CRISPR-screening-vocabulary

This collection is inspired by awesome-single-cell / awesome-CRISPR / single-cell-vocabulary.

Terms

List of terms related to CRISPR screening, etc.

• Forward genetics

  • Screening approach in which genes involved in the phenotype of interest are identified by screening genetically perturbed cells.

• Pooled CRISPR screen

  • A technique in which genetically encoded perturbations are introduced in bulk and read out with sequencing or imaging technology.

• Arrayed CRISPR screens

  • A technique in which perturbations are introduced in individual reaction compartments and remain physically separated.

• High-content CRISPR screens

  • Screens combining complex models, perturbations and stimuli with data-rich read-outs.

• Biological replicates

  • Separately conducted repetitions of the same CRISPR screen using cells from different individuals or different passages of a cell line

• Coverage

  • The average number of cells per guide RNA (gRNA) in a CRISPR screen.

• Multiplicity of infection (MOI)

  • The average number of virions (and, by extension, guide RNAs (gRNAs)) delivered per cell during infection.

• Genetic interactions

  • The combined effect of the simultaneous perturbation of several genes, which may deviate from the sum of the individual effects.

• Positive selection screens

  • Also known as enrichment screens. Cells with the phenotype of interest are selected (enriched) in the screens; other cells are depleted.

• Negative selection screens

  • Also known as dropout screens. Cells with the phenotype of interest are depleted in the screen; other cells are maintained.

• Effective dose

  • The intensity of a perturbation (such as a drug or virus) that causes an effect (such as cell death) in a specified percentage of cells.

• Screening hits

  • Target genes identified as being associated with the phenotype of interest in a CRISPR screen.

• scCRISPR-seq

  • An umbrella term for a group of methods that combine pooled CRISPR sequencing with a single-cell sequencing read-out.

• Manifold learning

  • A set of machine learning methods that seek to uncover hidden structures in the data through dimensionality reduction.

• Variants of uncertain significance

  • Genetic variants for which there is insufficient genetic evidence to support or exclude a causal phenotypic effect.

• Saturation genome editing

  • Introduction of many genome edits into a gene or regulatory element, with the goal of comprehensively assessing their phenotypic impact.

• Synthetic lethality

  • Special case of a genetic interaction in which knockouts of two genes are individually tolerated, but their combination is lethal to cells.

• False positives

  • Putative CRISPR screening hits that do not validate, which can be caused by technical biases.

• False negatives

  • Potential CRISPR screening hits that would have validated but were missed, which can be caused by suboptimal screening conditions.

• Population bottlenecks

  • Reductions in the genetic diversity among a pool of cells owing to external events.

• Genetic drift

  • Genetic changes over time in a pool of cells, caused by random and uncontrolled events.

• Unique molecular identifiers

  • Short barcodes that uniquely identify individual DNA or RNA molecules.

References

• High-content CRISPR screening. Nat Rev Methods Primers (2022)