Investigating the genetic aetology of three facial dysostoses in South Africa

Abstract

Treacher Collins (TCS), Nager (NS) and Miller syndromes (MS) are genetic developmental disorders that show overlapping clinical features. No molecular testing for these facial dysostoses (FDs) disorders is available in South Africa (SA). This is due to a number of challenges, most notably that we have no published data on the genetics of these disorders in the South African populations. Clinicians therefore depend on family history and clinical features to make a diagnosis, a task complicated by the variable expression and reduced penetrance seen in these conditions. Diagnosis of these disorders is further complicated by features overlapping with condition such as Broncho-oto-renal (BOR) syndrome, Mandibulofacial dysostosis with microcephaly (MFDM) and CHARGE syndrome. Fifteen South African patients with TCS and NS including their differential diagnoses of BOR- and CHARGE syndrome were recruited from the participating clinics of the Division of Human Genetics, Wits and NHLS. Of the 15 patients recruited, ten were Africans, four were Caucasians and one was of Indian ancestry. The majority (7/15) of the patients had a provisional clinical diagnosis of TCS followed by CHARGE syndrome (5/15). Two patients had a suspected diagnosis of TCS, BOR- or CHE syndrome and a single patient was clinically diagnosed with NS. Genomic DNA was extracted from whole blood and targeted next-generation sequencing-based (NGS) mutation screening was performed to analyse twelve genes known to cause or interact with causative genes of the disorders under study. Sequencing was performed on an Illumina MiSeq platform. Putative pathogenic variants were identified through a tiered filtering approach. Firstly, variants with a minor allele frequency of more than 0.05 in gnomAD exomes and genomes datasets were excluded. Subsequently, bioinformatics prediction tools and the mode of inheritance were then used to prioritise variants. Lastly, the American College of Medical Genetics (ACMG) guidelines for variant interpretation were used to classify and identify putative disease-causing variants.Seven putative disease-causing variants were identified in seven of 15 unrelated patients. Putative disease-causing variants were identified within three genes: CHD7, POLR1D and TCOF1 genes. These consisted of five deletions (CHD7 c.1931delA, CHD7 c.3309_3310delCA, TCOF1 c.4369_4373delAAGAA, TCOF1 c.3708delC and POLR1D c.261delA) and two single nucleotide variants (CHD7 c.232C>T and CHD7 c.643C>T). Of the seven putative disease-causing variants identified, three (TCOF1 c.4369_4373delAAGAA, TCOF1 c.3708delC and POLR1D c.261delA) were identified in patients with TCS and four (CHD7 c.232C>T, CHD7 c.1931delA, CHD7 c.3309_3310delCA and CHD7 c.643C>T) were identified in patients with CHARGE syndrome. Six of these variants (CHD7 c.232C>T, CHD7 c.1931delA, CHD7 c.3309_3310delCA, CHD7 c.643C>T TCOF1 c.3708delC and POLR1D c.261delA) are not reported in public mutation databases and one (TCOF1 c.4369_4373delAAGAA) is a common recurring TCS pathogenic mutation. The overall diagnostic yield of this study was 47%. In addition, a variant of unknown significance (VUS) (TCOF1 c.3183G>C) predicted to affect splicing was also identified in one patient with TCS. The present study is, to the best of our knowledge, the first study to perform a molecular analysis on TCS, NS, MS, BOR and CHARGE syndrome in South African patients. This study has produced a baseline mutation profile of TCS and CHARGE syndrome in the South African population and has demonstrated that targeted NGS with multigene panel testing is an acceptable diagnostic method which could be successfully implemented for the molecular diagnosis of TCS and CHARGE syndrome in the South African population. The successful implementation of an NGS-based diagnostic approach for TCS and CHARGE syndrome in SA will enable their molecular diagnosis and this will be important for confirmation of a clinical diagnosis. Furthermore, understanding the genetic basis of these conditions in the South African population will thus not only have practical implication for the patients and their families but also address the paucity of data on genetic conditions in SA.