Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing.
Alleles
Cleft Lip
/ genetics
Cleft Palate
/ genetics
Fibroblast Growth Factors
GTPase-Activating Proteins
Genetic Predisposition to Disease
Genome-Wide Association Study
/ methods
High-Throughput Nucleotide Sequencing
/ methods
Humans
Peptide Elongation Factors
Polymorphism, Single Nucleotide
Ribonucleoprotein, U5 Small Nuclear
Gene panel
NGS
Orofacial clefts
Pathogenic variants
Journal
Molecular genetics and genomics : MGG
ISSN: 1617-4623
Titre abrégé: Mol Genet Genomics
Pays: Germany
ID NLM: 101093320
Informations de publication
Date de publication:
Sep 2022
Sep 2022
Historique:
received:
20
02
2022
accepted:
12
06
2022
pubmed:
2
7
2022
medline:
31
8
2022
entrez:
1
7
2022
Statut:
ppublish
Résumé
For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.
Identifiants
pubmed: 35778651
doi: 10.1007/s00438-022-01919-w
pii: 10.1007/s00438-022-01919-w
doi:
Substances chimiques
ARHGAP29 protein, human
0
EFTUD2 protein, human
0
FGF12 protein, human
0
GTPase-Activating Proteins
0
Peptide Elongation Factors
0
Ribonucleoprotein, U5 Small Nuclear
0
Fibroblast Growth Factors
62031-54-3
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1315-1327Subventions
Organisme : European Social Fund and Wielkopolska Voivodeship (Regional Operational Programme for Wielkopolskie Voivodeship 2014-2020)
ID : RPWP.07.02.02-30-0037/16
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
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