has been done through utilizing nucleotide probes that are homologous to the mutations being searched for. Through such applications, treatment of genetic diseases is now being studied, thus, emphasizing on the effective and significant application of genetics in the field of medicine. In this sense, the development of the field of human genetics to medical genetics has become one of the most significant contributions of genetics in the world, being able to provide diagnosis, research, and treatment to many individuals.
Microsatellites and SNPs
DNA polymorphisms are variations in the nucleotide sequence of DNA, which are functionally silent. These are important and widely used genetic markers tagging particular allelic chromosomal regions similar to signposts along roads. Such polymorphic alleles are present in the constitutional DNA of each individual and passed on in the germline to the progeny (2004). In this regard, such polymorphisms are important, most especially in detecting mutations and changes in the pairing of genes. It has been mentioned previously that the detection of gene linkages and mutation can be done using gene markers. This is because gene markers serve to display the sequence of repeats and pairing of genes in a certain organism. Gene markers that serve this purpose include microsatellites and SNPs or single nucleotide polymorphisms.
Molecular markers known as microsatellites are small, heritable repeating DNA sequences that vary among and within species of many organisms ( 2004). Microsatellites or STRs (short tandem repeat polymorphisms) are sequences composed of runs of repeat units 2-5bp in length, which are found in the genomes of many eukaryotes (1998). These repeated sequences are ubiquitous in the genomes of a wide range of organisms, and the number of repeats within many of them is highly variable in the population of a particular species. The most common microsatellites in mammals are of the form (dC – dA) (dG – dT) (2002), and in the human genome, there are perhaps 35,000 microsatellite loci, occurring on average every 100,000bp, and with allele lengths of usually between 2 and 50 repeats per locus. The importance of microsatellites lies in their high mutation rates, between 10-2 and 10-5 per gamete, per generation, so that they also vary greatly in copy number between individuals. Such high levels of genetic diversity coupled with neutral evolution, codominance and simple Mendelian inheritance mean that they are also in ideal, and currently extremely popular, set of molecular markers ( 1998). At present, microsatellite polymorphisms or MSPs are now being used for a wide range of applications in genetics, including the construction of genetic linkage maps, linkage mapping of disease genes and quantitative traits, diagnosis of genetic disorders, studies of loss of heterozygosity in tumors, paternity testing, forensic analysis, and selective breeding in the dairy and beef industries (2002). Another molecular marker that indicates polymorphism is the SNP, or the single-nucleotide polymorphisms, which are the most common type of repeated genetic elements. These variations are associated with diversity in the population, individuality, susceptibility to diseases, and individual responses to medicine. This type of variation is particularly noted in the untranslated regions of the genome, that is, in the 5’ and 3’ untranslated regions of the gene, within introns, and in the extragenic regions of DNA, where variations in sequence can occur without as great an impact on function. These polymorphisms are points that normal person in the population and another have. One person has an A-T pair, whereas another has a G-C pair. More than 90% of all human genes contain at least one SNP, and approximately 3 million have been discovered since the human genome sequence was determined (2006). In this regard, both of these polymorphisms can be regarded as important means of detecting genetic sequences and mutations, thus, are both important in medical genetic diagnostics and research.
Using Microsatellites and SNPs: Implications and Research
It has been reported that genetic diseases caused by mutations in one gene are referred to as single gene disorders, while complex or multigene disorders result from a combination of mutations, polymorphisms, and or environmental influences (2004). As emphasized, genetic diseases caused by genetic alterations can be detected through researches and studies using both the microsatellites and SNPs. In this regard, both gene markers are being used as effective and significant gene markers in different researches, most especially in the medical field, in order to help detect and treat genetic mutations and genetic diseases in individuals.
Application of using microsatellites may be of medical importance, as a number of human genetic diseases, such as fragile X syndrome, Huntington’s disease, myotonic dystrophy, and spino-bulbo-muscular dystrophy are associated with a dramatic increase in the copy number of trinucleotide microsatellite repeats. For example, fragile X syndrome, the most common form of inherited (X-linked) mental retardation, and recognized by a fragile or breakable site in the X chromosome, appears to be caused by expansion of a CGG repeat in exon 1 of the FMRI gene. Normally alleles contain between 6 and 50 repeat units whereas clinically affected individuals have more than 200 repeats and frequently more than 1000 ( 1998). The practical laboratory definition of several thousand microsatellite markers for use in pooled genomic screens is an enormous task, but most only be completed once to make the method generally available for association mapping of human disease and trait loci. An automated sequencer or scanner for detection of fluorescently labeled PCR products is the ideal instrument for initial association screening with pooled DNA samples using microsatellites, because it allows a large amount of information to be obtained from each gel ( 2001). On the other hand, SNP markers are clearly the genetic tool of the future, especially for high-throughput, automated research laboratories with resources to purchase sophisticated instruments. SNPs can serve as genetic markers with experiments relying on linkage diequilibrium to detect associations of SNP alleles and phenotypic traits. SNPs also have the possibility of being directly responsible for the phenotype. SNP maps in humans are currently under development, and these maps are leading to an enhanced understanding of human disease (2004). In this regard, SNP technologies are now being used in improving our understanding of the etiology of complex human disease, such as in gene mapping, candidate polymorphism association testing, pharmacogenetics, diagnostics and risk profiling, prediction of response to nonpharmacologic environmental stimuli, and homogeneity testing and epidemiologic study design. While only a few of these areas are currently areas of active research in human genetics, it is most likely that some or all of these areas will become relevant to investigations of the genetic susceptibility to human disease (E2002). However, despite the perceived efficacy and effectiveness of the use of both genetic markers in medical genetic diagnostic and research, comparison of both the use of microsatellites and SNPs are being stressed. Comparison of the two genetic markers emphasizes that SNPs must be used significantly, as abundant and more highly dense SNPs can be obtained in the genome, compared with the use of microsatellites. In addition, using SNPs can also provide at least approximately the same amount of information as the common set of microsatellites (2005). However, SNP markers are somewhat more difficult to type than microsatellites and often have lower rates of heterozygosity in populations and crosses. Nevertheless, they can be designed to virtually any sequence and are less prone to mutation than microsatellites, thus, are particularly useful for association mapping, haplotype, and phylogenetic studies (2007). In its use in medical diagnostics and research, a higher number of SNP loci are required, thus, multiplying the costs in reagents and manpower by 6 to 10 fold. Choosing SNPs over microsatellites also involves considerable investment in equipment that often has higher operating costs than the sequencers used for typing microsatellites. Nowadays, microsatellite libraries can be ordered from companies at a reasonable cost and can be ordered with pre-evaluated primer pairs, thus, significantly cutting down the costs of manpower required for these steps ( 2006). In the end, to reduce labor and cost, the most efficient scheme for completing a pooled screen, including the preliminary marker optimization phase for both microsatellites and SNPs, would be a large collaborative study of several diseases with independent laboratories typing all diseases, and a division of microsatellite markers among laboratories (2001). However, in the process, the use of both genetic markers would be able to make the diagnosis and treatment of genetic or hereditary diseases easier and earlier, thus, significantly allowing the field of genetics to significantly contribute to the preservation of life of individuals. In addition, utilizing such genetic markers in the field of medicine would allow advancement of genetic engineering, which emphasizes genetic testing and gene therapy, in its aim to predict genetic diseases and to override or replace defective genes. Genome scanning using genetic markers can also allow pharmaceutical manufacturers to custom-tailor drugs to a person’s genome, thus, providing more effective treatment (2004). As such, it can be perceived that the use of both microsatellites and SNPs, despite its costs, would allow the significant contribution of genetics in the field of medicine.
Conclusion
From the discussion, it can be understood that the use of both microsatellites and SNPs involves costs and measures, which may somehow hinder its effective research. However, from the significance of its use in genome scanning, the field of medicine would then be developed and improved, most especially in terms of the diagnosis and treatment of individuals, suffering from various genetic disorders. Such findings would be assisted by the use of such genetic markers in the field of research, as certain developments would be useful in developing new drugs and therapies for genetic disorders. In addition, the use of microsatellites and SNPs would augment the field of medical diagnosis, thus, making findings regarding the disease of individuals easier to detect and examine, thus, helping to provide early detection and early treatment.
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