Evidence map›Paper›PMID 38827422›Full record

ArticleGenetics in medicine open2023

Clinical variants in

Christopher E Hopkins, Kathryn McCormick, Trisha Brock, Matthew Wood, Sarah Ruggiero, Kolt Mcbride, Christine Kim, Jennifer A Lawson, Ingo Helbig, Matthew N Bainbridge

Abstract read
In one paragraph

Article in Genetics in medicine open, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Review
  6. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Christopher E HopkinsInVivo Biosystems, Eugene, OR.
Kathryn McCormickInVivo Biosystems, Eugene, OR.
Trisha BrockInVivo Biosystems, Eugene, OR.
Matthew WoodCodified Genomics, LLC, Houston, TX.
Sarah RuggieroDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA.
Kolt McbrideInVivo Biosystems, Eugene, OR.
Christine KimInVivo Biosystems, Eugene, OR.
Jennifer A LawsonInVivo Biosystems, Eugene, OR.
Ingo HelbigDivision of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA.
Matthew N BainbridgeCodified Genomics, LLC, Houston, TX.ORCID 0000-0003-3016-1545

Funding

Function-based Variant Assessment of Epilepsome Genes to Increase Diagnostic YieldR43NS113691 · NINDS · NEMAMETRIX, INC. · PI HOPKINS, CHRISTOPHER E · 2019 to 2019
$664k
Functional Assessment of Variants in Organisms of Research (FAVOR) - Profiling Canonical Human Genes and their Variants through Disease Model Phenotyping.R43HG010852 · NHGRI · NEMAMETRIX, INC. · PI BROCK, TRISHA, HOPKINS, CHRISTOPHER E · 2020 to 2021
$475k
Testing Lifespan/Healthspan Pharmacological Interventions in Humanized C. elegans Knock-In Models of DementiaR43AG061978 · NIA · NEMAMETRIX, INC. · PI BROCK, TRISHA, HART, ANNE CHURCH · 2018 to 2018
$350k
Humanized LMNA Animal Model for Detecting Pathogenicity in Clinical VariantsR43GM133229 · NIGMS · NEMAMETRIX, INC. · PI HOPKINS, CHRISTOPHER E · 2019 to 2019
$225k
Resubmission: Systems for Exploring Pathogenicity in Clinical Variants of a Presynaptic Protein Involved in EpilepsyR43NS108847 · NINDS · NEMAMETRIX, INC. · PI HOPKINS, CHRISTOPHER E · 2019 to 2019
$225k
NHGRI NIH HHS R43 HG010852NIA NIH HHS R43 AG061978NIGMS NIH HHS R43 GM133229NINDS NIH HHS R43 NS108847NINDS NIH HHS R43 NS113691
6 · The paper itself

Abstract

Purpose: Modeling disease variants in animals is useful for drug discovery, understanding disease pathology, and classifying variants of uncertain significance (VUS) as pathogenic or benign. Methods: Using Clustered Regularly Interspaced Short Palindromic Repeats, we performed a Whole-gene Humanized Animal Model procedure to replace the coding sequence of the animal model's Results: Using multiple models, we were able to obtain a diagnostic sensitivity near 0.9. Twenty-three VUS were also interrogated and 8 of 23 (34.8%) were observed to be functionally abnormal. Interestingly, unsupervised clustering identified 2 distinct subsets of known pathogenic variants with distinct phenotypic features; both p.Tyr75Cys and p.Arg406Cys cluster away from other variants and show an increase in swim speed compared with hSTXBP1 worms. This leads to the hypothesis that the mechanism of disease for these 2 variants may differ from most STXBP1-mutated patients and may account for some of the clinical heterogeneity observed in the patient population. Conclusion: We have demonstrated that automated analysis of a small animal system is an effective, scalable, and fast way to understand functional consequences of variants in

Indexed as

Clinical variantCRISPRSTXBP1unc-18Variant of uncertain significance

Identifiers

PMID38827422
PMCPMC11141691

What OpenQuestion holds

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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.