Skip to main content
Fig. 3 | Genome Biology

Fig. 3

From: Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects

Fig. 3

Gene copy-number ratio association with CRISPR-Cas9 loss of fitness effect. a Diagram of the different genomic rearrangements captured by the gene copy-number ratio and their potential effect in CRISPR-Cas9 response. b FISH of MYC amplifications (green signal) in HCC1954 tetraploid cell line. In the left panel, representative metaphase (80% of cells) with high MYC amplifications and low copy-number ratio. In the right panel, detailed view of the chromosomes containing MYC signal (upper) and the corresponding derivative chromosomes identified by M-FISH (lower). c Similar to b, FISH of MYC amplifications (green signal) in NCI-H2087 diploid cell line. In the left panel, representative metaphase (90% of cells) with high MYC copy-number ratio. For both cell lines, 10 cells were analyzed in the FISH experiments. d High copy-number ratios are enriched for strong CRISPR-Cas9 LOF effects. Recall curves of non-expressed genes grouped by their copy-number ratio profile across CRISPR-Cas9 fold changes. e Matrix of gene and chromosome copies representing the mean gene-level CRISPR-Cas9 fold change of non-expressed genes in the respective group. f Representative example of an amplified non-expressed gene with strong LOF effects associated with gene copy-number ratio (right panel) and to a lesser extent with absolute gene copy-number (left panel). CRISPR-Cas9 fold changes in e and f are scaled (known essential genes mean fold change = − 1)

Back to article page