Next-generation sequencing of genes for hereditary hearing loss: from gene identification to diagnostic implementation
17 september 2018
UAntwerp, Campus Drie Eiken, Building O, Auditorium O1 - Universiteitsplein 1 - 2610 Wilrijk (Antwerp) (route: UAntwerpen, Campus Drie Eiken
16 - 18 uur
Guy Van Camp
PhD defence Manou Sommen - Department of Biomedical Sciences
Hearing loss (HL) is the most common sensory disorder in developed countries with far-reaching social, psychological and cognitive implications. Furthermore, it is an extremely heterogeneous disorder, both genetically and phenotypically, with a poor genotype-phenotype correlation, complicating molecular testing. In the first part of this thesis, we aimed to develop a comprehensive molecular diagnostic test by the use of next-generation sequencing (NGS). Via a pilot study on a limited set of HL genes the sensitivity, specificity, pro and contras were evaluated. This showed the capability and flexibility of the technique for a systematic high-throughput screening in a cost-effective way. In a large follow-up study, we evaluated the challenges of a NGS-based testing for HL in relation to single nucleotide variations (SNV), small insertions and deletions (Indel) and copy-number variation (CNV) detection, which resulted in the implementation of a NGS-based test for HL at the Center of Medical Genetics Antwerp (CMG). In order to get insight in the yield of this test and the frequency of different HL genes and mutations in the Belgian population, a retrospective study was performed on all HL patients referred to the CMG in the period 2014-2018, which showed a diagnosis in 27%-35% of patients.
Although NGS-based testing for HL resulted in a great improvement of the etiological work-up for HL, for the majority of patients no genetic diagnosis is obtained. This is partially due to the fact that there are still causative HL genes yet to be identified. In the second part of this thesis we aimed to identify and characterize new causative genes for HL-related syndromes using the hypothesis-free whole-exome sequencing (WES) approach. As such, we showed the c.11483A>G [p.(Asp3828Gly)] variant in LRP2 to be the genetic cause in a consanguineous Iraqi family presenting a Stickler-like phenotype. Furhermore, WES in families presenting Heimler syndrome (HS) showed biallelic mutations in PEX1 or PEX6. Both genes are known to be associated with autosomal recessive peroxisome-biogenesis disorders. A detailed genetic and functional characterization of the identified mutations showed that each HS-affected family has at least one hypomorphic allele resulting in an extremely mild peroxisomal dysfunction. Finally, the utility of WES in combination with NGS-based targeted resequencing for the identification of disease-causing mutations and risk factors in phenotypic disorders related to the same molecular pathophysiological mechanism was demonstrated. This study approach sowed mutations in MEPE to be associated with hereditary congenital facial paresis (HCFP) and otosclerosis.