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What different methods exist for studying genetic variation at a molecular level? How could an allele polymorphism mutation be shown to contribute to a disease/ trait?

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Introduction

What different methods exist for studying genetic variation at a molecular level? How could an allele polymorphism mutation be shown to contribute to a disease/ trait? Almost all human genetic variation is relatively insignificant biologically- that is, it has no apparent adaptive significance. Some variation such as a neutral mutations, alter the amino acid sequence of the resulting protein but produces no detectable change in its function. Other variation, for example, silent mutations, do not even change the amino acid sequence of a polypeptide. Furthermore, only a small percentage of the DNA sequences in the human genome are coding sequences (sequences that are ultimately translated into protein) or regulatory sequences (sequences that can influence the level, timing, and tissue specificity of gene expression). However, these supposedly silent variations may be useful in mapping specific genes in the human genome, is not allowing the study of variation amongst individuals in a population flourish. The co-existence of more than one variant of an allele is called genetic polymorphism. More precisely, an allele is usually defined as polymorphic if it is present at a frequency of >1% in a population. Variation among individuals however, need not only occur in base sequences in deoxyribonucleic acid (DNA), which codes for the production of a polypeptide molecule (gene) or even promoters. It is therefore essentail to determine the types of polymorphism inherent in individuals of a species, before these DNA variations can be studied on a molecular level. Single-nucleotide polymorphs (SNPs) consist of differences in the identity and frequency of a single nucleotide pair at a particular locus. For example, some individuals in a population may have the base pair T-A at the chromosomal site whereas others may have the pair C-G instead. SNPs are the most common form of genetic variation amongst individuals of a species because they are distributed uniformly along all 46 chromosomes. In the human genome, any two randomly chosen DNA molecules are likely to differ at loci every 1000-3000bp in gene-coding DNA, in comparison to one SNP site in every 500-1000bp of non-coding DNA1. ...read more.

Middle

Nevertheless, a large number of alleles contained in the population produce a large number of possible genotypes; subsequently STRPs are highly constructive in their ability to establish an individual's identification during DNA fingerprinting (or typing), due to this broad variance amongst a populace. Once variations at allele polymorphic sites have been distinguished amongst individuals, how could a particular polymorphism then be proven to contribute to a particular genetic disease or trait? When one seeks to identify a gene responsible for a disease, unless there are gross deletions or other obvious changes which identify the damaged gene in patients, we have a choice of approximately 80,000 DNA gene loci from which to determine a disease causing gene. This typical problem occurs when a mutation (polymorphism) has a known effect on the organism's phenotype and there is some idea of the gene locus on a chromosome yet no corresponding knowledge of the actual gene or altered protein transcribed and translated from it. In such cases, the utility of DNA polymorphisms in locating and identifying disease genes resulting from genetic linkage (the tendency for genes that are sufficiently close together on a chromosome to be inherited together) is evident. For instance, if restriction polymorphisms are known to occur at random in the genome, some should occur near any particular target gene. Thus, the closer the marker to the disease causing gene, the less likely that recombination will occur between the two. Any gene that is not separated from a particular polymorphism is therefore a candidate for a disease locus. So, if the inheritance of a disease is traced through a family by observing the individuals' phenotypes, together with a traced inheritance of particular polymorph markers, one can comprehend that certain DNA markers must be sufficiently close to a disease gene on a particular chromosome if they tend to be inherited in a pedigree, concluding that the closer the marker, the stronger the association with the disease gene. ...read more.

Conclusion

Such information does not prove a severe handicap for well studied organisms e.g. domesticated, selectively bred animals, as research materials and sequencing information is readily available. However, for less documented organisms, genetic analysis of various traits within a population, arising from polymorphisms, can be carried out using a technique referred to as random amplified polymorphic DNA (RAPD.) RAPD draws on a set of polymerase chain reaction primers with a length of 8-10 nucleotides long, whose sequence is effectively random. The genomic DNA of an organism is extracted and subjected to these random primers, usually in pairs. Due to the short length of the primers, they often anneal at multiple sites along the DNA of the individual. Primers that anneal in the correct orientation and at a suitable distance from each other, amplify unknown DNA sequences between them. The resulting amplified sequences from a genome will vary from organism to organism in a given species, emphasising the presence or absence of a polymorphic site within a population. The RAPD may then be subjected to gel electrophoresis and analysis after staining with ethidium bromide. When comparing band variations between individuals of a species, those that have the same amplified bands are deemed as monomorphic whereas those with divergence in band patterns contain RAPD polymorphisms. Note that discussions of variations of such organisms are very often referring to the objective band patterns observed after genetic analysis rather than varying physiological or morphological characteristics. In conclusion, it is possible to measure variations in single nucleotide polymorphisms and variable number tandem repeats amongst a population when restriction enzymes are applied. The resulting random fragment length polymorphs produced can then be used as genetic markers to further identify hereditary predispositions to certain diseases. The polymerase chain reaction allows a small sample of a desired DNA to be augmented so that many copies are available for further investigation of the gene. Variations in 'alleles' between individuals can be clearly portrayed after their translation to an x-ray micrograph, after carrying out gel electrophoresis and Southern blotting (created by Edward Southern) on desired DNA fragments produced by restriction endonucleases. ...read more.

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