Exam 11: Genetic Testing From Genes to Genomes, and the Ethics of Genetic Testing and Therapy

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-Benefits. A major benefit will be that the guesswork can be taken out of drug doses (even now, prescriptions for drugs such as warfarin are usually routinely made on a one-size fits all approach; knowing a person's genome sequence will allow more optimal dosing according to the profile of variants in the key drug-metabolizing enzymes). In the case of infectious disease, there is the prospect of rapid-response sequencing of the genomes of individual pathogen strains within hours of disease outbreaks, allowing rapid, innovative responses to epidemics across the globe.
-Challenges. The development of massively parallel genome sequencing has meant that the bottleneck has moved from data acquisition to data analysis. The sheer volume of sequencing data poses challenges for how to both store the data safely and provide a means of rapid ready access to the data while at the sane time maintaining data security and confidentiality.
When even highly trained geneticists struggle to understand current genome sequencing outputs reports, how can we expect physicians to make sense of them? There is a long way to go, and significant challenges in working out out what all the genetic variants mean, which will require very significant development of bioinformatics capabilities allied with functional studies.

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1) Amplification refractory mutation system (ARMS)
2) Oligonucleotide ligation assay
3) Pyrosequencing
4) DNA sequencing

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DNA samples, almost always genomic DNA samples, are treated with a suitable restriction endonuclease that cleaves the DNA into double-stranded fragments of a manageable size. The DNA fragments are separated according to size by agarose gel electrophoresis (DNA is negatively charged and will migrate towards the positive electrode through the porous agarose gel; small fragments move faster through the gel because there is less frictional resistance than with the larger fragments ).
After electrophoresis, the gel is immersed in strong alkaline solution and the resulting denatured DNA is transferred by capillary action to a nylon membrane that is placed in contact with the gel ("blotting"). The individual DNA fragments become immobilized on the membrane at positions which are a faithful record of the size separation achieved by agarose gel electrophoresis.
Subsequently, the immobilized single-stranded test sample DNA sequences are allowed to associate with labeled single-stranded probe DNA. The probe will bind only to highly related DNA sequences in the test sample DNA, and their position on the membrane can be related back to the original gel in order to estimate their size.