Whole-Genome Sequencing Improves the Diagnosis of DFNB1 Monoallelic Patients

Hearing loss is the most common sensory defect, due in most cases to a genetic origin. Variants in the GJB2 gene are responsible for up to 30% of non-syndromic hearing loss. Today, several deafness genotypes remain incomplete, confronting us with a diagnostic deadlock. In this study, whole-genome sequencing (WGS) was performed on 10 DFNB1 patients with incomplete genotypes. New variations on GJB2 were identified for four patients. Functional assays were realized to explore the function of one of them in the GJB2 promoter and confirm its impact on GJB2 expression. Thus, in this study WGS resolved patient genotypes, thus unlocking diagnosis. WGS afforded progress and bridged some gaps in our research.

The Cause of Hereditary Hearing Loss in GJB2 Heterozygotes—A Comprehensive Study of the GJB2/DFNB1 Region

Hearing loss is a genetically heterogeneous sensory defect, and the frequent causes are biallelic pathogenic variants in the GJB2 gene. However, patients carrying only one heterozygous pathogenic (monoallelic) GJB2 variant represent a long-lasting diagnostic problem. Interestingly, previous results showed that individuals with a heterozygous pathogenic GJB2 variant are two times more prevalent among those with hearing loss compared to normal-hearing individuals. This excess among patients led us to hypothesize that there could be another pathogenic variant in the GJB2 region/DFNB1 locus. A hitherto undiscovered variant could, in part, explain the cause of hearing loss in patients and would mean reclassifying them as patients with GJB2 biallelic pathogenic variants. In order to detect an unknown causal variant, we examined 28 patients using NGS with probes that continuously cover the 0.4 Mb in the DFNB1 region. An additional 49 patients were examined by WES to uncover only carriers. We did not reveal a second pathogenic variant in the DFNB1 region. However, in 19% of the WES-examined patients, the cause of hearing loss was found to be in genes other than the GJB2. We present evidence to show that a substantial number of patients are carriers of the GJB2 pathogenic variant, albeit only by chance.

A Novel Truncating Mutation in HOMER2 Causes Nonsyndromic Progressive DFNA68 Hearing Loss in a Spanish Family

Nonsyndromic hereditary hearing loss is a common sensory defect in humans that is clinically and genetically highly heterogeneous. So far, 122 genes have been associated with this disorder and 50 of them have been linked to autosomal dominant (DFNA) forms like DFNA68, a rare subtype of hearing impairment caused by disruption of a stereociliary scaffolding protein (HOMER2) that is essential for normal hearing in humans and mice. In this study, we report a novel HOMER2 variant (c.832_836delCCTCA) identified in a Spanish family by using a custom NGS targeted gene panel (OTO-NGS-v2). This frameshift mutation produces a premature stop codon that may lead in the absence of NMD to a shorter variant (p.Pro278Alafs*10) that truncates HOMER2 at the CDC42 binding domain (CBD) of the coiled-coil structure, a region that is essential for protein multimerization and HOMER2-CDC42 interaction. c.832_836delCCTCA mutation is placed close to the previously identified c.840_840dup mutation found in a Chinese family that truncates the protein (p.Met281Hisfs*9) at the CBD. Functional assessment of the Chinese mutant revealed decreased protein stability, reduced ability to multimerize, and altered distribution pattern in transfected cells when compared with wild-type HOMER2. Interestingly, the Spanish and Chinese frameshift mutations might exert a similar effect at the protein level, leading to truncated mutants with the same Ct aberrant protein tail, thus suggesting that they can share a common mechanism of pathogenesis. Indeed, age-matched patients in both families display quite similar hearing loss phenotypes consisting of early-onset, moderate-to-profound progressive hearing loss. In summary, we have identified the third variant in HOMER2, which is the first one identified in the Spanish population, thus contributing to expanding the mutational spectrum of this gene in other populations, and also to clarifying the genotype–phenotype correlations of DFNA68 hearing loss.

Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistani families

Background: Hearing loss is the most common sensory defect, and it affects over 6% of the population worldwide. Approximately 50%-60% of hearing loss patients are attributed to genetic causes. Currently, more than 100 genes have been reported to cause non-syndromic hearing loss. It is possible and efficient to screen all potential disease-causing genes for hereditary hearing loss by whole exome sequencing (WES).Methods: We collected 5 consanguineous pedigrees from Pakistan with hearing loss and applied WES in selected patients for each pedigree, followed by bioinformatics analysis and Sanger validation to identify the causal genes.Results: Variants in 7 genes were identified and validated in these pedigrees. We identified single candidate variant for 3 pedigrees: GIPC3 (c.937T>C), LOXHD1 (c.6136G>A) and TMPRSS3 (c.941T>C). The remaining 2 pedigrees each contained two candidate variants: TECTA (c.4045G>A) and MYO15A (c.3310G>T and c.9913G>C) for one pedigree and DFNB59 (c.494G>A) and TRIOBP (c.1952C>T) for the other pedigree. The candidate variants were validated in all available samples by Sanger sequencing.Conclusion: The candidate variants in hearing-loss genes were validated to be co-segregated in the pedigrees, and they may indicate the aetiologies of hearing loss in such patients. We also suggest that WES may be a suitable strategy for hearing-loss gene screening in clinical detection.

Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistan families

Background Hearing loss is the most common sensory defect that affects over 6% of the population worldwide. About 50%-60% of hearing loss patients are attributed to genetic causes. Currently more than 100 genes have been reported to cause non-syndromic hearing loss. It’s possible and efficient to screen all potential disease-causing genes for hereditary hearing loss by whole exome sequencing (WES). Methods We collected 5 consanguineous pedigrees with hearing loss from Pakistan and applied WES on selected patients for each pedigree, followed by bioinformatics analysis and Sanger validation to identify the causing genes for them. Results Variants in 7 genes were identified and validated in these pedigrees. We identified single candidate for 3 pedigrees, which were GIPC3 (c.937T>C), LOXHD1 (c.2935G>A) and TMPRSS3 (c.941T>C). And the remaining 2 pedigrees each contained two candidates, which were TECTA (c.4045G>A) and MYO15A (c.3310G>T and c.1705G>C) for one pedigree and DFNB59 (c.494G>A) and TRIOBP (c.1952C>T) for the other pedigree. The candidates were validated in all available samples by Sanger sequencing. Conclusion The candidate variants in hearing loss genes were validated to be co-segregated in the pedigrees, which may indicate the reasons for such patients. We also suggested that WES may be suitable strategy for hearing loss screening in clinical detection.

T26. VISUO-TACTILE TRANSFER AND AUDIO-VISUAL INTEGRATION IMPAIRMENT AS A NEW VULNERABILITY MARKER IN CHILDREN-AT-RISK OF SCHIZOPHRENIA, BIPOLAR DISORDER OR RECURRENT DEPRESSIVE DISORDER

Background Major psychiatric disorders (MPD) such as schizophrenia, bipolar disorder and recurrent major depression have shared neurodevelopmental vulnerability due to early neuronal and sensory defect as revealed by sensory and cognitive endophenotypes observed in our cohorts (e.g. Gagné et al., Schizophr. Res., 2019). There is considerable evidence that a harmonious self-development - known to be disrupted in MPDs - requires a synchronized multisensory perception and an adequate integration of sensory afferences (e.g. tactile, visual, auditory and proprio / interoception) with cognition. Early impairment in intermodal transfer (IMT) and multisensory integration (MSI) may jeopardize a stable and unified self’s and world’s representation and then would undermine self-development and represent a risk factor for MPD. IMT is the capability to transfer a percept coming exclusively from a sensory modality (e.g. tactile) to another modality (e.g. visual). MSI is the ability to integrate sensory inputs from different modalities (e.g. visual and auditory) to have a better information processing. This study shows that impairment in IMT/MSI may be a vulnerability marker in children genetically at-risk. Methods Sample: Forty-four offspring (21 girls) of patients suffering from a MPD and thus genetically at-risk for MPD (GatR) aged from 9–15 years old (mean age = 12.06) were recruited from the cohort study INTERCEPT through the HoPE program of the CIUSSS de la Capitale-Nationale. Twenty-five controls (19 girls) with no family history of MPD and no DSM-V disorder aged from 9–15 years old (mean age = 12.87) were recruited using advertisements or control bank. IMT Task: Each condition has 12 trials and the shapes are hidden from sight during palpation. MSI Task: - Simple reaction time (RT) task comprising 80 trials with unimodal stimuli (Auditory OR Visual) and 40 trials with AV (Auditory and Visual simultaneously) multimodal stimuli presented randomly. Results IMT task: When compared to controls, GatR were impaired in the three conditions (T-T: 9.77 vs. 10.32, T-V: 9.89 vs. 9.96, V-T: 9,11 vs. 9.92) with significant impairments both for T-T (t(60.53) = 2.18, p = 0.017) and V-T (t (57.28) = 2.33, p = 0.012) conditions. MSI task: GatR showed a deficit in MSI for almost all RT ranges (except for a peak at 185 ms), while control participants showed MSI facilitation for ranges from 150 to 200 ms. Discussion Developmentally genetically high-risk children would show significant impairments both in IMT and MSI that might enter into the group of indicators of brain dysfunctions, or risk endophenotypes, that both children at risk and adult patients carry (Paccalet et al., Schizophr. Res., 2016; Maziade, New Eng J Medicine, 2017). In addition, the two tasks would be valid and sensitive to the early sensory alterations in self-development. Finally, the battery is brief, user-friendly and playful for children.

Joint Attention and Sensitivity to Orienting Gaze in Children with Atypical Development

The article is devoted to the study of the relationship between the mechanism of joint attention and the subsequent normative and atypical development of the child. It is shown that the ability to establish joint attention based on the direction of the interlocutor's gaze is a precursor of the emergence of social and cognitive abilities. The study examined the differences between typical developmental children and atypical development control groups in their ability to be sensitive to social behavioral signals, namely the orientation direction of the interlocutor's gaze. On a sample of 120 children with typical development, mental retardation, hearing impairment, speech disorders and visual impairment, a number of tasks were developed to assess the ability to use the character's direction of sight in the picture to determine its intentions. The task measured such a skill of joint attention as the child’s ability to calculate and report what the other person was looking at and what he intended to choose. We also used tasks with a central hint with an explicit indication of an arrow and a peripheral hint to check the recognition of social and non-social orienting signals. Based on the comparison of contrasting groups, the variability of the formation and age-related changes in skills of joint attention, or rather the presence of differences in recognition, synthesis and interpretation orienting social information coming from eye contact. It was found that children with atpic development have a low level of "downward" joint attention. Impaired joint attention may be one of the earliest signs in children with atypical development at a later age. The results showed that deficiencies in the behavior of joint attention vary depending on mental age and level of development, a sensory defect, so the level of development can really affect the ability of children to joint attention.

Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistan families

Background: Hearing loss is the most common sensory defect that affects over 6% of the population worldwide. About 50%-60% of hearing loss patients are attributed to genetic causes. Currently more than 100 genes have been reported to cause non-syndromic hearing loss. It’s possible and efficient to screen all potential disease-causing genes for hereditary hearing loss by whole exome sequencing (WES).Methods: We collected 5 consanguineous pedigrees with hearing loss from Pakistan and applied WES on selected patients for each pedigree, followed by bioinformatics analysis and Sanger validation to identify the causing genes for them.Results: Variants in 7 genes were identified and validated in these pedigrees. We identified single candidate for 3 pedigrees, which were GIPC3 (c.937T>C), LOXHD1 (c.2935G>A) and TMPRSS3 (c.941T>C). And the remaining 2 pedigrees each contained two candidates, which were TECTA (c.4045G>A) and MYO15A (c.3310G>T and c.1705G>C) for one pedigree and DFNB59 (c.494G>A) and TRIOBP (c.1952C>T) for the other pedigree. The candidates were validated in all available samples by Sanger sequencing.Conclusion: The candidate variants in hearing loss genes were validated to be co-segregated in the pedigrees, which may indicate the reasons for such patients. We also suggested that WES may be suitable strategy for hearing loss gene screening in clinical detection.