Saturation Genome Editing (SGE) is a CRISPR/Cas9-based method to functionally test the effects of large numbers of variants in their native genomic context ( Findlay et al. Nature 2014 ). For SGE of BRCA1 , we developed an assay in a haploid human cell line (HAP1) in which BRCA1 is essential ( Blomen et al. Science 2015 ). In each SGE experiment, nearly all possible single nucleotide variants (SNVs) over a ~100 bp region of BRCA1 are introduced via multiplex homology-directed repair, such that each cell acquires a single variant in the targeted exon. Because BRCA1 is essential in this cell line, incorporation of SNVs that cause loss of BRCA1 function are depleted from the population of cells over time, an effect quantified with massively parallel DNA sequencing.

Function scores are reported here for 3,893 SNVs located within or near the thirteen exons that encode for the RING and BRCT domains of BRCA1 (exons 2-5 and 15-23, respectively). Function scores quantify the depletion of SNVs, and are log2-scaled such that the median synonymous SNV scores as 0. More negative function scores are indicative of loss-of-function variants; the median nonsense SNV scored -2.12. Each SNV was placed into one of three broad functional classes based on its function score: 'functional'/'FUNC' (score > -0.748, 72.5%), 'intermediate'/'INT' ( -0.748 > score > -1.328, 6.4%), and 'non-functional'/'LOF' (score < -1.328, 21.1%).

Targeted RNA sequencing was performed to assess how each exonic SNV impacts BRCA1 mRNA levels. RNA scores are log2-based ratios reporting how depleted each SNV is in mRNA (relative to the median synonymous SNV in each experiment).

For more details and/or to cite these scores, please refer to the following manuscript:

Findlay, G.M., Daza, R.M., Martin, B., Zhang, M.D., Leith, A.P., Gasperini, M., Janizek, J.D., Huang, X., Starita, L.M., Shendure, J. Accurate classification of BRCA1 variants with saturation genome editing. Nature (2018). https://doi.org/10.1038/s41586-018-0461-z.


SGE function scores and data are the copyright of the University of Washington.


SGE function scores and data are the copyright of the University of Washington.

Citation:

Findlay, G.M., Daza, R.M., Martin, B., Zhang, M.D., Leith, A.P., Gasperini, M., Janizek, J.D., Huang, X., Starita, L.M., Shendure, J. Accurate classification of BRCA1 variants with saturation genome editing. Nature (2018). https://doi.org/10.1038/s41586-018-0461-z.


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