ArticleNature genetics2024
High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing.
Article in Nature genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed.
- Black-box data: a new paradigm for biomedicine in the AI era.Chemical science · 2026Review
- CRISPR screening redefines therapeutic target identification and drug discovery with precision and scalability.Journal of pharmaceutical analysis · 2026Review
- A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture.bioRxiv : the preprint server for biology · 2026Article
- Improved in vivo gene knockout with high specificity using multiplexed Cas12a sgRNAs.Nature communications · 2026Article
- Large scale compound selection guided by cell painting reveals activity cliffs and functional relationships.Communications biology · 2026Article
- Quantitative analysis of genetic interactions in human cells from genome-wide CRISPR-Cas9 screens.bioRxiv : the preprint server for biology · 2026Article
- Feature representation for explainable CRISPR off-target prediction and base editing efficiency.Frontiers in bioinformatics · 2026Article
- Evaluating transportability of in vitro cellular models to in vivo human phenotypes using gene perturbation data.Nature communications · 2025Article
- Generalizable morphological profiling of cells by interpretable unsupervised learning.Nature communications · 2025Article
- Functional genomics for improving adoptive T-cell transfer therapies.Journal for immunotherapy of cancer · 2025Review
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy.PLoS computational biology · 2025Article
- The Potential of NGTs to Overcome Constraints in Plant Breeding and Their Regulatory Implications.International journal of molecular sciences · 2025Review
- Megabase-scale loss of heterozygosity provoked by CRISPR-Cas9 DNA double-strand breaks.Molecular cell · 2025Article
- Precision T cell correction platform for inborn errors of immunity.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Engineering B cells to treat and study human disease.Nature biotechnology · 2025Review
- Morphological map of under- and overexpression of genes in human cells.Nature methods · 2025Article
- BaCoN (Balanced Correlation Network) improves prediction of gene buffering.Molecular systems biology · 2025Article
- Live-cell painting: Image-based profiling in live cells using acridine orange.Molecular biology of the cell · 2025Article
- Causal machine learning for single-cell genomics.Nature genetics · 2025Review
- Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a powerful tool for introducing targeted mutations in DNA, but recent studies have shown that it can have unintended effects such as structural changes. However, these studies have not yet looked genome wide or across data types. Here we performed a phenotypic CRISPR-Cas9 scan targeting 17,065 genes in primary human cells, revealing a 'proximity bias' in which CRISPR knockouts show unexpected similarities to unrelated genes on the same chromosome arm. This bias was found to be consistent across cell types, laboratories, Cas9 delivery methods and assay modalities, and the data suggest that it is caused by telomeric truncations of chromosome arms, with cell cycle and apoptotic pathways playing a mediating role. Additionally, a simple correction is demonstrated to mitigate this pervasive bias while preserving biological relationships. This previously uncharacterized effect has implications for functional genomic studies using CRISPR-Cas9, with applications in discovery biology, drug-target identification, cell therapies and genetic therapeutics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.