Dataset Information

Diagnostic Gene Panel Testing in (Non)-Syndromic Patients with Cleft Lip, Alveolus and/or Palate in the Netherlands.

ABSTRACT:

Objectives

Clefts of the lip, alveolus and/or palate (CLA/P) are the most common craniofacial congenital malformations in humans. These oral clefts can be divided into non-syndromic (isolated) and syndromic forms. Many cleft-related syndromes are clinically variable and genetically heterogeneous, making it challenging to distinguish syndromic from non-syndromic cases. Recognition of syndromic/genetic causes is important for personalized tailored care, identification of (unrecognized) comorbidities, and accurate genetic counseling. Therefore, next generation sequencing (NGS)-based targeted gene panel testing is increasingly implemented in diagnostics of CLA/P patients. In this retrospective study, we assess the yield of NGS gene panel testing in a cohort of CLA/P cases.

Methods

Whole exome sequencing (WES) followed by variant detection and interpretation in an a priori selected set of genes associated with CLA/P phenotypes was performed in 212 unrelated CLA/P patients after genetic counseling between 2015 and 2020. Medical records including family history and results of additional genetic tests were evaluated.

Results

In 24 CLA/P cases (11.3%), a pathogenic genetic variant was identified. Twenty out of these 24 had a genetic syndrome requiring specific monitoring and follow-up. Six of these 24 cases (25%) were presumed to be isolated CLA/P cases prior to testing, corresponding to 2.8% of the total cohort. In eight CLA/P cases (3.8%) without a diagnosis after NGS-based gene panel testing, a molecular diagnosis was established by additional genetic analyses (e.g., SNP array, single gene testing, trio WES).

Conclusion

This study illustrates NGS-based gene panel testing is a powerful diagnostic tool in the diagnostic workup of CLA/P patients. Also, in apparently isolated cases and non-familial cases, a genetic diagnosis can be identified. Early diagnosis facilitates personalized care for patients and accurate genetic counseling of their families.

SUBMITTER: Wurfbain LF

PROVIDER: S-EPMC10425715 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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Publications

Diagnostic Gene Panel Testing in (Non)-Syndromic Patients with Cleft Lip, Alveolus and/or Palate in the Netherlands.

Wurfbain Lisca Florence LF Cox Inge Lucia IL van Dooren Maria Francisca MF Lachmeijer Augusta Maria Antonia AMA Verhoeven Virginie Johanna Maria VJM van Hagen Johanna Maria JM Heijligers Malou M Klein Wassink-Ruiter Jolien Sietske JS Koene Saskia S Maas Saskia Mariska SM Veenstra-Knol Hermine Elisabeth HE Ploos van Amstel Johannes Kristian JK Massink Maarten Pieter Gerrit MPG Mink van der Molen Aebele Barber AB van den Boogaard Marie-José Henriette MH

Molecular syndromology 20230608 4

<h4>Objectives</h4>Clefts of the lip, alveolus and/or palate (CLA/P) are the most common craniofacial congenital malformations in humans. These oral clefts can be divided into non-syndromic (isolated) and syndromic forms. Many cleft-related syndromes are clinically variable and genetically heterogeneous, making it challenging to distinguish syndromic from non-syndromic cases. Recognition of syndromic/genetic causes is important for personalized tailored care, identification of (unrecognized) com ...[more]

PMID: 37589029

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Project description:BackgroundTreatment of cleft lip and palate (CLP) requires a comprehensive interdisciplinary approach and long-term follow-up. Only a few studies are available that reported on changes after treatment, which showed that in particular the transverse dimension, in patients with CLP is prone to changes after treatment. However, those studies did not pay attention to concomitant changes in the mandibular arch that occur after treatment.ObjectivesTo evaluate mandibular transverse dental arch dimensions and interarch transverse changes in patients with complete non-syndromic unilateral cleft lip, alveolus, and palate (CUCLAP) up to five years after treatment.Material and methodsRetrospective longitudinal study in 75 consecutive patients with CUCLAP directly after comprehensive treatment (T0), two (T2), and 5 years after treatment (T5). Great Ormond Street, London and Oslo (GOSLON) scores were available for all patients. Three-dimensional scans of all dental casts were made. Inter premolar and intermolar distances between the mandibular contralateral teeth were measured. The modified Huddart Bodenham (MHB index) was applied to assess the transverse interarch relationship. Paired t-tests and ANOVA were used to analyze transverse and interarch transverse changes. Linear regression analysis was done to define contributing factors.ResultsPaired t-tests showed a significant decrease of the mandibular inter first and second premolar distances (p < 0.05) and an increase of the inter second molar distance, whilst the MHB Index deteriorated at all time points for all segments and for the total arch score (p < 0.05). Linear regression showed no significant contributing factors on the decrease of the transverse distances. However, inter arch transverse relationship was significantly affected by age at the end of treatment, missing maxillary lateral incisor space closure, and the GOSLON Yardstick score at the end of treatment (p < 0.05), especially during the first two years after treatment.ConclusionsChanges occurred in the mandibular arch expressed as changes in the transverse dimensions and interarch relationship measured by the MHB Index. A younger age at the end of treatment, space closure for a missing maxillary lateral incisor and a higher GOSLON score at the end of treatment negatively influence the interarch transverse deterioration especially in the first two years after treatment. For the transverse dimensional changes in the mandibular arch such influencing factors could not be determined.

Project description:The etiology and pathogenesis of non-syndromic cleft lip and palate (NSCL/P) are largely unknown. Long non-coding RNAs (lncRNA) are thought to play important roles in NSCL/P, but reports on the underlying processes are currently unavailable. Our study focused on children diagnosed with NSCL/P alone. Based on the morphology, patients were categorized as either cleft lip with or without cleft palate (CL/P) or cleft palate-only (CPO). When patients received surgery for NSCL/P, tissue excised from the trimmed wound edge was reserved to serve as experimental samples; adjacent normal tissue was used as a positive control. Target lncRNAs in the collected tissues were identified using microarray and quantitative reverse transcription PCR (RT-qPCR). Immunohistochemical (IHC) staining and RT-qPCR were used to verify the target mRNAs. Pathway, gene ontology (GO) enrichment, and TargetScan prediction were employed to construct endogenous RNA networks (ceRNA networks) and explore their potential functions. RNA-Seq analysis revealed 24 upregulated and 43 downregulated lncRNAs in the CL/P and CPO groups compared with those in the control group; of these, MALAT1and NEAT1 were screened and validated using RT-qPCR. Common NSCL/P risk factors positively correlated with MALAT1 and NEAT1 expression (ORMALAT1 = 28.111, 95% CI: 4.054-194.923; ORNEAT1 = 30.556, 95% CI: 4.422-211.142; P < 0.05). Bioinformatics predicted four ceRNA networks: MALAT1-hsa-miR-1224-3p-SP1, MALAT1-hsa-miR-6734-5p/hsa-miR-1224-3p-WNT10A, NEAT1-hsa-miR-140-3p.1-CXCR4, and NEAT1-hsa-miR-3129-5p/hsa-miR-199a-3p/hsa-miR-199b-3p-ZEB1. GO enrichment focused on the potential functions of ceRNA networks, including biosynthesis of organic cyclic compounds, formation of membrane-enclosed and organelle lumens, and Wnt-protein binding. The results of RT-qPCR were consistent with those of IHC staining with regard to expression of related mRNAs. MALAT1 and NEAT1, which are upregulated in NSCL/P, are associated with the severity of NSCL/P. This study provides a new insight into NSCL/P pathogenesis and suggests that MALAT1 and NEAT1 act as potential therapeutic targets and prognostic biomarkers for NSCL/P.

Dataset Information

Diagnostic Gene Panel Testing in (Non)-Syndromic Patients with Cleft Lip, Alveolus and/or Palate in the Netherlands.

Objectives

Methods

Results

Conclusion

Publications

Diagnostic Gene Panel Testing in (Non)-Syndromic Patients with Cleft Lip, Alveolus and/or Palate in the Netherlands.

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