Additional file 1 of Minimal genome-wide human CRISPR-Cas9 library
Creators: name: Gonçalves, Emanuel
name: Thomas, Mark
name: Behan, Fiona M.
name: Picco, Gabriele
name: Pacini, Clare
name: Allen, Felicity
name: Vinceti, Alessandro
name: Sharma, Mamta
name: Jackson, David A.
name: Price, Stacey
name: Beaver, Charlotte M.
name: Dovey, Oliver
name: Parry-Smith, David
name: Iorio, Francesco
name: Parts, Leopold
name: Yusa, Kosuke
name: Garnett, Mathew J.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Cancer

description: Additional file 1: Figure S1. Randomised selection of n sgRNAs per gene. ROC curve derived from previously defined sets of essential and non-essential genes [6]. Standardized partial area under the ROC curve (AROC) calculated per cell line over the range of maximum false discovery rate of 20%. AROCs are compared between down-sampled sgRNAs and all sgRNAs available for all the covered genes. 10 random sgRNAs permutations without replacement per cell line and per n guides were performed and AROCs mean values are plotted. AROC were calculated for each replicate of Project Score [13] (n = 663). Figure S2. MinLibCas9 sgRNA rank and selection flowchart and sgRNA metrics comparison. a, flowchart describing the sgRNA selection procedure. b, efficiency metrics of Project Score library sgRNAs - KS metric (Kolmogorov Smirnov test) comparison to non-targeting guides, JACKS scores [14], Rule Set 2 [9] scores, and FORECasT [21] predicted percentage of in frame deletions produced - plotted together with guides median fold-changes calculated across 663 samples. Spearman correlation coefficients are reported in the lower triangle of the grid. Plots in the diagonal represent the distribution of the respective metric. Figure S3. Down-sample analysis of top n sgRNAs ranked using KS and JACKS metrics. Combined score discards sgRNAs with a JACKS score outside the range of [0, 2] and then selects the top n sgRNAs according to the KS score (descending order, stronger KS scores and thereby stronger absolute fold-changes). Essential/Non-essential AROCs are the area under the ROC curve (at 20ýR) using known essential and non-essential genes. Precision and recall rates are calculated between the sets of significant gene-level dependencies (at 1% FDR) estimated using the original library and the down-sampled library. Each box-and-whisker plot shows 1.5 x interquartile ranges and 5–95th percentiles, centres indicate medians (n = 245 cancer cell lines from Project Score [13]). Figure S4. MinLibCas9 benchmarking. a, distributions of CRISPOR sgRNA scores. b,distributions of KS, JACKS and RuleSet2 scores for sgRNAs from Project Score library that contain T-stretches of 4 and 5. c, significant dependencies identified using different FDR rates between essential and nonessential genes (1%, 5%, 10%, 15%, 20% and 25%). MinLibCas9 fold-change thresholds at each FDR rate and the average precision (AP) of the gene dependencies identified in MinLibCas9 that are also found with Project Score library. Error bars represent standard deviation. d, average precision scores per cell line of established dependencies with MinLibCas9 fold-changes, calculated through downsampling the original screens, correlated with Project Score data quality as measured by the area under the ROC curve (AROC) using known essential and non essential genes. e,MinLibCas9 fold-change threshold for each cell line identified at 1% FDR of essential versus non-essential genes plotted against those identified with Project Score library . Colour represents density. f, cumulative number of dependencies (at 1% FDR) identified in 245 cancer cell lines for each gene with both the full original library and the minimal library. g,scaled fold-changes (median essential genes fold-change = 1; median non-essential genes fold-change = 0) of dependencies recapitulated (n = 251,387) and missed (n = 36,996) with the minimal library (two-sided Welch’s t-test p-value