Hi,
Our team is currently trying to study the mechanisms behind the formation of certain specific genomic variations.
We have observed that abnormalities in certain genes and drug treatments may lead to changes in the frequency of these genomic variations. As a result, we have established knockout /drug-induced cell models for validation.
We aim to detect and compare expected genomic variations in WT/KO/drug-treated cell lines. Typically, for statistical analysis, this means that we need to have biological replicates for WT/KO/drug conditions. However, we have noticed that setting biological replicates in WGS experiments is not a common practice, as seen in projects such as 1kg, TCGA, and CCLE, where replicates are rarely used for WGS. This has left us confused.
I would appreciate any advice or criticism from the community.
Do you expect the replicate populations to have different changes? Then doing sequencing of multiple replicates makes sense.
Generally people are interested in identifying germline mutations with WGS so it is not essential to do replicate samples. Clonal population cancer sequencing on the other hand looks for variation in clones. Somatic variants identified can then be used to create clonal trees.
In fact, we anticipate that a certain treatment (for example) will result in cells (in a specific model) being more prone to accumulating a certain type of variation. Therefore, we actually hope to observe no such variation in the wild-type (WT) group, while the frequency of variation in the treatment group changes. These mutations are not derived from germ cells, but are induced during the cultivation process through an inducer.
If you expect the mutations to be located in different genes/locations then using replicates may not produce identical results. If these mutations are rare then you may not observe them for a while (until enough cells with that accumulate).
Are you going to sample at a single time point? You could do multiple treatment replicates but the mutation a) may not be immediately visible/apparent b) may not be the same in the replicates (unless there is a specific enzyme/pathway that is the target of the treatment).