PETRO enables robust estimation of on-target perturbation effects in Perturb-seq
- 1University of Wisconsin-Madison
Abstract
Perturb-seq uses multiple guides per target as replicates, but off-target effects can bias target-level estimates even with efficient target perturbation. We present PETRO, which recovers the on-target perturbation effect while allowing, for each outcome, an unknown minority of guides to have arbitrary off-target effects. Across CRISPRa and CRISPRi datasets, sequence-associated off-target bias persisted after pooling cells across guides and nearly doubled in one CRISPRa dataset after a published guide filter. PETRO largely removed this bias and reduced transmission of effects from independently flagged promiscuous guides. In simulations, PETRO nearly matched pooling in power without off-target effects; with off-target effects, pooling remained biased as cell numbers increased, whereas PETRO recovered the on-target perturbation effect. In cortical Perturb-seq, most ZNF219 pathway enrichments from pooling rested on one guide and did not survive majority-supported aggregation, unlike those for targets with concordant guides. PETRO enables robust target-level Perturb-seq analysis from replicate-guide agreement.
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BibTeX
@misc{sun2026petro,
title = {{PETRO enables robust estimation of on-target perturbation effects in Perturb-seq}},
author = {Z. Sun and H. Kang and S. Keles},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.15.759256},
url = {https://www.biorxiv.org/content/10.64898/2026.10.15.759256v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - PETRO enables robust estimation of on-target perturbation effects in Perturb-seq
AU - Z. Sun
AU - H. Kang
AU - S. Keles
PY - 2026
DA - 2026/10/15
PB - bioRxiv
DO - 10.64898/2026.10.15.759256
UR - https://www.biorxiv.org/content/10.64898/2026.10.15.759256v1
AB - Perturb-seq uses multiple guides per target as replicates, but off-target effects can bias target-level estimates even with efficient target perturbation. We present PETRO, which recovers the on-target perturbation effect while allowing, for each outcome, an unknown minority of guides to have arbitrary off-target effects. Across CRISPRa and CRISPRi datasets, sequence-associated off-target bias persisted after pooling cells across guides and nearly doubled in one CRISPRa dataset after a published guide filter. PETRO largely removed this bias and reduced transmission of effects from independently flagged promiscuous guides. In simulations, PETRO nearly matched pooling in power without off-target effects; with off-target effects, pooling remained biased as cell numbers increased, whereas PETRO recovered the on-target perturbation effect. In cortical Perturb-seq, most ZNF219 pathway enrichments from pooling rested on one guide and did not survive majority-supported aggregation, unlike those for targets with concordant guides. PETRO enables robust target-level Perturb-seq analysis from replicate-guide agreement.
ER -