Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG)

Coalition for Global Hearing Health Hearing Care Pathways Working Group: Guidelines for Clinical Guidance for Readiness and Development of Evidence-Based Early Hearing Detection and Intervention Programs

Editor's Note: The following article discusses the timely topic Clinical Guidance in the areas of Evidence-Based Early Hearing Detection and Intervention Programs. This article aims to discuss areas of services needed, guidance to countries/organizations attempting to initiate early hearing detection and intervention systems. Expert consensus and systematic/scoping reviews were combined to produce recommendations for evidence-based clinical practice. In Ear and Hearing, our long-term goal for the Point of View article is to stimulate the field's interest in and to enhance the appreciation of the author's area of expertise. Hearing is an important sense for children to develop cognitive, speech, language, and psychosocial skills. The goal of universal newborn hearing screening is to enable the detection of hearing loss in infants so that timely health and educational/therapeutic intervention can be provided as early as possible to improve outcomes. While many countries have implemented universal newborn hearing screening programs, many others are yet to start. As hearing screening is only the first step to identify children with hearing loss, many follow-up services are needed to help them thrive. However, not all of these services are universally available, even in high-income countries. The purposes of this article are (1) to discuss the areas of services needed in an integrated care system to support children with hearing loss and their families; (2) to provide guidance to countries/organizations attempting to initiate early hearing detection and intervention systems with the goal of meeting measurable benchmarks to assure quality; and (3) to help established programs expand and improve their services to support children with hearing loss to develop their full potential. Multiple databases were interrogated including PubMed, Medline (OVIDSP), Cochrane library, Google Scholar, Web of Science and One Search, ERIC, PsychInfo. Expert consensus and systematic/scoping reviews were combined to produce recommendations for evidence-based clinical practice. Eight essential areas were identified to be central to the integrated care: (1) hearing screening, (2) audiologic diagnosis and management, (3) amplification, (4) medical evaluation and management, (5) early intervention services, (6) family-to-family support, (7) D/deaf/hard of hearing leadership, and (8) data management. Checklists are provided to support the assessment of a country/organization's readiness and development in each area as well as to suggest alternative strategies for situations with limited resources. A three-tiered system (i.e., Basic, Intermediate, and Advanced) is proposed to help countries/organizations at all resource levels assess their readiness to provide the needed services and to improve their integrated care system. Future directions and policy implications are also discussed.

Diagnostic yield of genetic testing in adults with sensorineural hearing loss

INTRODUCTION

The contribution of genetic causes to sensorineural hearing loss (SNHL) in adults is less clear than in children, and genetic diagnosis is still not standardized in adults. In this study we present the genetic results obtained in a cohort of adult patients with SNHL.

MATERIALS AND METHODS

We included 63 adults with SNHL that received genetic testing between 2019 and 2022. Whole exome sequencing was performed and variants in genes related to hearing loss (virtual panel with 244 genes) were prioritised and analysed.

RESULTS

24% (15/63) of patients were genetically diagnosed: 87% (13/15) of patients had non-syndromic hearing loss and 13% (2/15) had syndromic hearing loss. We identified pathogenic and likely pathogenic variants in 11 different genes.

CONCLUSIONS

Our results show that a significant proportion of adults with SNHL have a genetic origin, and that implementation of genetic testing improves diagnostic accuracy and allows personalized management of these patients.

Reevaluating the splice-altering variant in TECTA as a cause of nonsyndromic hearing loss DFNA8/12 by functional analysis of RNA

PURPOSE

The aim of this study was to determine the genetic cause of early onset autosomal dominant hearing loss segregating in five-generation kindred of Chinese descent and provide preimplantation genetic testing (PGT)for them.

METHODS

Clinical examination, pedigree analysis and exome sequencing were carried out on the family. Minigene-based splicing analysis, in vivo RNA analysis and protein structure prediction by molecular modeling were conducted on the candidate variant. PGT for the causative variation and chromosome aneuploidis based on SNP analysis has been used for avoidance of hearing loss in this family.

RESULTS

All the affected individuals presented with moderate down-sloping hearing loss and whole-exome sequencing identified a novel splice-site variant c.5383+6T>A in the tested subjects within the TECTA locus. Genotyping of all the 32 family members confirmed segregation of this variant and the hearing loss phenotype in the extended family. Functional analysis of RNA and molecular modeling indicates that c.5383+6T>A is a pathogenic splice-site variant and should be considered as genetic cause of the hearing loss. Furthermore, a successful singleton pregnancy with no variation in TECTA c.5383+6 was established and a healthy male child was born by PGT.

CONCLUSION

We have identified a novel variant c.5383+6T>A in TECTA ZA-ZP inter-domain, which could be attributable to the early-onset autosomal dominant hearing loss. The implications of our study are valuable in elucidating the disrupted RNA splicing and uncovering the genetic cause of hearing loss with TECTA pathogenic variants, as well as providing reproductive approaches to healthy offspring.

The congenital hearing phenotype in GJB2 in Queensland, Australia: V37I and mild hearing loss predominates

GJB2 was originally identified in severe, non-syndromic sensorineural hearing loss (SNHL), but was subsequently associated with mild and moderate SNHL. Given the increasing utilisation of genetic testing pre-conceptually, prenatally, and neonatally, it is crucial to understand genotype-phenotype correlations. This study evaluated the nature and frequency of GJB2 variants in an Australian paediatric population with varying degrees of SNHL ascertained through newborn hearing screening. Audiograms from individuals with GJB2 variants and/or a GJB6 deletion (GJB6-D13S11830) were retrospectively reviewed (n = 127). Two-thirds were biallelic (homozygous/compound heterozygous) for pathogenic/likely pathogenic variants of GJB2 and/or GJB6 (n = 80). The most frequent variant was c.109 G > A, followed by c.35delG and c.101 T > C. Compared to biallelic carriage of other GJB2 variants, c.109 G > A positive individuals (homozygous/compound heterozygous) were more likely to have mild HL at their initial and latest audiograms (p = 0.0004). Biallelic carriage of c.35delG was associated with moderately-severe or greater SNHL at both initial and latest audiograms (p = 0.007). The c.101 T > C variant presented with milder SNHL and U-shaped audiograms (p = 0.02). In this agnostically identified cohort, mild SNHL predominated in GJB2/GJB6 carriers in contrast to previous studies targeting individuals with significant loss. Consequently, c.109 G > A, associated with milder phenotypes, was the most frequent. This study provides valuable data to support prognostic confidence in genetic counselling.

Genetic diagnosis of childhood sensorineural hearing loss

INTRODUCTION

Congenital/early-onset sensorineural hearing loss (SNHL) is one of the most common hereditary disorders in our environment. There is increasing awareness of the importance of an etiologic diagnosis, and genetic testing with next-generation sequencing (NGS) has the highest diagnostic yield. Our study shows the genetic results obtained in a cohort of patients with bilateral congenital/early-onset SNHL.

MATERIALS AND METHODS

We included 105 children with bilateral SNHL that received genetic testing between 2019 and 2022. Genetic tests were performed with whole exome sequencing, analyzing genes related to hearing loss (virtual panel with 244 genes).

RESULTS

48% (50/105) of patients were genetically diagnosed. We identified pathogenic and likely pathogenic variants in 26 different genes, and the most frequently mutated genes were GJB2, USH2A and STRC. 52% (26/50) of variants identified produced non-syndromic hearing loss, 40% (20/50) produced syndromic hearing loss, and the resting 8% (4/50) could produce both non-syndromic and syndromic hearing loss.

CONCLUSIONS

Genetic testing plays a vital role in the etiologic diagnosis of bilateral SNHL. Our cohort shows that genetic testing with NGS has a high diagnostic yield and can provide useful information for the clinical workup of patients.

Genetics evaluation outcomes of patients with pediatric hearing loss: 2008-2022 retrospective study

OBJECTIVE

This study aims to explore how genetics evaluation and testing for patients with pediatric onset hearing loss affects their diagnosis and management.

METHODS

Retrospective chart review was completed for patients with pediatric hearing loss that were evaluated by a genetic counselor from 2008 to 2022 with data entry into a REDCap database. Descriptive statistical analysis was completed.

RESULTS

Four hundred twenty-nine patients with pediatric onset hearing loss were evaluated by genetics. Majority of patients presented with bilateral (67 %) and sensorineural (83 %) hearing loss. Genetic testing was recommended for 76 % of patients with pediatric hearing loss evaluated by a genetic counselor with 70 % completing some or all recommended tests. Overall genetic testing diagnostic rate was 34 %, with 41 % of diagnoses syndromic. Yearly trends noted an increasing number of patients evaluated, tests ordered, and subsequently an increased number of diagnoses overtime. For diagnostic results, management recommendations were made for 45 % of patients (35/78) and for 92 % of family members (72/78). This compared to total management recommendations for all patients (82/429, 19 %) and family members (110/429, 26 %).

CONCLUSION

This study identified a genetic testing diagnostic rate for pediatric hearing loss of 34 % over 14 years. This study notes the beneficial outcomes of patients with hearing loss and their families meeting with a genetic counselor and the importance of collaboration with hearing loss management colleagues. It highlights the value a genetic counselor consult can add to a patient's diagnostic journey, in addition to how genetic testing impacts management for patients and their families.

Hearing Loss: Genetic Testing, Current Advances and the Situation in Latin America

Congenital hearing loss is the most common birth defect, estimated to affect 2-3 in every 1000 births, with ~50-60% of those related to genetic causes. Technological advances enabled the identification of hundreds of genes related to hearing loss (HL), with important implications for patients, their families, and the community. Despite these advances, in Latin America, the population with hearing loss remains underdiagnosed, with most studies focusing on a single locus encompassing the GJB2/GJB6 genes. Here we discuss how current and emerging genetic knowledge has the potential to alter the approach to diagnosis and management of hearing loss, which is the current situation in Latin America, and the barriers that still need to be overcome.

Hereditary deafness carrier screening in 9,993 Chinese individuals

Background: Preconception or prenatal carrier screening plays an important role in reproductive decision-making, but current research on hereditary deafness is limited. This study aimed to investigate the carrier frequencies of common deafness genes in the Chinese population who underwent carrier screening and to follow up on pregnancy outcomes in high-chance couples. Methods: Individual females or couples in preconception or early pregnancy were recruited from two hospitals in China. Carrier screening for common deafness genes in the Chinese population, including the GJB2 and SLC26A4 genes, was performed using next-generation sequencing technology. Genetic counseling was provided to subjects before and after testing. Results: Of the 9,993 subjects screened, the carrier rate was 2.86% for the GJB2 gene and 2.63% for the SLC26A4 gene. The variant with the highest carrier frequency in GJB2 was c.235delC (1.89%), and c.919-2A>G (1.08%) in SLC26A4. Of the six high-chance couples, four made alternative reproductive decisions (three with prenatal diagnosis and one with preimplantation genetic testing), with consequent termination of the birth of two affected fetuses. Conclusion: These findings confirmed the clinical utility of preconception or prenatal carrier screening for hereditary deafness.

Co-Occurrence of Sensorineural Hearing Loss and Congenital Heart Disease: Etiologies and Management

OBJECTIVES/HYPOTHESIS

The co-occurrence of sensorineural hearing loss (SNHL) and congenital heart disease (CHD) is a rare condition with complex etiologies. The purpose of this study is to assess the etiologies, clinical features, and outcomes of cochlear implant (CI) in this patient population.

STUDY DESIGN

Case series and literature review.

METHODS

Clinical data of children who were diagnosed with SNHL and CHD and received CIs at a tertiary hospital from 2016 to 2021 were retrospectively analyzed. A literature review was performed to identify patients with SNHL and CHD.

FINDINGS

Of the 382 children who underwent cochlear implantation at our center, eight (2.1%) were diagnosed with SNHL and CHD. A literature review identified 1525 patients from 254 studies; the database therefore consisted of 1533 patients. The most common genetic etiologies of co-occurring SNHL and CHD were CHARGE syndrome (36.3%), Turner syndrome (8.4%), 22q11.2 deletion (3.0%), Noonan syndrome (2.9%), and Down syndrome (2.5%), whereas the most common non-genetic etiologies were congenital rubella syndrome (22.9%) and SNHL after early cardiac surgery (5.5%). Most of the patients presented with congenital, bilateral, severe-profound SNHL requiring early rehabilitation. Of the 126 children who received CIs at a median age of 2.5 years, half showed delayed speech development at last follow-up.

CONCLUSIONS

Co-occurring SNHL and CHD is a rare condition with complex etiologies. Timely hearing intervention with long-term follow-up and proper timing of heart surgery is essential for these children.

LEVEL OF EVIDENCE

4, case series Laryngoscope, 134:400-409, 2024.

Non-Syndromic Sensorineural Hearing Loss in Children

Pediatric hearing loss is common with significant consequences in terms of language, communication, social and emotional development, and academic advancement. Radiological imaging provides useful information regarding hearing loss etiology, prognosis, therapeutic options, and potential surgical pitfalls. This review provides an overview of temporal bone imaging protocols, an outline of the classification of inner ear anomalies associated with sensorineural hearing loss and illustrates some of the more frequently encountered and/or important causes of non-syndromic hearing loss.

Next-generation sequencing improves precision medicine in hearing loss

Background: An early etiological diagnosis of hearing loss positively impacts children's quality of life including language and cognitive development. Even though hearing loss associates with extremely high genetic and allelic heterogeneity, several studies have proven that Next-Generation Sequencing (NGS)-based gene panel testing significantly reduces the time between onset and diagnosis. Methods: In order to assess the clinical utility of our custom NGS GHELP panel, the prevalence of pathogenic single nucleotide variants, indels or copy number variants was assessed by sequencing 171 nuclear and 8 mitochondrial genes in 155 Spanish individuals with hearing loss. Results: A genetic diagnosis of hearing loss was achieved in 34% (52/155) of the individuals (5 out of 52 were syndromic). Among the diagnosed cases, 87% (45/52) and 12% (6/52) associated with autosomal recessive and dominant inheritance patterns respectively; remarkably, 2% (1/52) associated with mitochondrial inheritance pattern. Although the most frequently mutated genes in this cohort were consistent with those described in the literature (GJB2, OTOF or MYO7A), causative variants in less frequent genes such as TMC1, FGF3 or mitCOX1 were also identified. Moreover, 5% of the diagnosed cases (3/52) were associated with pathogenic copy number variants. Conclusion: The clinical utility of NGS panels that allows identification of different types of pathogenic variants-not only single nucleotide variants/indels in both nuclear and mitochondrial genes but also copy number variants-has been demonstrated to reduce the clinical diagnostic odyssey in hearing loss. Thus, clinical implementation of genomic strategies within the regular clinical practice, and, more significantly, within the newborn screening protocols, is warranted.

Hearing Assessment in Infants, Children, and Adolescents: Recommendations Beyond Neonatal Screening

Children who are deaf or hard of hearing (D/HH) are at high risk for permanent deficits in language acquisition and downstream effects such as poor academic performance, personal-social maladjustments, and emotional difficulties. Identification of children born D/HH through newborn hearing screening and subsequent timely early intervention can prevent or reduce many of these adverse consequences. Ongoing surveillance for changes in hearing thresholds after infancy is also important and should be accomplished by subjective assessment for signs of atypical hearing and with objective screening tests. Scheduled hearing screening may take place in the primary care setting, or via referral to an audiologist according to the Bright Futures/American Academy of Pediatrics "Recommendations for Preventive Pediatric Health Care" (also known as the periodicity schedule). This report covers hearing assessment beyond the newborn period, reviews risk factors for hearing level change, and provides guidance for providers of pediatric primary care on the assessment and care of children who are D/HH.

Exome Sequencing Expands the Genetic Diagnostic Spectrum for Pediatric Hearing Loss

OBJECTIVES

Genetic testing is the standard-of-care for diagnostic evaluation of bilateral, symmetric, sensorineural hearing loss (HL). We sought to determine the efficacy of a comprehensive genetic testing method, exome sequencing (ES), in a heterogeneous pediatric patient population with bilateral symmetric, bilateral asymmetric, and unilateral HL.

METHODS

Trio-based ES was performed for pediatric patients with confirmed HL including those with symmetric, asymmetric, and unilateral HL.

RESULTS

ES was completed for 218 probands. A genetic cause was identified for 31.2% of probands (n = 68). The diagnostic rate was 40.7% for bilateral HL, 23.1% for asymmetric HL, and 18.3% for unilateral HL, with syndromic diagnoses made in 20.8%, 33.3%, and 54.5% of cases in each group, respectively. Secondary or incidental findings were identified in 10 families (5.52%).

CONCLUSION

ES is an effective method for genetic diagnosis for HL including phenotypically diverse patients and allows the identification of secondary findings, discovery of deafness-causing genes, and the potential for efficient data re-analysis.

LEVEL OF EVIDENCE

4 Laryngoscope, 133:2417-2424, 2023.

Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome

Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are "variants of uncertain significance" (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆GFold) for all DVD missense variants. We find that 5772 VUSs have a large, destabilizing ∆∆GFold that is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3456 VUSs are likely pathogenic at a probability of 99.0%. Of the 224 genes in the DVD, 166 genes (74%) exhibit one or more missense variants predicted to cause a pathogenic change in protein folding stability. The VUSs prioritized here affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.

Association of Genetic Diagnoses for Childhood-Onset Hearing Loss With Cochlear Implant Outcomes

Importance

In the US, most childhood-onset bilateral sensorineural hearing loss is genetic, with more than 120 genes and thousands of different alleles known. Primary treatments are hearing aids and cochlear implants. Genetic diagnosis can inform progression of hearing loss, indicate potential syndromic features, and suggest best timing for individualized treatment.

Objective

To identify the genetic causes of childhood-onset hearing loss and characterize severity, progression, and cochlear implant success associated with genotype in a single large clinical cohort.

Design, Setting, and Participants

This cross-sectional analysis (genomics) and retrospective cohort analysis (audiological measures) were conducted from 2019 to 2022 at the otolaryngology and audiology clinics of Seattle Children's Hospital and the University of Washington and included 449 children from 406 families with bilateral sensorineural hearing loss with an onset younger than 18 years. Data were analyzed between January and June 2022.

Main Outcomes and Measures

Genetic diagnoses based on genomic sequencing and structural variant analysis of the DNA of participants; severity and progression of hearing loss as measured by audiologic testing; and cochlear implant success as measured by pediatric and adult speech perception tests. Hearing thresholds and speech perception scores were evaluated with respect to age at implant, months since implant, and genotype using a multivariate analysis of variance and covariance.

Results

Of 406 participants, 208 (51%) were female, 17 (4%) were African/African American, 32 (8%) were East Asian, 219 (54%) were European, 53 (13%) were Latino/Admixed American, and 16 (4%) were South Asian. Genomic analysis yielded genetic diagnoses for 210 of 406 families (52%), including 55 of 82 multiplex families (67%) and 155 of 324 singleton families (48%). Rates of genetic diagnosis were similar for children of all ancestries. Causal variants occurred in 43 different genes, with each child (with 1 exception) having causative variant(s) in only 1 gene. Hearing loss severity, affected frequencies, and progression varied by gene and, for some genes, by genotype within gene. For children with causative mutations in MYO6, OTOA, SLC26A4, TMPRSS3, or severe loss-of-function variants in GJB2, hearing loss was progressive, with losses of more than 10 dB per decade. For all children with cochlear implants, outcomes of adult speech perception tests were greater than preimplanted levels. Yet the degree of success varied substantially by genotype. Adjusting for age at implant and interval since implant, speech perception was highest for children with hearing loss due to MITF or TMPRSS3.

Conclusions and Relevance

The results of this cross-sectional study suggest that genetic diagnosis is now sufficiently advanced to enable its integration into precision medical care for childhood-onset hearing loss.

Assessing Variants of Uncertain Significance Implicated in Hearing Loss Using a Comprehensive Deafness Proteome

Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6,328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are "variants of uncertain significance" (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆G Fold ) for all DVD missense variants. We find that 5,772 VUSs have a large, destabilizing ∆∆G Fold that is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3,456 VUSs are likely pathogenic at a probability of 99.0%. These VUSs affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.