Identification of transgene insertion sites via short- and long-read whole genome sequencing.

Lew Kaplan, Sierra J Edgerton, Brennan D Mahoney, Catherine A Ray, Thomas A Reh

Abstract read

In one paragraph

Article in Methods (San Diego, Calif.), 2026. 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

Update of
Identification of transgene insertion sites via short- and long-read whole genome sequencing.2026

5 · Who and what money

Authors and funding

5 authors.

Lew KaplanDepartment of Neurobiology and Biophysics, University of Washington, 1959 NE Pacific Street, Seattle 98195-7420, WA, USA,. Electronic address: lewkap@uw.edu.

Sierra J EdgertonDepartment of Neurobiology and Biophysics, University of Washington, 1959 NE Pacific Street, Seattle 98195-7420, WA, USA,. Electronic address: sierraedgerton@gmail.com.

Brennan D MahoneyDepartment of Neurobiology and Biophysics, University of Washington, 1959 NE Pacific Street, Seattle 98195-7420, WA, USA,. Electronic address: bdm37@uw.edu.

Catherine A RayDepartment of Neurobiology and Biophysics, University of Washington, 1959 NE Pacific Street, Seattle 98195-7420, WA, USA,. Electronic address: catray@uw.edu.

Thomas A RehDepartment of Neurobiology and Biophysics, University of Washington, 1959 NE Pacific Street, Seattle 98195-7420, WA, USA,. Electronic address: tomreh@uw.edu.

Funding

Supplement to EY021482 to carry out a screen for retinal regeneration using CRISPR-Cas9 gene activation.R01EY021482 · NEI · UNIVERSITY OF WASHINGTON · PI THOMAS A REH · 2011 to 2026

$6.3M

NEI NIH HHS R01 EY021482

6 · The paper itself

Abstract

Transgenic mouse lines are essential to uncover organ or system level genotype-phenotype relationships. The generation of such lines via transgene addition may lead to the insertion into unknown genomic loci potentially leading not only to the disruption of native genes but also attenuation of transgene expression. Additionally, this often results in the inability to determine transgene zygosity which in turn complicates breeding and interpretation of experimental results. In this study we present two whole genome sequencing based pipelines that allow the identification and genotyping of even complex multi transgenic inserts. As they use widely available reagents and bioinformatic tools, they can easily be applied to develop genotyping strategies in potentially any laboratory animal species.

Indexed as

Mutagenesis, InsertionalTransgenesWhole Genome SequencingAnimalsMiceMice, TransgenicInsertion site analysisLong-readSequencingWhole genome

Identifiers

PMID42551815

DOI10.1016/j.ymeth.2026.08.003

What OpenQuestion holds

Textmetadata

Read underepoch 390

Registered trials

None linked

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.