Evidence map›Paper›PMID 40672186›Full record

ArticlebioRxiv : the preprint server for biology2025

Synthesis errors in oligonucleotides are propagated into the genome by homology-directed repair.

Stacia K Wyman, Zulema Romero, Seok-Jin Heo, Marian Navarrete, Netravathi Krishnappa, Donald B Kohn, David Ik Martin, Mark C Walters, Dario Boffelli

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Stacia K WymanInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Zulema RomeroDepartments of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
Seok-Jin HeoLaboratory for Genomics Research, University of California, San Francisco, CA 94158.
Marian NavarreteDepartments of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
Netravathi KrishnappaInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
Donald B KohnInnovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
David Ik MartinUCSF Benioff Children's Hospital Oakland, Oakland, CA 94609, USA.
Mark C WaltersUCSF Benioff Children's Hospital Oakland, Oakland, CA 94609, USA.
Dario BoffelliCedars-Sinai Medical Center, Department of Pediatrics, Los Angeles CA 90069, USA.ORCID 0000-0003-2529-9056

Funding

Cure Sickle CellOT3HL147741 · NHLBI · MEDICAL COLLEGE OF WISCONSIN · PI MARY EAPEN, Mary Maresca Horowitz · 2018 to 2026
$37.7M
Curing Sickle Cell Disease with CRISPR-Cas9 genome editingOT2HL151319 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WALTERS, MARK C · 2019 to 2021
$2.2M
NHLBI NIH HHS OT2 HL151319NHLBI NIH HHS OT3 HL147741
6 · The paper itself

Abstract

Single-stranded oligonucleotides (ssODNs) are used as donor templates for gene editing by targeted endonuclease cleavage and homology directed repair (HDR). We probed their sequence fidelity by deep sequencing ssODNs from three manufacturers, and genomes derived from editing using these ssODNs as templates for HDR. The ssODNs carry single-nucleotide and small deletion synthesis errors in proportions differing widely among manufacturers; these are propagated into the genome by HDR; therapeutic gene correction strategies will need to this additional source of editing errors.

Identifiers

PMID40672186
PMCPMC12265553

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

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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 OpenQuestion graph.