BRCA1/BRCA2 - Achilles common essential

Q&A
1

Hi,

Thanks so much for all your work supporting this fantastic project.

Apologies if this question has previously been addressed, but I am uncertain why BRCA1 and BRCA2 are annotated as common essential genes in the downloadable “Achilles_common_essential.csv” but not when browsing the website GUI?

Thanks,

Otto.

2

Hello,

I believe the inconsistency is due to the which dataset is being shown in the portal for that gene, and the file you referenced is for a related, but slightly different dataset.

There are actually multiple CRISPR datasets: one generated at the Broad, “Achilles”, one generated at Sanger, “Score”, and a last dataset which is a harmonized version incorporating data from both Sanger and Broad.

On the gene page, we default to using the largest dataset which has data for the given gene, which for most genes, is the combined dataset.

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(The “CRISPR (DepMap 22Q1 Public+Score, Chronos)” is referring to the merged dataset and indicating what is being shown here is using that data)

So, while BRCA1 and BRCA2 are present in “Achilles_common_essentials.csv” (which is derived from only the Broad data), they are missing from “CRISPR_common_essentials.csv” (which is derived from the Broad and Sanger data). That suggests that based on the merged dataset these genes did not meet the cutoff and is consistent with what’s being shown on the portal.

Thanks,
Phil

1 Like
3

Thanks Phil! That’s a great help