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

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Question 1

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Give a summary of the principal anticipated benefits and challenges that might be expected from widespread clinical genome sequencing.

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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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A genetic test for a marker M was carried out in 500 people affected by disease X and showed that 480 of the affected individuals typed positive for the marker. In a suitably matched set of 1000 healthy controls, just 80 people typed positive for marker. i) Establish the sensitivity and specificity of the test. ii) Work out the false positive rate and the positive predictive value iii) Work out the false negative rate and the negative predictive value.

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The working hypothesis is that there is ...

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Concerning preimplantation genetic diagnosis, which, if any, of the following statements is incorrect? a) It is carried out within the context of assisted reproduction. b) The analyses always involve genotyping just a single cell and so are technically difficult. c) Sometime a single blastomere is analysed from the embryo. d) Sometimes a polar body is analysed to infer the genotype of the embryo.

What is the basis of the ACCE framework for genetic testing?

What are the main uses of chromosome fluorescence in situ hybridization in a genetic service laboratory?

What is involved in Southern blot hybridization?

Describe the principles of arrayCGH and its applications in a diagnostic DNA laboratory.

Why is there still a need for conventional karyotyping using chromosome banding techniques?

What is meant by cascade testing?

What are the main applications of Southern blot-hydridization as an assay in a genetics service laboratory?

Explain the principles underlying target-sequence enrichment from a complex nucleic acid population.

What is involved in chromosome fluorescence in situ hybridization?

Give an outline of the different laboratory approaches to testing for aneuploidies and discuss their relative merits.

List four different ways in which a known, specific single nucleotide mutation can be detected within a defined exon.

What is involved in preimplantation genetic diagnosis, and why is it carried out?

Prenatal diagnosis involves analysing samples originating from fetal cells (either recovered directly from fetal tissue, or from maternal blood samples). What are the aims of these procedures?

Two ethical controversies relating to preimplantation genetic diagnosis involve sex selection and HLA selection. What are the issues involved?

Match the disorder a) to h) with the likelihood that it would be a focus for a genetic procedure listed in i) to vi)

The triplet repeat-primed PCR assay is commonly used in analysing samples from individuals with unstable trinucleotide repeat expansions. What is involved in this method?

With reference to genetic screening, what is the primary motivation for a) pregnancy screening, b) newborn screening, and c) carrier screening, and what types of disorders are involved?