Missing CRISPRGeneEffect values in 23Q2 release

Issues and Bugs
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1

Hi,

There seem to be some missing values in the CRISPRGeneEffect.csv-file in the 23Q2 release, a total of 184,785 by my counting. In contrast, that same file in the 22Q4 release had no missing values. The missing values are both on genes that were already included in the 22Q4 release and on genes that are added in this release. One missing value, for example, is for the gene ACSM2B in the cell line NIH:OVCAR-3 (ACH-000001).

Could you please advise what is happening? Am I looking at the wrong file?

Thanks in advance,
Bastiaan

2

Hi Bastiaan,

Most of these are cases where a gene has inadequate sgRNA representation (minimum of 2) in one or more libraries. Models screened in only those libraries will have NAs for the gene. Previously, such genes were simply dropped. Some existing genes also had block NAs introduced because 22Q4 had a bug that only required 1 sgRNA to be present for a gene, which was corrected in 23Q4. There may be a couple additional edge cases where germline SNPs affected all the sgRNAs for a gene in a given model.