**4. Syndromic hearing loss**

In contrast to the nonsyndromic hearing impairment, the syndromic hearing impairment is defined as a part of a syndrome, and it is associated with malformations of the external ear, malformations of other organs or other medical problems. HL is identified in more than 400 different syndromes [29]. The most common type of autosomal dominant syndrome with sensorineural HL is **Waardenburg syndrome** (WS types 1-4; OMIM#193500, #193510, #148820, and #277580), an auditory-pigmentary syndrome caused by pathogenic variants in *PAX*3, *MITF*, *EDNRB*, *EDN*3, or *SOX*10 genes and characterized by the presence of pigmentary anomalies of skin, hair, and eyes. The second most common are **branchiootorenal spectrum disorders** (OMIM#113650, #610896 #602588, #166780), where conductive/sensorineural HL is accompanied by branchial cleft cysts or fistulas, malformations of outer ear, preauricular pits, and renal anomalies resulting from pathogenic variants in *EYA*1, *SIX*1, or *SIX*5. The third most common cause of autosomal dominant syndromic hearing impairment is **neurofibromatosis type 2** (NF2, OMIM#101000), a multiple neoplasia syndrome with HL secondary to the usually bilateral vestibular schwannomas (acoustic neuroma) and other tumors of the central nervous system (meningioma, schwannoma, glioma, or neurofibroma). NF2 is caused by heterozygous pathogenic variants in a gene-encoding neurofibromin-2 (NF2 gene) [30].

The **Stickler syndrome** (STL) is a connective tissue disorder with eye findings (high myopia, vitreoretinal degeneration, retinal detachment, and cataract) being the most constant traits. Other features are sensorineural or conductive HL, midline clefting (cleft palate, bifid uvula), Pierre Robin sequence, flat midface, mild spondyloephiphyseal dysplasia, and early-onset osteoarthritis [31]. Currently, four types of STL syndrome are distinguished autosomal dominant STL1 (OMIM#108300) and STL2 (OMIM# 604841) caused by pathogenic variants in *COL*2*A*1 and *COL*11*A*1, and autosomal recessive STL4 (OMIM#614134) and STL5 (OMIM#614284) due to pathogenic variants in *COL*9*A*1 and *COL*9*A*2 genes, respectively. The **Usher syndrome** (USH) is a combination of HL and visual impairment as a consequence of retinitis pigmentosa. The autosomal recessive condition is classified into three types: USH1 (OMIM#276900) with severe-to-profound deafness and defective vestibular function, USH2 (OMIM#276901) with mild-to-severe hearing impairment and normal vestibular function and USH3 (OMIM#276902) with progressive postlingual HL and vestibular dysfunction. Pathogenic variants in one of six genes (*MYO*7*A*, *USH*1*C*, *CDH*23, *PCDH*15, *USH*1*G*, or *CIB*2) may lead to USH1 [32], in one of three genes (*ADGRV*1, *WHRN*, or *USH*2*A*) to USH2 and in one of two genes (*CLRN*1 or *HARS*) to USH3. The second most common autosomal recessive syndrome with sensorineural HL is the **Pendred syndrome** (PDS, OMIM#274600), characterized by severe-to profound deafness that is congenital or develops in early childhood and euthyroid/hypothyroid goiter that arises in early puberty or adulthood. It is associated with developmental abnormalities of the cochlea (Mondini dysplasia or enlarged vestibular aqueduct) that can be diagnosed by a CT examination of temporal bones. The cause of the PDS is pathogenic variants in the *SLAC*26*A*4 gene encoding an anion transporter named pendrin. The third most common autosomal recessive syndrome with deafness is the **Jervell and Lange-Nielsen syndrome** (JLN), which is marked by congenital profound sensorineural HL and prolongation of the QT interval (corrected QT (QTc) > 440 msec), syncopal episodes due to ventricular arrhythmias and a high risk of sudden death. In patients with JLNS1 (OMIM#220400) pathogenic variants in *KCNQ*1 and in patients with JLNS2 (OMIM#612347) pathogenic variants in *KCNE*1 are found.

Considering the significant contribution of genetic factors to HL and the recent guideline for clinical evaluation and etiologic diagnosis of HL, one may conclude that single-gene testing is justified if a specific genetic etiology of HL is suspected. If there are no specific clinical indications, testing for the DFNB1-related HL should be performed. If the investigations do not provide conclusive results, HL genes may be analyzed by the NGS approaches such as multigene panels, whole exome or whole genome sequencing [16]. All known nonsyndromic deafness loci (locus denotes the position in the genome linked with the disease) are labeled as DFN (DeaFNess) and classified according to the type of inheritance (DFNA: autosomal dominant; DFNB: autosomal recessive; DFNX: X-linked) followed by a number indicating the order of locus discovery. In **Table 1**, some of the most common HL causative loci are gathered. As it was previously stated, HL is a genetically heterogenous disease; nevertheless, there are some common, characteristic features, which may be a valuable asset in the process of dissecting the genetic reason of HL. Examples of pedigrees, characteristic audiometric features, and

Despite quite a large number of genes causative for HL, the first step in the diagnostic approach should be the analysis of the DFNB1 locus, as the testing is inexpensive and fast [28]. Apart from obvious clinical indications, such as IP3 malformation for the *POU*3*F*4 gene

In contrast to the nonsyndromic hearing impairment, the syndromic hearing impairment is defined as a part of a syndrome, and it is associated with malformations of the external ear, malformations of other organs or other medical problems. HL is identified in more than 400 different syndromes [29]. The most common type of autosomal dominant syndrome with sensorineural HL is **Waardenburg syndrome** (WS types 1-4; OMIM#193500, #193510, #148820, and #277580), an auditory-pigmentary syndrome caused by pathogenic variants in *PAX*3, *MITF*, *EDNRB*, *EDN*3, or *SOX*10 genes and characterized by the presence of pigmentary anomalies of skin, hair, and eyes. The second most common are **branchiootorenal spectrum disorders** (OMIM#113650, #610896 #602588, #166780), where conductive/sensorineural HL is accompanied by branchial cleft cysts or fistulas, malformations of outer ear, preauricular pits, and renal anomalies resulting from pathogenic variants in *EYA*1, *SIX*1, or *SIX*5. The third most common cause of autosomal dominant syndromic hearing impairment is **neurofibromatosis type 2** (NF2, OMIM#101000), a multiple neoplasia syndrome with HL secondary to the usually bilateral vestibular schwannomas (acoustic neuroma) and other tumors of the central nervous system (meningioma, schwannoma, glioma, or neurofibroma). NF2 is caused by heterozygous

The **Stickler syndrome** (STL) is a connective tissue disorder with eye findings (high myopia, vitreoretinal degeneration, retinal detachment, and cataract) being the most constant traits. Other features are sensorineural or conductive HL, midline clefting (cleft palate, bifid uvula), Pierre Robin sequence, flat midface, mild spondyloephiphyseal dysplasia, and

analysis, the remaining cases should be rather streamed to wide, multigenic analysis.

additional remarks for some common HL genes are shown in **Table 2**.

pathogenic variants in a gene-encoding neurofibromin-2 (NF2 gene) [30].

**4. Syndromic hearing loss**

36 An Excursus into Hearing Loss

The two following autosomal recessive syndromic forms of HL represent rare metabolic disorders that, however, should not be missed out as their symptoms may resolve by appropriate treatment and dietary modifications. The **Biotinidase deficiency** (BTD, OMIM#253260) is a form of multiple carboxylase deficiency characterized by primarily neurologic (seizures, hypertonia, developmental delay, ataxia) and cutaneous (skin rash, dermatitis, alopecia) features. Patients lose vision and three-fourth of those who become symptomatic have some degree of HL. Laboratory findings show organic aciduria, mild hyperammonemia, and biotinidase deficiency. The BTD begins usually within the two first years of life and results from recessive pathogenic variants in the *BTD* gene. Treatment with biotin resolves neurologic and cutaneous manifestations, while HL and optic atrophy are usually irreversible.

The **Refsum disease** (OMIM#266500) is an inborn error of lipid metabolism with anosmia and early-onset retinitis pigmentosa being two universal findings. Other variable clinical features include neuropathy, ataxia, progressive severe HL, ichthyosis, cardiac, and skeletal (metacarpals/ metatarsals shortening) involvement. Increased serum concentration of phytanic acid establishes the diagnosis. The symptoms present an insidious onset usually during the late first through third decades of life. Causative recessive variants are found in the *PHYH* and *PEX*7 genes. In the medical care, diet modifications aimed at reduction of chlorophyll from the diet (exclusion of green vegetables (phytanic acid), and animal fat (phytol), and plasmapheresis) are used.

Syndromic X-linked HL is represented by the **Alport** (OMIM#301050) and **Mohr-Tranebjaerg** (MTS, OMIM#304700) **syndromes**. The Alport syndrome is characterized by glomerulonephropathy leading to progressive renal failure, varying severity of progressive sensorineural HL (occurs typically after 10 years of age and affects mainly high frequencies), and variable ocular anomalies. In 85% of patients with Alport syndrome, dominant pathogenic variants in the *COL*4*A*5 gene on the X chromosome are found. Approximately 15% of patients develop Alport syndrome due to recessive variants in the *COL*4*A*4 or *COL*4*A*3 genes, cases with autosomal dominant inheritance, have also been occasionally reported.

due to characteristic deterioration of hearing during patient's life. The algorithm is based on the computational analysis of specific audiometric data deposited in the database. Furthermore, the machine-learning method is applied to select and prioritize possibly causative genes for

Genetic Basis of Hearing Loss

39

http://dx.doi.org/10.5772/intechopen.73557

The Pictures of Standard Syndromes and Undiagnosed Malformations (POSSUM) (https:// www.possum.net.au/) is a comprehensive dysmorphology database designed for the diagnosis of multiple malformations, metabolic, teratogenic, chromosomal, and skeletal syndromes as well as their images. This database consists of information on over 4000 different syndromes and searching is based on the selected features and results in a specific list of possible

In almost all genetically related diseases (included hearing impairment), there is a need for tailored diagnostic strategies in searching for their molecular background. The milestone in this research area was the development of the method for the DNA sequencing by Frederick Sanger in 1975 [39]. Whereas the direct sequencing (called also Sanger sequencing—tribute to its inventor) allows to debunk the molecular cause of disease in a limited number of genes, e.g., when HL background analyses were limited to the *GJB*2 gene, there was a significant gap in our knowledge and diagnostic capabilities. This gap has been filled out by introducing NGS technology, also called massive parallel sequencing (MPS) or high-throughput DNA sequencing. The NGS developed over the last decade has revolutionized the genetic research and diagnostic practice, mainly because of reducing costs and time of DNA sequencing. This technology gives a unique opportunity to analyze in one experiment the sequence of more than 1 million base pairs, thus sequencing of the whole genome or thousands of genes simultaneously in a few days has become possible [40]. The most commonly used forms of NGS in searching for pathogenic variants underling HL are whole exome sequencing (WES) and

An undisputable advantage of the WES is the possibility of simultaneous sequencing of the whole coding DNA sequence (protein coding part within all human genes ~20,000) regardless of the disease studied. This makes WES a universal test for almost all known genetic diseases. The multigene panel sequencing is a more economical solution, especially dedicated for the diagnostic purpose. It should be noted that with the panel sequencing, only already known genes associated with a given disease are analyzed. Although the targeted NGS has many advantages, whole-genome sequencing (WGS) is still the state of art approach with its high cost representing a main drawback. The application of high-throughput DNA sequencing methods generates a vast amount of information, which accelerated the discovery of new, causative genes for many diseases. Also in the field of genetically related HL, with the NGS technology, novel genes have been discovered for all modes of inheritance described above. The important, newly discovered genes causative of recessive HL are: *ADCY*1*, BDP*1*, SYNE*4*, ELMOD*3*, CABP*2*, GRXCR*2*, OTOGL, TPRN*, and *TSPEAR*. For dominant HL, the *CEACAM*16, *P*2*RX*2, and *OSBPL*2 genes

**6. Next-generation sequencing technology in dissecting the** 

pathogenic variant screening [36, 37].

**background of hearing loss**

diagnoses [38].

multigene panels.

In the Mohr-Tranebjaerg syndrome, also known as progressive deafness syndrome with blindness, dystonia, fractures and mental deficiency, progressive pre- or postlingual sensorineural deafness occurs in the early childhood and is a presenting symptom. MTS is caused by recessive variants of the *TIMM*8*A* gene.

Mutations in the **mitochondrial genome** can lead to HL that is an isolated feature or part of genetic syndrome, i.e., mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), myoclonic epilepsy with ragged-red fibers (MERFF) or Kearns-Sayre syndrome (KSS), a mitochondrial myopathy, characterized by ptosis, ophthalmoplegia, muscle weakness, cerebellar ataxia, diabetes mellitus, and/or endocrinopathies [33]. Aminoglycoside ototoxicity has been associated with pathogenic variants in *MT-RNR1* [34]. Pathogenic variant m.3243A > G in the *MT-TL1* gene, which is causative of MELAS, was found in patients with diabetes mellitus and HL or HL exclusively [35]. The data raise questions on mitochondrial variant penetrance, tissue specificity, and heteroplasmy level.
