Germline variation contributes to false negatives in CRISPR-based experiments with varying burden across ancestries.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
07 Jun 2024
07 Jun 2024
Historique:
received:
05
12
2023
accepted:
20
05
2024
medline:
8
6
2024
pubmed:
8
6
2024
entrez:
7
6
2024
Statut:
epublish
Résumé
Reducing disparities is vital for equitable access to precision treatments in cancer. Socioenvironmental factors are a major driver of disparities, but differences in genetic variation likely also contribute. The impact of genetic ancestry on prioritization of cancer targets in drug discovery pipelines has not been systematically explored due to the absence of pre-clinical data at the appropriate scale. Here, we analyze data from 611 genome-scale CRISPR/Cas9 viability experiments in human cell line models to identify ancestry-associated genetic dependencies essential for cell survival. Surprisingly, we find that most putative associations between ancestry and dependency arise from artifacts related to germline variants. Our analysis suggests that for 1.2-2.5% of guides, germline variants in sgRNA targeting sequences reduce cutting by the CRISPR/Cas9 nuclease, disproportionately affecting cell models derived from individuals of recent African descent. We propose three approaches to mitigate this experimental bias, enabling the scientific community to address these disparities.
Identifiants
pubmed: 38849329
doi: 10.1038/s41467-024-48957-z
pii: 10.1038/s41467-024-48957-z
doi:
Substances chimiques
RNA, Guide, CRISPR-Cas Systems
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
4892Subventions
Organisme : U.S. Department of Defense (United States Department of Defense)
ID : WX81XWH-21-1-0934
Organisme : U.S. Department of Defense (United States Department of Defense)
ID : W81XWH-21-1-0901
Informations de copyright
© 2024. The Author(s).
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