Evidence map›Paper›PMID 31685013›Full record

ArticleClinical epigenetics2019

A genome-wide DNA methylation signature for SETD1B-related syndrome.

I M Krzyzewska, S M Maas, P Henneman, K V D Lip, A Venema, K Baranano, A Chassevent, E Aref-Eshghi, A J van Essen, T Fukuda and 17 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical epigenetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
39citing papers in PubMed, 1 pooled it
7.5field-weighted citation impact, top 2% 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

39 citing papers in PubMed, 1 synthesis or guideline pooled it, 65 citations in OpenAlex.

  1. Pooled it
  2. Syndromic diabetes and hypergonadotropic hypogonadism in a boy with a 12q24.31-32 chromosomal deletion involvingClinical pediatric endocrinology : case reports and clinical investigations : official journal of the Japanese Society for Pediatric Endocrinology · 2026
    Article
  3. Article
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  7. Article
  8. [Clinical characteristics of epilepsy with intellectual disability associated withZhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2025
    Review
  9. Article
  10. Article
  11. Article
  12. Article
  13. Review
  14. Article
  15. Review
  16. Article
  17. Review
  18. Delineation of a KDM2B-related neurodevelopmental disorder and its associated DNA methylation signature.Genetics in medicine : official journal of the American College of Medical Genetics · 2023
    Article
  19. Article
  20. Episignature Mapping ofInternational journal of molecular sciences · 2022
    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

27 authors at 15 institutions in 7 countries.

I M KrzyzewskaAmsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
S M MaasAmsterdam UMC, Department of Pediatrics, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
P HennemanAmsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
K V D LipAmsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
A VenemaAmsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
K BarananoKennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA.
A ChasseventKennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA.
E Aref-EshghiDepartment of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada.
A J van EssenUniversity Medical Centre Groningen, University of Groningen, Department of Medical Genetics, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
T FukudaDepartment of Pediatrics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.
H IkedaNational Epilepsy Centre, NHO, Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan.
M JacquemontDepartment of medical genetics, CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France.
H-G KimNeurological Disorder Center Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar.
A LabalmeDepartment of medical genetics, Hospices Civils de Lyon, Bron, France.
S M E LewisDepartment of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada.
G LescaDepartment of medical genetics, Hospices Civils de Lyon, Bron, France.
I MadrigalBiochemistry and Molecular Genetics Service, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Center for Biomedical Network Research on Rare Diseases (CIBERER), Barcelona, Spain.
S MahidaKennedy Krieger Institute, Department of Neurogenetics, 801 N. Broadway, Rm 564, Baltimore, MD, 21205, USA.
N MatsumotoDepartment of Human Genetics, Graduate School of Medicine, Yokohama City University, Fukuura 3-9, Kanazawa-ku, Yokohama, 236-0004, Japan.
R RabionetDepartment of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, av diagonal 643, 08028, Barcelona, Spain.
E Rajcan-SeparovicDepartment of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada.
Y QiaoDepartment of Medical Genetics, Children's & Women's Health Centre of British Columbia University of British Columbia, C234-4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada.
B SadikovicDepartment of Pathology and Laboratory Medicine, Western University, 800 Commissioner's Road E, London, ON, N6A 5W9, Canada.
H SaitsuDepartment of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan.
D A SweetserMassGeneral Hospital, Division of Medical Genetics and Metabolism, 175 Cambridge St, Suite 500, Boston, Massachusetts, 02114, USA.
M AldersAmsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands. m.alders@amsterdamumc.nl.
M M A M MannensAmsterdam UMC, Department of Clinical Genetics, Genome Diagnostics laboratory Amsterdam, Reproduction & Development, University of Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands.
Amsterdam University Medical Centers · NLKennedy Krieger Institute · USUniversity of British Columbia · CAHamamatsu University School of Medicine · JPHospices Civils de Lyon · FRWestern University · CACentre for Biomedical Network Research on Rare Diseases · ESCentre Hospitalier Universitaire de La Réunion · FRHamad bin Khalifa University · QAMaineGeneral Medical Center · USNational Epilepsy Center · JPUniversitat de Barcelona · ESUniversity of Amsterdam · NLUniversity of Groningen · NLYokohama City University · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

SETD1B is a component of a histone methyltransferase complex that specifically methylates Lys-4 of histone H3 (H3K4) and is responsible for the epigenetic control of chromatin structure and gene expression. De novo microdeletions encompassing this gene as well as de novo missense mutations were previously linked to syndromic intellectual disability (ID). Here, we identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases. We demonstrate the clinical utility of this unique epi-signature by reclassifying previously identified SETD1B VUS (variant of uncertain significance) in two patients.

Indexed as

DNA MethylationLoss of Function MutationAdolescentAdultAnxietyAutism Spectrum DisorderChildChild, PreschoolCpG IslandsEpigenesis, GeneticEpilepsyF-Box ProteinsFemaleGenetic MarkersHistone-Lysine N-MethyltransferaseHumansF-Box ProteinsGenetic MarkersHistone-Lysine N-MethyltransferaseJumonji Domain-Containing Histone DemethylasesKDM2A protein, humanSETD1B protein, human

Identifiers

PMID31685013
PMCPMC6830011
OpenAlexW2986189881

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.