Exercise 5: A Diagnostic Copy Number Screen

TODO Convert this to h5p

In diagnostic screens all samples are important: you cannot leave out samples and all measurements need to be of the highest quality possible. In my qPCR experiment I want to study copy number variation of 16 genes
(genes of interest and reference genes) and 2 calibrator samples (samples with known copy number). Since we need high quality data we will use 4 technical replicates.

Are we going to use sample maximization ?
No. In contrast to gene expression studies, where we want to compare expression levels of a gene between different groups of samples, copy number analyses do compare genes. It means that in this case the sample maximization approach (placing all samples of the same gene on the same plate) is not valid. Instead we use a gene maximization approach here (placing same sample for different genes on the same plate).

| How many samples can I fit on a 384 well plate ? |
| :—————————— |
| We have 16 (genes) * 4 (replicates) = 64 reactions per sample.
This means that we can fit 6 samples on a 384 well plate: 4 unknowns and 2 calibrators.