Evidence map›Paper›PMID 39294130›Full record

ArticleNature communications2024

Complex trait associations in rare diseases and impacts on Mendelian variant interpretation.

Craig Smail, Bing Ge, Marissa R Keever-Keigher, Carl Schwendinger-Schreck, Warren A Cheung, Jeffrey J Johnston, Cassandra Barrett, Genomic Answers for Kids Consortium, Keith Feldman, Ana S A Cohen and 4 more

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. GEN-KnowRD: Reframing AI for Rare Disease Recognition.medRxiv : the preprint server for health sciences · 2026
    Article
  5. Article
  6. Article
  7. Review
  8. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Craig SmailGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA. csmail@cmh.edu.ORCID 0000-0001-8045-6021
Bing GeDepartment of Human Genetics, McGill University, Montreal, Canada.
Marissa R Keever-KeigherGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.ORCID 0000-0002-0317-8774
Carl Schwendinger-SchreckGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.
Warren A CheungGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.ORCID 0000-0003-0267-7464
Jeffrey J JohnstonGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.ORCID 0000-0002-8962-6186
Cassandra BarrettGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.
Genomic Answers for Kids Consortium
Keith FeldmanUKMC School of Medicine, University of Missouri Kansas City, Kansas City, USA.
Ana S A CohenGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.ORCID 0000-0002-6353-6350
Emily G FarrowGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.ORCID 0000-0002-8864-7073
Isabelle ThiffaultGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.ORCID 0000-0001-7987-6731
Elin GrundbergGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA.ORCID 0000-0001-5415-7896
Tomi PastinenGenomic Medicine Center, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, USA. tpastinen@cmh.edu.ORCID 0000-0003-4016-5021

Funding

Mapping causal genetic processes in non-Mendelian pediatric rare diseaseR35GM146966 · NIGMS · CHILDREN'S MERCY HOSP (KANSAS CITY, MO) · PI Craig Smail · 2022 to 2026
$1.9M
Novel computational approaches to characterize the effects of rare functional outlier variants on cis- and trans-regulatory disease processesR21HG012422 · NHGRI · CHILDREN'S MERCY HOSP (KANSAS CITY, MO) · PI SMAIL, CRAIG · 2022 to 2023
$429k
NHGRI NIH HHS R21 HG012422NIGMS NIH HHS R35 GM146966U.S. Department of Health & Human Services | National Institutes of Health (NIH) R21HG012422U.S. Department of Health & Human Services | National Institutes of Health (NIH) R35GM146966Wellcome Trust
6 · The paper itself

Abstract

Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - in the onset and phenotypic presentation of rare diseases. Here, we comprehensively map individual polygenic liability for 1102 open-source PGS in a cohort of 3059 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. Using this resource, we demonstrate increased polygenic liability in probands with an inherited candidate disease variant (VUS) compared to unaffected carrier parents. Further, we show an enrichment for large-effect rare variants in putative core PGS genes for associated complex traits. Overall, our study supports and expands on previous findings of complex trait associations in rare diseases, implicates polygenic liability as a potential mechanism underlying variable penetrance of candidate causal variants, and provides a framework for identifying novel candidate rare disease genes.

Indexed as

Genetic Predisposition to DiseaseMultifactorial InheritancePhenotypeRare DiseasesChildCohort StudiesFemaleGenetic VariationGenome-Wide Association StudyHumansMalePenetrance

Identifiers

PMID39294130
PMCPMC11411080

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.