Genetic screening for deafness

Non-Syndromic Hearing Loss in a Romanian Population: Carrier Status and Frequent Variants in the GJB2 Gene

The genetic causes of autosomal recessive nonsyndromic hearing loss (ARNSHL) are heterogeneous and highly ethnic-specific. We describe GJB2 (connexin 26) variants and carrier frequencies as part of our study and summarize previously reported ones for the Romanian population. In total, 284 unrelated children with bilateral congenital NSHL were enrolled between 2009 and 2018 in northwestern Romania. A tiered diagnostic approach was used: all subjects were tested for c.35delG, c.71G>A and deletions in GJB6 (connexin 30) using PCR-based methods. Furthermore, 124 cases undiagnosed at this stage were analyzed by multiplex-ligation-dependent probe amplifications (MLPA), probe mix P163, and sequencing of GJB2 exon 2. Targeted allele-specific PCR/restriction fragment length polymorphism (RFLP) established definite ethio-pathogenical diagnosis for 72/284 (25.35%) of the cohort. Out of the 124 further analyzed, in 12 cases (9.67%), we found compound heterozygous point mutations in GJB2. We identified one case of deletion of exon 1 of the WFS1 (wolframin) gene. Carrier status evaluation used Illumina Infinium Global Screening Array (GSA) genotyping: the HINT cohort-416 individuals in northwest Romania, and the FUSE cohort-472 individuals in southwest Romania. GSA variants yielded a cumulated risk allele presence of 0.0284. A tiered diagnostic approach may be efficient in diagnosing ARNSHL. The summarized contributions to Romanian descriptive epidemiology of ARNSHL shows that pathogenic variants in the GJB2 gene are frequent among NSHL cases and have high carrier rates, especially for c.35delG and c.71G>A. These findings may serve in health strategy development.

Screening Consanguineous Families for Hearing Loss Using the MiamiOtoGenes Panel

Background: Hearing loss (HL) is one of the most common and genetically heterogeneous sensory disorders in humans. Genetic causes underlie 50-60% of all HL and the majority of these cases exhibit an autosomal recessive model of inheritance. Methods: In our study, we used our targeted custom MiamiOtoGenes panel of 180 HL-associated genes to screen 23 unrelated consanguineous Iranian families with at least two affected children to identify potential causal variants for HL. Results: We identified pathogenic variants in seven genes (MYO7A, CDH23, GIPC3, USH1C, CAPB2, LOXHD1, and STRC) in nine unrelated families with varying HL profiles. These include five reported and four novel mutations. Conclusion: For small consanguineous families that were unsuitable for conventional linkage analysis the employment of the MiamiOtoGenes panel helped identify the genetic cause of HL in a cost-effective and timely manner. This rapid methodology provides for diagnoses of a significant fraction of HL patients, and identifies those who will need more extensive genetic analyses such as whole exome/genome sequencing.

Genetic Predisposition to Sporadic Congenital Hearing Loss in a Pediatric Population

Discriminating between inherited and non-inherited sporadic hearing loss is challenging. Here, we attempted to delineate genetic inheritance in simplex cases of severe-to-profound congenital hearing loss in Korean children. Variations in SLC26A4 and GJB2 in 28 children with bilateral severe-to-profound non-syndromic hearing loss (NSHL) without familial history were analyzed using Sanger sequencing. Genetic analysis of individuals without mutations in SLC26A4 and GJB2 was performed by whole exome sequencing (WES). Bi-allelic mutations in SLC26A4 and GJB2 were identified in 12 and 3 subjects, respectively. Of the 13 individuals without mutations in SLC26A4 and GJB2, 2 and 1 carried compound heterozygous mutations in MYO15A and CDH23, respectively. Thus, 64.3% (18/28) of individuals with NSHL were determined to be genetically predisposed. Individuals with sporadic severe-to-profound NSHL were found to mostly exhibit an autosomal recessive inheritance pattern. Novel causative candidate genes for NSHL were identified by analysis of WES data of 10 families without mutations in known causative genes. Bi-allelic mutations predisposing to NSHL were identified in 64.3% of subjects with sporadic severe-to-profound NSHL. Given that several causative genes for NSHL are still unidentified, genetic inheritance of sporadic congenital hearing loss could be more common than that indicated by our results.

Deafness gene mutations in newborns in Beijing

OBJECTIVE

To determine the incidence of congenital hearing loss (HL) in newborns by the rate of deafness-related genetic mutations.

DESIGN

Clinical study of consecutive newborns in Beijing using allele-specific polymerase chain reaction-based universal array.

STUDY SAMPLE

This study tested 37 573 newborns within 3 days after birth, including nine sites in four genes: GJB2 (35 del G, 176 del 16, 235 del C, 299 del AT), SLC26A4 (IVS7-2 A > G, 2168 A > G), MTRNR1 (1555 A > G, 1494 C > T), and GJB3 (538 C > T). The birth condition of infants was also recorded.

RESULTS

Of 37 573 newborns, 1810 carried pathogenic mutations, or 4.817%. The carrier rates of GJB2 (35 del G, 176 del 16, 235 del C, 299 del AT), GJB3 (538 C > T), SLC26A4 (IVS7-2 A > G, 2168 A > G), and MTRNR1 (1555 A > G, 1494 C > T) mutations were 0.005%, 0.104%, 1.924%, 0.551%, 0.295%, 0.253%, 1.387%, 0.024%, and 0.274%, respectively. Logistic regression analysis indicated no statistically significant relationship between mutations and infant sex, premature delivery, twin status, or birth weight.

CONCLUSIONS

The 235delC GJB2 mutation was the most frequent deafness-related mutation in the Chinese population. Genetic screening for the deafness gene will help detect more cases of newborn congenital HL than current screening practices.

Whole-exome sequencing reveals diverse modes of inheritance in sporadic mild to moderate sensorineural hearing loss in a pediatric population

PURPOSE

This study was designed to delineate genetic contributions, if any, to sporadic forms of mild to moderate sensorineural hearing loss (SNHL) not related to GJB2 mutations (DFNB1) in a pediatric population.

METHODS

We recruited 11 non-DFNB1 simplex cases of mild to moderate SNHL in children. We applied whole-exome sequencing to all 11 probands. We used a filtering strategy assuming that de novo variants of known autosomal dominant (AD) deafness genes, biallelic mutations in autosomal recessive (AR) genes, monoallelic mutations in X chromosome genes for males, and digenic inheritance could be associated. Candidate variants first were prioritized with allele frequency in public databases and confirmed by a phase or a segregation test in each family. Additional information from the literature or public databases was used to identify strong candidate variants.

RESULTS

Strong candidate variants were detected in 5 of 11 probands (45.4%). A diverse mode of inheritance implicated the sporadic occurrence of the phenotype. AR mutations in OTOGL and SERPINB6 and digenic inheritance involving two deafness genes, GPR98 and PDZ7, were detected. A de novo AD mutation also was detected in TECTA and MYH14. No syndromic feature was detected in individuals with GPR98/PDZ7 or MYH14 variants in our cohort at this moment.

CONCLUSION

Mild to moderate pediatric SNHL, even if sporadic, features a strong genetic etiology and can manifest via diverse modes of inheritance. In addition, a multidisciplinary approach should be used for a correct diagnosis.

Hearing impairment in Estonia: an algorithm to investigate genetic causes in pediatric patients

PURPOSE

The present study was initiated to establish the etiological causes of early onset hearing loss (HL) among Estonian children between 2000-2009.

METHODS

The study group consisted of 233 probands who were first tested with an arrayed primer extension assay, which covers 199 mutations in 7 genes (GJB2, GJB6, GJB3, SLC26A4, SLC26A5 genes, and two mitochondrial genes - 12S rRNA, tRNASer(UCN)). From probands whose etiology of HL remained unknown, DNA analysis of congenital cytomegalovirus (CMV) infection and G-banded karyotype and/or chromosomal microarray analysis (CMA) were performed.

RESULTS

In 110 (47%) cases, the etiology of HL was genetic and in 5 (2%) congenital CMV infection was diagnosed. We found mutations with clinical significance in GJB2 (100 children, 43%) and in 2 mitochondrial genes (2 patients, 1%). A single mutation in SLC26A4 gene was detected in 5 probands (2.2%) and was considered diagnostic. In 4 probands a heterozygous IVS2-2A>G change in the SLC26A5 gene was found. We did not find any instances of homozygosity for this splice variant in the probands. CMA identified in 4 probands chromosomal regions with the loss of one allele. In 2 of them we were able to conclude that the found abnormalities are definitely pathogenic (12q13.3-q14.2 and 17q22-23.2 microdeletion), but the pathogenity of 2 other findings (3p26.2 and 1p33 microdeletion) remained unknown.

CONCLUSION

This practical diagnostic algorithm confirmed the etiology of early onset HL for 115 Estonian patients (49%). This algorithm may be generalized to other populations for clinical application.

Predictors of genetic testing decisions: a systematic review and critique of the literature

Genetic testing is increasingly available in medical settings and direct-to-consumer. However, the large and growing literature on genetic testing decisions is rife with conflicting findings, inconsistent methodology, and uneven attention across test types and across predictors of genetic testing decisions. Existing reviews of the literature draw broad conclusions but sacrifice nuanced analysis that with a closer look reveals far more inconsistency than homogeny across studies. The goals of this paper are to provide a systematic review of the empirical work on predictors of genetic testing decisions, highlight areas of consistency and inconsistency, and suggest productive directions for future research. We included all studies that provided quantitative analysis of subjective (e.g., perceived risk, perceived benefits of testing) and/or objective (e.g., family history, sociodemographic variables) predictors of genetic testing interest, intentions, or uptake, which produced a sample of 115 studies. From this review, we conclude that self-reported and test-related (as opposed to disorder-related or objective) predictors are relatively consistent across studies but that theoretically-driven efforts to examine testing interest across test types are sorely needed.

Inherited hearing loss: molecular genetics and diagnostic testing

BACKGROUND

Hearing loss is a clinically and genetically heterogeneous condition with major medical and social consequences. It affects up to 8% of the general population.

OBJECTIVE

This review recapitulates the principles of auditory physiology and the molecular basis of hearing loss, outlines the main types of non-syndromic and syndromic deafness by mode of inheritance, and provides an overview of current clinically available genetic testing.

METHODS

This paper reviews the literature on auditory physiology and on genes, associated with hearing loss, for which genetic testing is presently offered.

RESULTS/CONCLUSION

The advent of molecular diagnostic assays for hereditary hearing loss permits earlier detection of the underlying causes, facilitates appropriate interventions, and is expected to generate the data necessary for more specific genotype-phenotype correlations.

Genetics of hearing loss: where are we standing now?

Hearing loss (HL) is the most common sensory impairment and is caused by a broad range of inherited to environmental causes. Inherited HL consists 50-60% of all HL cases. The inherited form of HL is further classified to different categories. More than 300 syndromes and 40 genes have been identified to result in different levels of HL. Although several diagnostic or screening tests have been developed, yet there are controversies around their use.

Access to genetic testing and genetic counseling in vulnerable populations: the d/Deaf and hard of hearing population

Genetic testing holds great potential for preventing morbidities and mortalities for a number of diseases through early detection and effective intervention. As the number of genetic tests expand, so will public demand for these services. Therefore, it is essential to evaluate access to genetic testing and genetic services to ensure that all Canadians, including vulnerable groups, have equitable access to all forms of health care, in keeping with the mandate of the Canadian Health Act. The purpose of this paper is to examine the literature to determine if and how the Deaf community, as a vulnerable group, is at an increased risk of inequitable access to genetic services in Canada and to discuss how those who are deaf and hard of hearing are subject to the same risks. First, we define vulnerability and describe why the Deaf community, as a social group, can be considered a vulnerable group, followed by a description of the benefits of genetic testing. Second, we describe the barriers to accessing genetic testing, and how the d/Deaf and hard of hearing population experience additional barriers. Third, we examine the difficulties incorporating genetic testing into medical practice, and how this creates additional barriers to those already at risk. Finally, we discuss the steps necessary to promote equitable access to genetic testing among the d/Deaf and hard of hearing populations within Canada, and provide recommendations for further research in this topic area. Lastly, we comment on how barriers to genetic testing vary among the d/Deaf and hard of hearing is dependent upon the type of health care system available (whether public or private).

Mutation analysis of GJB2 and GJB6 genes in Southeastern Brazilians with hereditary nonsyndromic deafness

In developed countries deafness has a genetic cause in over 60% of the cases. Contrastingly, in Brazil, it is estimated that only 16% of all deafnesses are caused by genetic factors. Among hereditary hearing deficiencies, approximately half is caused by mutations in the Gap Junction Protein Beta-2 (GJB2) gene, which encodes the protein Connexin 26 (Cx26). There are four mutations in this gene that present high prevalence in specific ethnical groups, namely, 35delG, 167delT, 235delC, and W24X. The 35delG mutation is the most frequent one, occurring in homozygosity or in compound heterozygosity with mutations in the GJB2 and GJB6 genes. This study aims to determine the prevalence of GJB2-35delG, GJB2-167delT, GJB2-235delC, GJB2-W24X, del (GJB6-D13S1830), and del (GJB6-D13S1854) mutations in patients with nonsyndromic deafness in the Espirito Santo State, Brazil. A total of 77 individuals were evaluated, from which 88.3% presented normal genotypes for all analyzed mutations, 1.3% were compound heterozygotes for 35delG-GJB2/D13S1830-GJB6, 1.3% were compound heterozygotes for 35delG/D13S1854-GJB6, 3.9% were homozygotes for the 35delG mutation and 5.2% were heterozygotes for 35delG/GJB2. The frequency of mutant alleles 35delG/GJB2, del (D13S1830/GJB6), and del (D13S1854/GJB6) was 7.8, 0.65, and 0.65%, respectively. Mutations 167delT, 235delC, and W24X were not detected. Determining the prevalence of specific mutations related to inherited deafness in a population can contribute to the development of more efficient and affordable molecular diagnostic protocols, and help in the genetic counseling of patients and their families.

Prevalence and Etiology of Hearing Loss in Rural Nicaraguan Children

OBJECTIVE/HYPOTHESIS

The prevalence and causes of pediatric hearing loss (HL) in the developing world are largely unknown. Infectious sequelae, ototoxic medications, and genetic causes may play a larger role in developing countries. In addition, the significance of GJB2 mutation gene in poorly developed areas remains unclear. The intent of this study is to investigate the prevalence and etiology of HL in children living in a remote, impoverished region of northern Nicaragua.

STUDY DESIGN

Cross-sectional study.

METHODS

Clinical data from two sources were analyzed: data from screening examinations performed in rural schools in the Department of Jinotega, Nicaragua (group A) and pediatric HL patients seen at the Otolaryngology and Audiology Clinic in Jinotega, Nicaragua (group B). Patients with congenital HL were offered a genetic test for GJB2 mutations. Comparisons were made using parametric (analysis of variance) and nonparametric (Kruskal-Wallis) tests.

RESULTS

School-based screening examinations (group A) revealed a high prevalence of significant HL (>30 dB) of 18%. The majority of these children had normal otoscopic examinations (58%). A family history of HL was seen in 24% of children who failed screening exams. Positive family history was more common in patients with HL (P < .01) and in specific schools (P < .05). Clinic-based evaluations (group B) reveal a population with predominantly severe-profound HL. Physical dysmorphism was common, yet identifiable syndromic HL was rare. Although familial HL was common (33%), there were no pathologic GJB2 mutations. Other common risk factors in this population were maternal infection during pregnancy, neonatal distress, low birth weight or prematurity, and gentamicin exposure.

CONCLUSIONS

HL in this rural, third world environment is more prevalent, and the etiologies responsible in this study group are different from those encountered in industrialized nations. Poor perinatal health care, infectious causes, gentamicin exposure, and hereditary HL are potentially preventable causes that play a major role in this population.

Genetic deafness in a preterm infant with a critical postnatal course

OBJECTIVE

We present a case of deafness in a preterm infant with several predisposing factors of an acquired hearing impairment that, however, turned out to have a genetic cause. We describe the severe postnatal course and review the relevant literature.

DESIGN

Case report.

SETTING

University-based tertiary neonatal intensive care unit.

PATIENT

Preterm infant (gestational age, 26/37; wks).

MEASUREMENTS AND MAIN RESULTS

A preterm infant exhibited hearing impairment after a complicated clinical course with pneumothoraces, a hemodynamically relevant patent ductus arteriosus, treatment with potentially ototoxic drugs, intraventricular hemorrhage, and periventricular leukomalacia. Despite the absence of a family history for deafness, genetic testing was performed. Surprisingly, genetic analysis revealed the presence of two compound heterozygous mutations in the patient's GJB2 gene as the cause for his early-onset nonsyndromic deafness.

CONCLUSION

To elucidate the nature of a hearing disorder, it is worthwhile to consider a genetic cause, despite the fact that it may seem unlikely in a severely sick preterm infant with numerous risk factors for a postnatally acquired hearing impairment and without a positive family history.

An overview of hereditary hearing loss

Understanding the genetic basis of hearing loss is important because almost 50% of profound hearing loss are caused by genetic factors and more than 120 independent genes have been identified. In this review, after a brief explanation of some genetic terms (allele, heterozygosis, homozygosis, polymorphism, genotype and phenotype), classification of genetic hearing loss (syndromic versus nonsyndromic, and recessive dominant, X-linked and mitochondrial) was performed. Some of the most common syndromes (Usher, Pendred, Jervell and Lange-Nielsen, Waardenburg, branchio-oto-renal, Stickler, Treacher Collins and Alport syndromes, biotinidase deficiency and Norrie disease) causing genetic hearing loss were also explained briefly. The genes involved in hearing loss and genetic heterogeneity were presented.

Nuclear and mitochondrial genes mutated in nonsyndromic impaired hearing

Half of the cases with congenital impaired hearing are hereditary (HIH). HIH may occur as part of a multisystem disease (syndromic HIH) or as disorder restricted to the ear and vestibular system (nonsyndromic HIH). Since nonsyndromic HIH is almost exclusively caused by cochlear defects, affected patients suffer from sensorineural hearing loss. One percent of the total human genes, i.e. 300-500, are estimated to cause syndromic and nonsyndromic HIH. Of these, approximately 120 genes have been cloned thus far, approximately 80 for syndromic HIH and 42 for nonsyndromic HIH. In the majority of the cases, HIH manifests before (prelingual), and rarely after (postlingual) development of speech. Prelingual, nonsyndromic HIH follows an autosomal recessive trait (75-80%), an autosomal dominant trait (10-20%), an X-chromosomal, recessive trait (1-5%), or is maternally inherited (0-20%). Postlingual nonsyndromic HIH usually follows an autosomal dominant trait. Of the 41 mutated genes that cause nonsyndromic HIH, 15 cause autosomal dominant HIH, 15 autosomal recessive HIH, 6 both autosomal dominant and recessive HIH, 2 X-linked HIH, and 3 maternally inherited HIH. Mutations in a single gene may not only cause autosomal dominant, nonsyndromic HIH, but also autosomal recessive, nonsyndromic HIH (GJB2, GJB6, MYO6, MYO7A, TECTA, TMC1), and even syndromic HIH (CDH23, COL11A2, DPP1, DSPP, GJB2, GJB3, GJB6, MYO7A, MYH9, PCDH15, POU3F4, SLC26A4, USH1C, WFS1). Different mutations in the same gene may cause variable phenotypes within a family and between families. Most cases of recessive HIH result from mutations in a single locus, but an increasing number of disorders is recognized, in which mutations in two different genes (GJB2/GJB6, TECTA/KCNQ4), or two different mutations in a single allele (GJB2) are involved. This overview focuses on recent advances in the genetic background of nonsyndromic HIH.