The Enigmatic Genetic Landscape of Hereditary Hearing Loss: A Multistep Diagnostic Strategy in the Italian Population

Abstract

Hearing loss is the most frequent sensorineural disorder, affecting approximately 1:1000 newborns. Hereditary forms (HHL) represent 50–60% of cases, highlighting the relevance of genetic testing in deaf patients. HHL is classified as non-syndromic (NSHL—70% of cases) or syndromic (SHL—30% of cases). In this study, a multistep and integrative approach aimed at identifying the molecular cause of HHL in 102 patients, whose GJB2 analysis already showed a negative result, is described. In NSHL patients, multiplex ligation probe amplification and long-range PCR analyses of the STRC gene solved 13 cases, while whole exome sequencing (WES) identified the genetic diagnosis in 26 additional ones, with a total detection rate of 47.6%. Concerning SHL, WES detected the molecular cause in 55% of cases. Peculiar findings are represented by the identification of four subjects displaying a dual molecular diagnosis and eight affected by non-syndromic mimics, five of them presenting Usher syndrome type 2. Overall, this study provides a detailed characterisation of the genetic causes of HHL in the Italian population. Furthermore, we highlighted the frequency of Usher syndrome type 2 carriers in the Italian population to pave the way for a more effective implementation of diagnostic and follow-up strategies for this disease.

Puzzling Out the Genetic Architecture of Endometriosis: Whole-Exome Sequencing and Novel Candidate Gene Identification in a Deeply Clinically Characterised Cohort

“…For each patient, a peripheral whole-blood sample was collected for genomic DNA extraction. The protocol for genomic DNA extraction was performed as already described in Spedicati et al [21].…”

“…WES was carried out on an Illumina NextSeq 550 instrument (Illumina Inc., San Diego, CA, USA) with the Twist Exome 2.0 plus Comprehensive Exome Spike-in kit (Twist Bioscience, South San Francisco, CA, USA), according to the manufacturer's protocol. The WES protocol and secondary and tertiary analyses were carried out as already reported in Spedicati et al [21].…”

Genome sequencing as a generic diagnostic strategy for rare disease

“…In clinical genomics, (de novo) single nucleotide and copy number variants (SNV/CNV) are the most commonly found aberrations [ 7 – 9 ], but to a lesser extent aneuploidy, expansions of short tandem repeats (STR), and (copy-neutral) structural variants (SV) also contribute to disease. To molecularly diagnose a rare disease, multiple workflows are often used, as a single disease can often be caused by multiple variant types [ 10 – 14 ]. Importantly, for diagnostic purposes, every technology needs to prove clinical, as well as analytical, validity [ 3 , 15 ].…”

Genome sequencing as a generic diagnostic strategy for rare disease

“…In clinical genomics, (de novo) single nucleotide and copy number variants (SNV/CNV) are the most found aberrations (7)(8)(9) , but to a lesser extent aneuploidy, expansions of short tandem repeats (STR), and structural variants (SV) also contribute to disease. To molecularly diagnose a rare disease, multiple workflows are often used, as a single disease can often be caused by multiple variant types (10)(11)(12)(13)(14) . Importantly, for diagnostic purposes, every technology needs to prove clinical, as well as analytical, validity (3,15) .…”