13 Using control samples

In order to interpret the genotypes of each individual in the three populations, you will need to compare the experimental C_t values you obtain with those in control DNAs. Your control DNA samples are from individuals with known genetic sequences. These are individuals with different known combinations of variants and gene copy number on each of their two copies of chromosome 22.

Table 1, below, shows you the information you need for five control DNAs. It tells you how many gene copies each chromosome 22 has and whether they are the ‘normal’ CYP2D6*1 allele or the mutant CYP2D6 *4 allele which encodes a defective CYP2D6 protein.

These DNAs are positive controls for gene copy number as we know what their CYP2D6 gene copy number is expected to be. For the CYP2D6 *4 variant, however, only control DNAs 1 and 2 also serve as true positive controls as they contain that particular allele in a known copy number.

You will also use a negative control, a sample that contains only ultraclean water and no DNA. This controls for the presence of any contaminants in the reaction mix itself.

Table 1  The genotypes of the five control DNAs used in the PCR experiments. For each sample, the genetic make-up in terms of CYP2D6 gene copy number and which variant is present on each chromosome 22 is indicated.