domains / families / science / base-editing-analysis

base-editing-analysis

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Analyzes base-editing screens for variant function. Covers library design (Hanna 2021 ClinVar-scale CBE screen benchmarked on BRCA1/2, Cuella-Martin 2021 DDR saturation), CBE vs ABE chemistry choice (BE3/BE4 vs ABE7.10/ABE8.20/ABE8e), editing-window math (positions 4-8 from PAM-distal end; 4-7 for ABE7.10), bystander-edit quantification and the variant-call ambiguity it creates, sgRNA-efficiency filtering before hit calling, indel byproduct interpretation, the substitution-vs-indel diagnostic, variant annotation against ClinVar / COSMIC, and the Broad be-validation-pipeline. Use when designing a BE variant screen, choosing CBE vs ABE for a specific edit, interpreting bystander-confounded hits, distinguishing functional signal from indel artifact, integrating CRISPResso2 output with screen scoring, or deciding BE vs PE for SNV installation.

When to use

• designing a BE variant screen
• choosing CBE vs ABE for a specific edit
• interpreting bystander-confounded hits
• distinguishing functional signal from indel artifact
• integrating CRISPResso2 output with screen scoring
• deciding BE vs PE for SNV installation
• quantifying per-sgRNA target-base conversion
• annotating variants against ClinVar / COSMIC

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