is CRIPSRGeneEffect X and Y chromosome aware

Q&A
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1

Hello,

I am pretty new to using this database, but I was recently trying to analyze CRISPRGeneeffect of certain paralog proteins that are present either on X or Y chromosomes. XX individuals would have two copies of X version (if it skips inactivation) but one copy each of X and Y proteins. When knocking out a gene that’s present on both X and Y chromosomes, does the screens have different guides to X and Y genes or if it’s the same. Trying to understand if there are any differences in cancer vulnerabilities dependent on X, Y paralogs and their potential differences between male and female cell lines

2

Hi bommisetti11,

We don’t distinguish X/Y paralogs. The bulk of screens were conducted in Avana, which only has reported alignments to X but I suspect that’s because it wasn’t aligned to Y. Humagne has guides that align to both. Cancer cell lines have high rates of aneuploidy in sex chromosomes, making the analysis even more complicated since you also have to account for different cutting toxicity based on the number of cut sites. If you want to study this question, I would strongly recommend starting from the individual sgRNA LFCs.