16 Collected data
What do we do with the data we’ve collected?
You will be able to interpret your experimental data obtained for each of the biobank DNA samples 1-90 by using the Ct values for control DNAs 1-5.
- Look at the Ct values for control DNAs 1-5 and work out a range of Ct values that represent the copy number for each of the genetic tests. You can base your interpretation upon your own control Ct values and on data pooled from your fellow students.
- In your spreadsheet enter the number of copies for each sample in a new column (see below for more detail).
A column for each population has been provided, coloured orange.
For this you may find it useful to first fill in the number of copies for the controls (Column J) and the range of Ct values for each positive control (Column K), and, in the case of copy number, the range of Ct values for each copy number (Column N on ‘copy number data’ sheet).
- For CYP2D6 *4: for each sample look at the Ct value and decide whether it contains zero, 1 or 2 copies of the CYP2D6 *4 variant.
- For CYP2D6 copy number: for each sample look at the Ct values and decide whether it contains 2, 3 or 4 copies of the gene.
Are there samples for which you have any anomalous results or results that you cannot interpret based upon the control dataset you have? If so, what might you suggest about the genetic make-up of these samples?
Answer
For the copy number data you may have spotted that one sample shows ‘not detected’. This could be an error, but you will have found the same result when you repeat the experiment. This suggests that the sample has no copies of the CYP2D6 gene on either chromosome 22.
You may have noticed that some samples have higher Ct values than for the control with 2 copies of the gene. This suggests that amplification started from fewer copies of the target DNA sequence and therefore suggests that there is only 1 copy of the gene (and so one chromosome 22 has no copies).
- Use your data to draw a suitable graph/chart that shows the distribution of the CYP2D6 *4 and/or CYP2D6 copy number within the populations you studied and compares with the other populations.
Alternatively, the ‘results’ sheets in the template spreadsheet automatically count the frequencies from your orange data columns and draw bar charts using these frequencies.
Remember to check that your graphs really do correspond to the data – it is easy to make mistakes!
15 Experiment continued