Orofacial clefts are the most common congenital anomalies of the head and neck. They arise early in embryonic development and are typically classified into two major groups: cleft lip with or without cleft palate, and cleft palate only. In addition to aesthetic problems, individuals with orofacial clefts often face functional difficulties, such as problems with feeding and speech. Orofacial clefts are complex congenital anomalies and, although they may occur as a result of monogenic genetic variants, they are more often of multifactorial origin, influenced by a combination of genetic and environmental factors. In this master's thesis, we aimed to identify genetic causes of orofacial clefts in 25 families with a family history of orofacial clefts of unknown origin. We obtained whole exome sequencing data for 28 index patients with orofacial cleft. First, we performed a bioinformatic analysis of whole exome sequencing data, where we screened 40 candidate genes to identify genetic variants that could influence the development of orofacial clefts. In total, 400 variants were evaluated, and their clinical significance was assessed using the Franklin (Genoox) platform according to the criteria of the American College of Medical Genetics and Genomics. Among the identified genetic variants, 55 were classified as variants of uncertain significance, 4 as likely pathogenic variants, and 2 as pathogenic variants. The presence of likely pathogenic and pathogenic variants in index patients and their affected and unaffected relatives was then confirmed using genotyping with hydrolysis probes or Sanger sequencing. Additionally, we verified the presence of two variants in the NOTCH2 and TRPS1 genes, which had been identified previously in another master's thesis. For the variant rs376493409 in gene CEP290, we demonstrated the possibility that it could segregate with the disease phenotype. For the variant rs73715573 in gene CFTR, we were unable to confirm or exclude segregation with the disease phenotype. For the variants rs113993960 in CFTR and rs374564199 in CDON, we confirmed that the variants do not segregate with the disease phenotype in the respective families. We did not confirm the presence of deletions in the CEP290, CNTNAP2, NOTCH2, and TRPS1 genes in the index patients and their relatives. Independently of whole exome sequencing results, we identified three additional variants in the CEP290, CFTR, and NOTCH2 genes. However these variants are predicted to be benign or likely benign.
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