Evidence map›Paper›PMID 39270651›Full record

ArticleStem cell reports2024

SeqVerify: An accessible analysis tool for cell line genomic integrity, contamination, and gene editing outcomes.

Merrick Pierson Smela, Valerio Pepe, Steven Lubbe, Evangelos Kiskinis, George M Church

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Stem cell reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Review
  2. Article
  3. Research progress of stem cells in the treatment of atherosclerosis.Frontiers in cell and developmental biology · 2025
    Review
  4. Induction of Meiosis from Human Pluripotent Stem Cells.bioRxiv : the preprint server for biology · 2024
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Merrick Pierson SmelaWyss Institute at Harvard University, Boston MA, USA. Electronic address: mpiersonsmela@g.harvard.edu.
Valerio PepeWyss Institute at Harvard University, Boston MA, USA.
Steven LubbeThe Ken & Ruth Davee Department of Neurology and Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
Evangelos KiskinisThe Ken & Ruth Davee Department of Neurology and Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
George M ChurchWyss Institute at Harvard University, Boston MA, USA; Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA, USA. Electronic address: george_church@hms.harvard.edu.

Funding

Human iPSC-derived ovarian follicles as a model of female reproductionF31HD108898 · NICHD · HARVARD UNIVERSITY · PI PIERSON SMELA, MERRICK DE FOREST · 2022 to 2024
$98k
NICHD NIH HHS F31 HD108898
6 · The paper itself

Abstract

Over the last decade, advances in genome editing and pluripotent stem cell (PSC) culture have let researchers generate edited PSC lines to study a wide variety of biological questions. However, abnormalities in cell lines such as aneuploidy, mutations, on-target and off-target editing errors, and microbial contamination can arise during PSC culture or due to undesired editing outcomes. The ongoing decline of next-generation sequencing prices has made whole-genome sequencing (WGS) a promising option for detecting these abnormalities. However, this approach has been held back by a lack of easily usable data analysis software. Here, we present SeqVerify, a computational pipeline designed to take raw WGS data and a list of intended genome edits, and verify that the edits are present and that there are no abnormalities. We anticipate that SeqVerify will be a useful tool for researchers generating edited PSCs, and more broadly, for cell line quality control in general.

Indexed as

Gene EditingSoftwareAnimalsCell LineComputational BiologyCRISPR-Cas SystemsGenomicsHigh-Throughput Nucleotide SequencingHumansPluripotent Stem CellsWhole Genome Sequencinganeuploidygenome editingmicrobial contaminationpluripotent stem cellquality controlSeqVerifysingle-nucleotide polymorphismssoftwarestem cellwhole-genome sequencing

Identifiers

PMID39270651
PMCPMC11561455

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.