Speaker
Description
Background: Orofacial clefts (OFCs) are the most frequent congenital craniofacial anomalies that occur during embryonic development. OFCs can occur as a cleft lip with or without a cleft palate (CL/P) and a cleft palate only (CP). The incidence is ~1 per 700 live births worldwide. OFCs may occur in isolation (nonsyndromic) or with other anomalies, such as limb deformities (syndromic). Congenital limb malformations are the second most prevalent birth defect, affecting ~1 per 500-1000 live births. This study investigated the genetic aetiology and potential pathways contributing to OFCs co-occurring with limb abnormalities within a Ghanaian cohort.
Methodology: Whole exome sequencing (WES) was performed on DNA samples from 9 Ghanaian families using the Illumina HiSeq platform at 100X read depth (GRCh38). Sentieon workflow was utilised for quality controls, read alignment, and variant calling. Normalised VCF files were annotated using Ensembl Variant Effect Predictor (VEP), focusing on rare variants (minor allele frequency <0.01) across multiple databases. Pathogenicity was determined using 11 dbNSFP-integrated predictors and others. Variants predicted as pathogenic by ≥6 tools were prioritised using the ACMG guidelines and VarElect, focusing on de novo variants or those with incomplete penetrance under dominant inheritance. Pathway enrichment analysis, protein-protein interactions and gene expression analysis were undertaken to decipher the biological functions of implicated genes.
Results: Key genes associated with OFCs, limb anomalies, and pathways necessary for normal craniofacial and limb development included TP63 (c.1027C>T; p.Arg343Trp), NIPBL (c.7617_7618del; p.Ser2540ProfsTer21), MYH3 (c.2015G>A; p.Arg672His), FGFR2 (c.755C>G; p.Ser252Trp), TP63 (c.952C>T; p.Arg318Cys), RGPD5 (c.4708G>A; p.Gly1570Arg), FOXD4L1 (c.329A>C; p.Tyr110Ser), DLG1 (c.1730G>A; p.Arg577Gln), TRIM74 (c.487C>T; p.Arg163Ter), TRIM73 (c.487C>T; p.Arg163Ter) and PRDM9 (c.2272_2273insTG; p.Arg758LeufsTer182).
Conclusion: The findings demonstrate that while some cases can be attributed to single-gene syndromes (e.g., NIPBL-associated Cornelia de Lange Syndrome), others may result from multiple co-occurring syndromes. These findings will help inform recurrence risk estimates and genetic counselling.