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Pooled CRISPR-Based Genetic Screens in Mammalian Cells
Published on: September 4, 2019
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Computational identification of clonal cells in single-cell CRISPR screens
Yihan Wang1, Shiqi Xie1, Daniel Armendariz1
1Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
BMC Genomics
|February 16, 2022
Summary
Clonal cell expansion in single-cell CRISPR screens can create false positives. Identifying and filtering these clonal cells improves the accuracy of genome function studies.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Single-cell CRISPR screens are vital for understanding genome function.
- Biased cell sampling, particularly from clonal expansion, can skew results.
- Accurate interpretation requires addressing clonal effects.
Purpose of the Study:
- To identify clonal cells within single-cell CRISPR screens.
- To assess the impact of clonal expansion on transcriptional data.
- To develop strategies for improving the reliability of these screens.
Main Methods:
- Utilized multiplexed sgRNAs as barcodes to tag and identify clonal cells.
- Analyzed transcriptional similarities and copy number variations within identified clones.
- Evaluated the contribution of clonal expansion to false positive results.
Main Results:
- Successfully identified clonal cells using multiplexed sgRNA barcodes.
- Demonstrated that cells within clones exhibit transcriptional similarity and genetic alterations.
- Confirmed that clonal expansion introduces false positives in single-cell CRISPR screens.
Conclusions:
- Clonal expansion is a significant confounder in single-cell CRISPR screens.
- Reducing clonal expansion or computationally filtering clonal cells enhances data reliability.
- Improved methods are crucial for accurate genome function analysis.
