You work for a private genetic analysis laboratory that tests for various alleles associated with different traits. The company wants to introduce testing for a specific SNP (rs4680) in the COMT gene on chromosome 22. COMT codes for the catecholamine-O-methyltransferase enzyme that helps inactivate various neurotransmitters and catecholamines such as dopamine and epinephrine.

The rs4680 SNP is a single nucleotide G to A substitution in exon 4 that changes GTG to ATG at codon 158, resulting in an amino acid change from valine to methionine within the polypeptide. This change leads to reduced catecholamine-O-methyltransferase enzyme activity and could increase levels of the associated neurotransmitters and catecholamines. Individuals carrying the rs4680 SNP may have a lower pain threshold but be more efficient at information processing under most conditions.

There are various ways in which the rs4680 SNP can be tested. Your line manager and company has requested for you and your colleagues to test different genotyping techniques that have already been designed, and then deliberate which would work best for your laboratory to routinely test for this SNP. They want you to complete a report to give your suggestions based on a certain set of criteria.

Laboratory criteria:

Cost-effectiveness.

Suitability for routine use.

Time effectiveness.

Reliability and repeatability.

Company criteria, ensure that you will routinely deliver:

“The right result every time at the right price.”

Do not include the guidelines in red in your final report

Delete guides as you work through!

Think about the various genotyping techniques outlined in the lab schedule. Describe how each of the genotyping techniques works. Note – you do not need to explain the basic principles of PCR, just the techniques used. Diagrams are useful for this, but they do need to be described.

You were provided with the primer sequences and enzymes to use throughout. Use this information to produce a figure(s) to illustrate the primer binding sites and expected products/results for each of the genotyping techniques.

One of the assays is incorrectly designed. Comment on which assay this is and suggest an alternative design. Also comment if you have suggestions for improvements to any of the other assays.

Use statistical methods and produce a suitable table which combines all the samples, assays and genotypes.

You do not need to include all the raw data, only processed data.

You need to concisely describe your results and how the genotypes were determined from the data.

From the literature, which technique is the gold standard? Compare the gold standard results to the other techniques. Comment on your findings.

Think back to your original aim.

They want you to deliberate which assay works best for the laboratory and then complete a report to give your suggestions on which assay is most suitable and why.

Remember your suggestion should be based on a set of criteria. How does each assay fare with the set criterion? Are there any additional criteria you suggest are important to consider? Critically review the advantages and disadvantages of each technique. You need to cross compare all the techniques.

The most important criteria for the lab is cost, find the costs of these processes. Which one is the best value for money whilst delivering the best results? You do not need to factor in the cost of the machines as you already have them.

Address the hospital criterion, think to the lectures about this (quality assurance), and use what you learn in the lectures to answer this.

Are there limitations to some of these techniques?

Finally, give your recommendations to your lab and to the hospital on the technique you think should be used.