Evidence map›Paper›PMID 37676273›Full record

ArticleHuman genetics2023

Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes.

Sarah W Curtis, Jenna C Carlson, Terri H Beaty, Jeffrey C Murray, Seth M Weinberg, Mary L Marazita, Justin L Cotney, David J Cutler, Michael P Epstein, Elizabeth J Leslie

Abstract read
In one paragraph

Article in Human genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
1.3field-weighted citation impact, top 17% of its field
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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. Article
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 at 5 institutions in 1 country.

Sarah W CurtisDepartment of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
Jenna C CarlsonDepartment of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA.
Terri H BeatyDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
Jeffrey C MurrayDepartment of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
Seth M WeinbergDepartment of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
Mary L MarazitaDepartment of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
Justin L CotneyDepartment of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, 06030, USA.
David J CutlerDepartment of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
Michael P EpsteinDepartment of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
Elizabeth J LeslieDepartment of Human Genetics, Emory University, Atlanta, GA, 30322, USA. ejlesli@emory.edu.ORCID http://orcid.org/0000-0002-5735-1712
Emory University · USUniversity of Pittsburgh · USJohns Hopkins University · USUniversity of Connecticut · USUniversity of Iowa · US

Funding

Extending the Phenotype of Nonsyndromic Orofacial CleftsR01DE016148 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L., WEINBERG, SETH M · 2004 to 2018
$19.7M
Molecular Genetic Epidemiology of Cleft Lip and PalateR37DE008559 · NIDCR · UNIVERSITY OF IOWA · PI MURRAY, JEFFREY C · 2004 to 2013
$6.8M
Unraveling mechanisms of genome regulation to understand and improvehuman healthR35GM119465 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI COTNEY, JUSTIN LEE · 2016 to 2025
$3.9M
Genetic modifiers of Van der Woude syndromeR01DE028342 · NIDCR · EMORY UNIVERSITY · PI LESLIE-CLARKSON, ELIZABETH JANE · 2019 to 2023
$2.7M
Functional characterization of craniofacial enhancers at single cell and single base pair resolutionR01DE028945 · NIDCR · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI COTNEY, JUSTIN LEE · 2019 to 2023
$1.9M
Human genomics analysis interface for FaceBase 2U01DE024425 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L. · 2014 to 2018
$1.2M
GENETIC MAPPING STUDIES OF ORAL-FACIAL CLEFTS IN CHINAR01DE009886 · NIDCR · VIRGINIA COMMONWEALTH UNIVERSITY · PI MARAZITA, MARY L · 1992 to 2002
$1.0M
Genetics of Craniofacial Disorders and Related PhenotypesR00DE025060 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LESLIE-CLARKSON, ELIZABETH JANE · 2017 to 2019
$732k
Improved Mediation Analyses in Case-Control StudiesR21DE029698 · NIDCR · EMORY UNIVERSITY · PI EPSTEIN, MICHAEL PHILIP · 2020 to 2021
$429k
Integrated multi-omics analyses of early mammalian craniofacial developmentR03DE028588 · NIDCR · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI COTNEY, JUSTIN LEE · 2020 to 2021
$328k
The role of noncoding regulatory variants in orofacial cleftsR03DE030118 · NIDCR · EMORY UNIVERSITY · PI LESLIE-CLARKSON, ELIZABETH JANE · 2021 to 2022
$313k
Planning International Orofacial Cleft Genetic StudiesR21DE016930 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L · 2006 to 2007
$293k
NHGRI NIH HHS U01 HG005925NIDCR NIH HHS DE025060NIDCR NIH HHS DE028342NIDCR NIH HHS DE030118NIDCR NIH HHS DE032260NIDCR NIH HHS F32 DE032260NIDCR NIH HHS R00 DE025060NIDCR NIH HHS R01 DE009886NIDCR NIH HHS R01 DE016148NIDCR NIH HHS R01 DE028945NIDCR NIH HHS R03 DE028588NIDCR NIH HHS R03 DE030118NIDCR NIH HHS R21 DE016930NIDCR NIH HHS R21 DE029698NIDCR NIH HHS R37 DE008559NIDCR NIH HHS U01 DE024425NIGMS NIH HHS R35 GM119465
6 · The paper itself

Abstract

As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10

Indexed as

Cleft LipCleft PalateAllelesBinding SitesChildHumansVesicular Transport ProteinsSEC24D protein, humanVesicular Transport Proteins

Identifiers

PMID37676273
PMCPMC13036755
OpenAlexW4386507049

What OpenQuestion holds

Textmetadata
LicenceTDM
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.