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3 Genetics of Hearing Loss
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
dierent between individuals within the same family. Autosomal
dominant conditions may also demonstrate reduced or incom­plete penetrance, where not every individual with a known pathogenic variant in the hearing loss gene manifests hearing loss. An autosomal dominant hearing loss phenotype tends to be late-onset and less severe than most recessive forms of hearing loss, and it may be progressive.
Common autosomal dominant hearing loss syndromes include branchio-oto-renal (BOR), Waardenburg, and Treacher Collins syndromes.
Pearl
The presentation of autosomal dominant hearing loss is quite variable but is typically late-onset and progressive, in contrast
a
b
X-Linked Inheritance
Father
Carrier Mother
to recessive hearing loss, which tends to be more severe and is more likely to have a congenital or prelingual presentation.
X-Linked Inheritance
Hearing loss may also be transmitted as an X-linked condition, indicating that the pathogenic variant is in a gene on the X chromosome. Boys are more likely to have hearing loss with this mode of inheritance than girls are, as they have only one X chro­mosome, and thus only one variant of these genes instead of two, as illustrated in Fig. 3.2c. If a woman has a pathogenic variant
on one of her X chromosomes, she will either have unaected
hearing or have a milder form of hearing loss than a man with the same variant. X-linked inheritance is characterized by a lack of male-to-male transmission.
Sons of a woman with a hearing loss variant on her X chromo-
some would have a 50% chance of hearing loss. Daughters of a
woman with a hearing loss variant on one of her X chromosomes would have a 50% chance of being carriers and having some hear­ing loss. All the daughters of a man with X-linked hearing loss will be carriers of the hearing loss gene, as they can inherit only the X chromosome with the pathogenic variant from their father. Alport syndrome is an example of a well-known X-linked disorder that
primarily aects men, yet aected women are common.
Mitochondrial Inheritance
The chromosomes in the nucleus are not the only location of DNA in a human cell. Mitochondria, organelles of the cell important for energy metabolism, have a small genome that consists of a small
Son
(25%)
c
Fig. 3.2 Inheritance patterns. (a) Autosomal recessive inheritance.
Unaected carrier parents have a 25% chance, in each pregnancy, to
have a child with hearing loss. (b) Autosomal dominant inheritance.
One aected parent with a 50% chance, in each pregnancy, to have a
child with hearing loss. (c) X-linked inheritance. Carrier mother has a 50% chance, in each pregnancy, to pass the pathogenic variant. There is a 25% chance in each pregnancy of a son with hearing loss. (Adapted from www.jnetics.org.)
Affected son
(25%)
Daughter
(25%)
Carrier daughter
(25%)
circular DNA approximately 16,000 base pairs in size containing a
small number of genes. Mitochondrial DNA (mtDNA) is inherited
from the mother, as it can be passed to ospring only through the egg cell; sperm contribute no mitochondria to ospring. The pedigree may show many aected siblings, and possibly variable expression, as the mother may be more mildly aected or unaected.
Sequence variants in mtDNA are associated with both nonsyn­dromic and syndromic hearing loss. Hearing loss occurs in over half of those with syndromic mitochondrial disorders, such as mito­chondrial encephalopathy, lactic acidosis, and stroke (MELAS).12 The
31
I Hearing Loss: Essential Information
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
m.1555A>G variant (that is, replacement of the base adenine with guanine at position 1,555 on the mitochondrial genome) is asso­ciated with aminoglycoside antibiotic exposure–induced hearing
loss as well as congenital hearing loss.13 Hearing loss phenotypes associated with nonsyndromic mitochondrial inheritance are most often moderate to profound in degree, and onset of mitochondrial hearing loss may be in childhood or later.14 When the hearing loss is triggered by administration of aminoglycosides, bilateral severe to profound hearing loss occurs within days.
15
Mosaicism
A person’s genetic makeup is typically the same in all of the cells of his or her body. In cases of mosaicism, genetic variants are present in some cells of the body, and not in others. A case report described by Schimmenti et al16 illustrates mosaicism in a child with profound hearing loss and a single hearing loss variant in GJB2. The parent was tested and did not have the allele in her blood. Subsequently, the parent was counseled that the hearing loss was likely recessive. The parent had a second child with a
di erent partner, and the second child also had hearing loss.
Tissue from a cheek swab revealed that the parent was mosaic for a single dominant allele in GJB2. Although the parent did not have hearing loss, she did have hyperkeratosis of the dorsal surfaces of her hands and feet.
3.6 Nonsyndromic Forms of
Genetic Hearing Loss
Nonsyndromic causes of hearing loss account for 70% of genetic
hearing loss (Fig. 3.1). In populations around the world, variants in
GJB2 account for 50% of cases with nonsyndromic recessive hearing
loss. Nonsyndromic dominant hearing loss accounts for approxi-
mately 20% of inherited nonsyndromic hearing loss.17 An overlap
exists in some genes that show both dominant and recessive inheritance patterns (Fig. 3.3). For example, most GJB2 variants are associated with recessive hearing loss, but some show dominant inheritance patterns.18 Further information about individual genes can be found at the Hereditary Hearing Loss Homepage19 and the Online Mendelian Inheritance in Man (OMIM) site.
20
Pearl
A majority of childhood hearing loss is autosomal recessive and
nonsyndromic, meaning that the child’s parents are una ected
carriers of the variant gene, and the hearing loss exists as an iso­lated condition without the involvement of other systems (e.g.,
una ected vision, normal kidney function).
Autosomal Recessive DFNB
MYO15A SLC26A4 TMIE TMPRSS3
OTOF CDH23 GIPC3 STRC USH1C
OTOG OTOA PCDH15 RDX GRXCR1
TRIOBP CLDN14 MYO3A WHRN
ESRRB ESPN MYO6 HGF ILDR1 ADCY1 CIB2 MARVELD2 BDP1
PJVK SLC22A4 SLC26A5 LRTOMT
DCDC2 LHFPL5 S1PR2 PNPT1 BSND MSRB3 SYNE4 LOXHD1
TPRN GPSM2 PTPRQ OTOGL
TBC1D24 ELMOD3 KARS
SERPINB6 CABP2 NARS2 MET
TSPEAR TMEM132E GRXCR2 EPS8
CLIC5 FAM65B CDC14A EPS8L2
WBP2 ROR1
66 Genes
COL11A2
X-linked DFNX
GJB2 GJB6
MYO7A
TMC1
TECTA
PRPS1
POU3F4
SMPX
COL4A6
AIFM1
Autosomal Dominant DFNA
CRYM DIAPH1 KCNQ4
GJB3 MYH14 CEACAM16
DFNA5 WFS1 COCH
EYA4 POU4F3 MYH9
ACTG1 MYO6 SIX1
SLC17A8 GRHL2 P2RX2
CCDC50 MIRN96 TJP2 TNC DIABLO TBC1D24
OSBPL2 HOMER2
MCM2 KITLG CD164
DMXL2
36 genes
Fig. 3.3 List of nonsyndromic hearing loss genes, arranged by inheritance mode. Based on http:// hereditaryhearingloss.org, accessed July 2017.
32
3 Genetics of Hearing Loss
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
3.6.1 Describing Nonsyndromic Hearing Loss: DFN Loci
As a rule, genes are identified by abbreviations that begin with a
letter and contain one or more letters or numbers, usually refer­ring to the protein they code for or a condition a variant causes. For example, the MYO7A gene codes for the protein myosin VIIa. For genes that have variants that cause hearing loss, there is another possible nomenclature system, where the name begins with the prefix DFN (for deafness), followed by a letter that des­ignates the mode of inheritance and a number to be used as a reference to hearing loss phenotypes associated with the locus.
Genetics professionals may use either system: they may refer to the specific gene to describe what causes the hearing loss or may
use the DFN nomenclature (Table 3.1). Both systems are recorded at the OMIM site.
Table 3.1 DFN nomenclature for hearing loss-related gene locations (loci)
DFN Term Inheritance
DFNA Dominant DFNA11 (autosomal dominant form of
DFNB Recessive DFNB2 (autosomal recessive form of
DFNX X-linked DFNX2 (X-linked form of POU3F4).
MT Mitochondrial MT-RNR1 (mitochondrial 12S ribosomal
20
Example Loci/Phenotypes
Mode
MYO7A). Nonsyndromic postlingual, progressive bilateral sensorineural hearing loss.
MYO7A). Nonsyndromic congenital or childhood-onset bilateral sensorineural hearing loss.
Nonsyndromic conductive hearing loss
with stapes xation.
RNA). Nonsyndromic 1555A>G variant related to aminoglycoside-induced hearing loss.
Pearl
Some genes may be inherited as dominant or recessive alleles (e.g., GJB2). Some genes (MYO7A) may be associated with recessive nonsyndromic hearing loss, dominant nonsyndromic hearing loss, or recessive syndromic hearing loss.
3.6.2 GJB2 (Connexin 26)
The gene GJB2 encodes connexin 26, a gap-junction protein expressed in the cochlea and important for the viability of hair cells and spiral ganglion neurons.21 Initially, GJB2 variants were thought to be associated with profound, congenital hearing loss; however, it is now known that GJB2 is related to many phenotypic variations,22 and hearing loss may escape diagnosis until later in life. Hearing loss due to GJB2 pathogenic variants is exclusively sensorineural, congenital, bilateral, and slowly pro­gressive, ranging from mild to profound in severity. loss due to GJB2 is more common in Asian and Caucasian groups than in other ethnic groups,
accounts for up to 70% of hearing loss–causing variants in many
populations.25 In Asian populations, c.235delC and p.V37I are more common.26 GJB2 variants are rare in Africa.
Rare, dominant GJB2 variants may be present as a syndromic
hearing loss associated with skin findings such as ichthyosis (dry, scaly, or aky skin, a common finding with keratitis-
ichthyosis-deafness [KID] syndrome) or other skin conditions such as hyperkeratosis in Vohwinkel syndrome and Bart-Pumphrey syndrome.
28,29
11, 24
and the single variant of c.35delG
22,27
22,23
Hearing
Special Consideration
Pearl
Detailed audiometric phenotyping should support genotypic information.
Pathogenic variants in the gene MYO7A are associated with Usher syndrome type 1B and profound, congenital sensorineu­ral hearing loss, yet this gene may also cause autosomal dom­inant and autosomal recessive nonsyndromic hearing loss. The g
enetic hearing loss can be described as DFNA11 if the MYO7A pathogenic variant is inherited as a nonsyndromic dominant hearing loss, or as DFNB2 if inherited as a nonsyndromic reces­sive hearing loss.
A complete reference of genetic variations associated with hearing loss phenotypes can be found at the Hereditary Hearing Loss Homepage.
19
For African and Hispanic populations, the genes that cause hearing loss are still not well known. However, this should not preclude genetic evaluation and testing for individuals from these population groups.
3.6.3 Nonsyndromic X-linked
Five known genes are associated with nonsyndromic X-linked hearing loss: PRPS1, POU3F4, COL4A6, SMPX, and AIFM1. The PRPS1 gene encodes an enzyme necessary for metabolism, and both over­activity (also called superactivity) and loss of function have been identified. Overactivity results in hearing loss in addition to neu­rological problems and hyperuricemia. The variant causing loss of function is referred to as DFNX1 (X-linked nonsyndromic deafness) and associated with forms of Charcot-Marie-Tooth (CMT) disease.
The POU3F4 gene regulates the activity of other genes, making its protein a transcription factor. This gene plays a role in the development of the middle and inner ears, with variants causing a mixed or conductive hearing loss.30 The conductive component is
due to congenital fixation of the stapes. Aected individuals are at
33
I Hearing Loss: Essential Information
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
risk for perilymphatic gusher during attempted surgery to repair
the stapes fixation at the oval window; perilymphatic gusher can
lead to total loss of hearing.
The COL4A6 gene encodes one of the subunits of type IV colla­gen found in membranes, which attaches layers of tissues in the body. Hearing loss is sensorineural in nature, with boys exhibiting a greater degree of loss than girls.
The SMPX gene is known to encode a protein responsible for the cytoskeleton of inner hair cells, with variants causing senso­rineural hearing loss. It may be mild and progressive in girls and women, whereas boys exhibit severe hearing loss early in life.
AIFM1, the gene that encodes a protein that plays roles in oxi­dative phosphorylation and programmed cell death, was recently
identified in two families with X-linked auditory neuropathy
and late-onset peripheral sensory neuropathy.33 This variant is designated DFNX5 as well as AUNX1 (for auditory neuropathy, X-linked, 1).
31
32
3.6.4 Nonsyndromic Mitochondrial
The MTRNR1 gene has variants associated with both aminogly­coside-induced hearing loss and nonsyndromic hearing loss. Variants in this gene are associated with sensorineural hearing loss even when there is no documented exposure to aminogly-
cosides. The m.1555 A > G variant in the mitochondrial 12S rRNA
gene (MTRNR1), the most frequently found variant, increases susceptibility to aminoglycoside ototoxicity. Most reports to
date show that the m.1555A>G variant has penetrance close to 100% when patients are exposed to aminoglycosides such as
gentamicin, tobramycin, amikacin, kanamycin, or streptomycin.
In the United States, nonsyndromic, prelingual mitochondrial
deafness is estimated to aect one out of every 20,000 to 40,000
babies.34 In Spain, it is estimated that a single mitochondrial
variant accounts for 15 to 20 percent of cases of nonsyndromic
hearing loss, even in the absence of exposure to aminoglycosides. Preventive measures for those who carry the variant may include avoidance of aminoglycosides and noise exposure, whenever possible.
35
3.7 Syndromic Forms of Genetic
Hearing Loss
Syndromic forms of hearing loss are associated with abnormal-
ities in other body systems, and more than 400 recognizable
patterns have been tied to hearing loss.6 Thirty percent of genetic hearing loss is associated with a syndrome. Additional syndromic causes of hearing loss are included in Table 3.2. Complete references can be found at OMIM,20 the Hereditary Hearing Loss Homepage,19 Genetics Home Reference,36 and the book Hereditary Hearing Loss and Its Syndromes.
37
Usher type 1 consists of profound hearing loss, vestibular
symptoms, and retinitis pigmentosa (RP) beginning in a child’s
first decade of life; Usher type 2 is characterized by congenital, sloping moderate-severe hearing loss and RP in the first to second
decade of life; and Usher type 3 is characterized by progressive hearing loss, variable vestibular symptoms, and variable onset of RP.19 A small percentage of people with Usher syndrome will have only one detectable pathogenic variant.
3.7.2 Pendred Syndrome
Pendred syndrome is an autosomal recessive endocrine disorder associated with variations in the SLC26A4 gene, thyroid goiter, enlarged vestibular aqueduct (EVA) and/or Mondini malforma­tion, possible balance problems, and hearing loss. loss is sensorineural or mixed, often severe to profound, and may be congenital, sudden, or progressive. Pendred syndrome is the most common syndromic hearing loss and accounts for
4 to 10% of all cases of hereditary hearing loss.
with Pendred syndrome typically carry two SLC26A4 variants. If EVA and variants of SLC26A4 exist in the absence of thyroid dys­function, the hearing loss is considered nonsyndromic (DFNB4). Individuals with DFNB4 tend to have one or no pathogenic vari­ants in SLC26A4.
42
39,40
Hearing
34,41
Individuals
Special Consideration
Individuals with unilateral hearing loss and genetic variants in SLC26A4 will typically experience hearing loss progression to the other ear, whereas individuals with Waardenburg syndrome usually do not demonstrate progression to the other ear.
3.7.3 Waardenburg Syndrome
Waardenburg syndrome (WS) can be identified by the clinical features of a white forelock; pale blue eyes, dierent-colored eyes, or two dierent colors in the same eye; wide-spaced eyes;
pigmentary anomalies; gastrointestinal disturbances; and hear­ing loss. There are four distinct types of WS. WS type 1 is char-
acterized by a white forelock or early graying of the hair in 45%
of individuals and by congenital bilateral or unilateral hearing
loss in 60% of cases. Hearing loss does not typically progress with
WS.43 Waardenburg syndrome is an autosomal dominant disor­der and has variable expression of its clinical features within families. A small number of cases may be autosomal recessive or may be due to new variants.
3.7.1 Usher Syndrome
Usher syndrome is the most common cause of concurrent deafness and blindness in adults. There are three types of Usher syndrome, all of which are transmitted via autosomal recessive
inheritance. In the United States, 4.4 per 100,000 individuals are
estimated to have Usher syndrome.
34
38
BOR syndrome is characterized by preauricular pits or tags; malformed or misshapen ears; middle or inner ear anatomical
dierences; defects in kidney structure or function; and hearing
loss, which may be conductive, sensorineural, or mixed. An
estimated 5% of individuals with BOR have profound hearing
loss.44 This autosomal dominant disorder occurs in 1 in 40,000
3.7.4 BOR Syndrome
3 Genetics of Hearing Loss
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
Table 3.2 Syndromes associated with genetic hearing loss
Syndrome Features Inheritance patterns Gene(s)
Alport syndrome Progressive hearing loss, blood in urine, hypertension 80% X-linked
Biotinidase deciency If untreated, seizures, hypotonia, breathing problems, vision
BOR syndrome Preauricular pits or tags, malformed or misshapen ears,
CHARGE syndrome Ocular, ear, and heart defects, delayed growth and
Craniosynostoses (Apert syndrome, Crouzon
syndrome, Pfeier syndrome)
Jervell and Lange-Nielsen syndrome
MELAS syndrome Stroke, cortical blindness, recurrent headaches, seizures,
MERRF syndrome Epilepsy, muscle twitches, muscle weakness, ataxia Mitochondrial MTTK, MTTL1, MTTH, MTTS1,
Neurobromatosis type 2 Vestibular schwannoma on cranial nerve VIII AD NF2 Pendred syndrome Thyroid goiter, EVA and/or Mondini malformation AR SLC26A4 (PDS), FOXI1 Stickler syndrome High myopia, risk of retinal detachment, very exible joints,
Treacher Collins syndrome Craniofacial malformations, malformed ears, small or absent
Usher syndrome Vestibular problems, retinitis pigmentosa AR Type 1: MYO7A, USH1C, CDH23,
Waardenburg syndrome White forelock; pale blue eyes, dierent colored eyes, or
Wolfram (DIDMOAD) syndrome
Abbreviations: AD, autosomal dominant; AR, autosomal recessive; BOR, branchio-oto-renal; CHARGE, coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies; DIDMOAD, diabetes insipidus, diabetes mellitus, optic atrophy, deafness; EVA, enlarged vestibular aqueduct; MELAS, mitochondrial
encephalopathy, lactic acidosis, strokelike episodes; MERRF, myoclonic epilepsy with ragged red bers.
Source: Information retrieved from Genetics Home Reference
loss, ataxia
middle or inner ear anatomic dierences, defects in kidney
structure or function
development, genital abnormalities Premature fusion of skull bones AD FGFR1, FGFR2, FGFR3
Heart arrhythmia, long QT syndrome, fainting spells AR KCNE1, KCNQ1
vomiting
arthritis, cleft palate, attened facial appearance, large
tongue, small lower jaw
ear canals, down-slanting eyes, dental problems, notched lower eyelids, missing eyelashes, and small jaw
two dierent colors in the same eye; wide-spaced eyes;
pigmentary anomalies; gastrointestinal disturbances
Low-frequency, progressive sensorineural hearing loss, diabetes insipidus, diabetes mellitus, optic atrophy
36
and OMIM,20 September 2016.
15% AR 5% AD
AR BTD
AD EYA1, SIX1, SIX5
AD CHD7, SEMA3E
Mitochondrial Most common: c.3243A in MTTL1.
AD COL2A1, COL11A1, COL11A2,
AD Less common: AR
AD Type 1: PAX3
AR WFS1, CISD2
X-linked: COL4A5 AR: COL4A4 AR/AD: COL4A3
Other genes include: MTTQ, MTTH,
MTTK, MTTC, MTTS1, MTND6. MTTS2, MTND1, MTND5, MTTL1
MTTS2, MTTF, MTND5
COL9A1, COL9A2
TCOF1, POLR1D, POLR1C
PCDH15, SANS, CIB2 Type 2: USH2A, GPR98, PDZD7, VLGR1, ADGRV1, WHRN
Type 3: CLRN1, HARS
Type 2: MITF, SNA12, SOX10 Type 3: PAX3 Type 4: EDNRB, EDN3, SOX10
individuals and is associated with the genes EYA1, SIX1, and SIX5.
Approximately 10% of cases of BOR are due to new variants.
45
70% of individuals who meet clinical criteria for CHARGE
syndrome.
48
3.7.5 CHARGE Syndrome
CHARGE syndrome is characterized by features abbreviated in
its name: coloboma (malformation in the eye), heart defects, choanal atresia, retarded growth and development, genital abnormalities, and ear anomalies. This disorder is inherited in an autosomal dominant pattern with an incidence of 1 in 12,000 babies46 and most cases being due to new variants. The hearing
loss associated with CHARGE can be conductive, sensorineural,
or mixed; may vary from mild to profound; and may progress over time. Temporal bone abnormalities are a hallmark of this
condition, specifically semicircular canal hypoplasia/aplasia.47
Pathogenic variants in the gene CHD7 are responsible for over
3.7.6 Jervell and Lange-Nielsen Syndrome and Other Syndromes Related to Cardiac Function
Jervell and Lange-Nielsen is an autosomal recessive disorder
characterized by heart arrhythmia, long QT syndrome, fainting
spells, and profound congenital hearing loss. Approximately one
in every 200,000 individuals in northern Europe is aected by
Jervell and Lange-Nielsen syndrome.
terized by a high risk of sudden death but, if identified early, can
be clinically managed.
49
This syndrome is charac-
35
I Hearing Loss: Essential Information
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
Other forms of genetic hearing loss associated with cardiac abnor­malities include sinoatrial node dysfunction and deafness (SANDD) and 22q11.2 deletion syndrome. SANDD disorder is characterized
by bradycardia (an abnormally low heart rate, less than 60 beats per
minute) and congenital severe to profound sensorineural hearing loss. SANDD is an autosomal recessive disorder, and, in contrast to Jervell and Lange-Nielsen syndrome, QT intervals are not pro­longed.50 The disorder of 22q11.2 deletion syndrome, also known
as DiGeorge syndrome or velocardiofacial syndrome, is related to
a constellation of cardiac and craniofacial abnormalities, including
an autosomal dominant unilateral or bilateral hearing loss in 78%
of individuals.51 Those with 22q11.2 deletion have structural heart disease rather than cardiac rhythm defects.
3.8 Chromosome Disorders
It is estimated that 1% of the general population has a chromo­some abnormality;52 however, very few conditions exist where an entire chromosome is added or deleted. More often, small portions of chromosomes are missing or duplicated.
3.8.1 Down Syndrome
The most common chromosome abnormality associated with hearing loss is Down syndrome. The incidence of Down syn­drome is 1/600 live births, making it the most common chro­mosome condition in humans. Hearing loss is reported in over
80% of children with Down syndrome53 and may be conductive,
mixed, or sensorineural, potentially involving stapes malforma­tions, stenotic ear canals, dysfunctional eustachian tubes, and/or middle ear infections.
For children with Down syndrome who also have hearing loss, one should not assume that Down syndrome is the sole cause of hearing loss. A case has been reported of a child with Down syndrome also having GJB2-related hearing loss.54 The incidence of co-occurring syndromic and nonsyndromic genetic diagnoses may be higher than previously estimated.
3.8.2 Microdeletions
Even submicroscopic regions of chromosomes can encode dozens of genes, and current genetic testing techniques can detect microdeletions through microarray. Microdeletions are char­acterized by dominant inheritance pattern in which one chro­mosome version is deleted and the other chromosome remains intact. The online parent support resource Unique55 can provide information for families regarding previously undescribed disor­ders. Williams syndrome and 22q11.2 deletion are examples of microdeletion disorders with associated hearing loss.
8,51
Features of ANSD include uctuating hearing, diculty listening
in noise, and speech perception abilities that are worse than would be predicted with cochlear hearing loss. The underlying
deficit is likely impaired inner hair cells, inner hair cell ribbon
synapses, or spiral ganglion neurons.
Approximately 40% of ANSD is genetic in origin, with both
syndromic and nonsyndromic findings,57 and inheritance patterns
that include autosomal dominant, autosomal recessive, X-linked, and mitochondrial modes. ANSD in its syndromic form may be seen as a component in degenerative neuropathies such as CMT disease or Friedreich ataxia, and auditory neuropathy may develop after the onset of the peripheral neuropathy. A mitochondrial form of auditory neuropathy has been associated with Leber’s hereditary optic neuropathy.
Nonsyndromic auditory neuropathy is most often autosomal recessive.59 The two genes frequently implicated are OTOF (DFNB9) and DFNB59. The OTOF gene codes for the protein otoferlin, which is known to have an impact on inner hair cell function. Variants in OTOF have been implicated in temperature-sensitive ANSD.60 DFNB59 codes for the protein pejvakin, which is associated with auditory nerve function, with some variants causing the ANSD phenotype,61 although this is controversial. Interestingly, GJB2 variants may also potentially cause ANSD.
The nonsyndromic autosomal dominant auditory neuropathy 1 (AUNA1) locus relates to pathogenic variants in the DIAPH3 gene. The X-linked locus, AUNX1, is characterized by childhood onset of auditory neuropathy and later-onset peripheral sensory neuropa-
thy and was recently identified to be AIFM1.
58
56
62
33
3.10 Genetic Evaluation of
Individuals with Hearing Loss
Only a few years ago, genetic testing for a child with apparently nonsyndromic hearing loss was limited to testing one gene at a time at a cost of nearly US $1,000 per gene. For a condition like hearing loss, where any one of over 100 genes could be the cause of hearing loss, exhaustive genetic testing was prohibitively expensive with limited availability. Combining this with months
of eort to sequence each gene, it could take years before the reason for a child’s hearing loss could be identified, if ever. The
list of individual genes that could be tested was quite short and consisted of sequencing GJB2, deletion detection in GJB6, sequencing SLC26A4, and possibly sequencing M YO7A . Although GJB2 sequence variants and GJB6 deletions account for 25% of sen- sorineural hearing loss in North American populations,24 limiting
testing to this gene identified only a small number of aected children. To overcome this limitation, nearly all confirmed hear­ing loss genes are now sequenced simultaneously through NGS.
3.9 Auditory Neuropathy Spectrum Disorder
Auditory neuropathy spectrum disorder (ANSD) is diagnosed
based on absent or abnormal auditory neural function reected
in the auditory brainstem response, with present cochlear microphonic or outer hair cell responses (otoacoustic emissions).
Special Consideration
Parents may feel guilty if a genetic basis of hearing loss is discov­ered through genetic testing. Audiologists can reassure parents that they are not at fault for the child’s hearing loss, and this message can be supported by the understanding of how genetic traits are inherited and how new traits develop.
36
3 Genetics of Hearing Loss
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
3.10.1 NGS and Sequence Variant
Nomenclature
NGS was developed in the 2000s and was first applied to hearing
loss in 2010 by Richard Smith and colleagues at the University of Iowa.63 NGS has also been called massively parallel sequencing. Sequencing can include the whole genome or subsets of the genome. For a patient with hearing loss, sequencing is targeted to genes that are associated with hearing loss. Hearing loss gene panels are designed to be comprehensive, because it is nearly impossible to determine clinically whether a child has syndromic or nonsyndromic hearing loss just by the audiogram. Furthermore, while most recessive forms of hearing loss present in infancy and most dominant forms present later on, this may not always be true. Thus, it is better to test comprehensively using a panel that includes dominant, recessive, and X-linked genes, given that sometimes inheritance patterns and hearing loss phenotypes may be misleading.
NGS requires a blood draw to obtain nucleated cells from
a whole blood sample. In some less common circumstances, cheek cells, obtained by scraping the inside of the cheek with a
brush, are acceptable. Genomic DNA is isolated and broken into
fragments. The fragments are captured to enrich the DNA for only those fragments that correspond to genes targeted to hearing loss.
The fragments are labeled and are injected into a microuidic cell,
where each fragment is then sequenced multiple times over. In this manner, sequences are accumulated from multiple genes at once and each area of the genome is sequenced many times over to ensure a quality sequence read for each nucleotide.
Bioinformatic approaches are used to map the sequence back to a reference genome, and the sequence is both computationally and manually curated for sequence variants. Sequence variants are then evaluated and given a designator. Furthermore, knowing whether or not a gene causes dominant or recessive hearing loss is taken into consideration as part of the interpretation. For example, if a child has
only one variant in a hearing loss–associated gene that is typically
inherited as a recessive, this variant alone may not be the cause of hearing loss. In addition to small genomic variants, larger variants,
called copy number variants (CNVs), may be identified, where a loss
or gain of a large genomic segment may remove a hearing loss gene.
Support of a clinical geneticist and genetic counselor is almost always needed to assist in interpretation of the sequencing report, much in the way a radiologist is needed to read an X-ray image.
There are three possible outcomes with an NGS result: negative, positive, and variant of uncertain significance (VUS).
64
loss is autosomal recessive, autosomal dominant, X-linked, or mitochondrial in origin.
VUS
VUS means that a change in the DNA sequence of a particular gene was detected, but it is not known whether the change explains the hearing loss. If a VUS is detected, the laboratory may request a blood sample from both parents to help clarify the child’s results and to help determine whether the VUS is benign (normal variant) or pathogenic. It is important that the parents understand that their samples may be needed for complete interpretation of their child’s results. Sometimes, even
after parental testing, a variant may still be classified as being of uncertain significance.
Advantages of NGS
NGS is advantageous because many genes can be sequenced at one time and the process of finding the right gene is accel­erated. NGS is particularly helpful for such conditions as Usher
syndrome, where the diagnosis typically does not become obvi­ous until a child has reached the teenage years65 yet decisions regarding habilitation, especially cochlear implantation, need to be made in infancy.
NGS hearing loss panels typically include between 70 and
120 genes and can be obtained through Clinical Laboratory Improvement Act (CLIA)-certified molecular diagnostic laborato­ries. Laboratory choice can be based on local provider or institu­tional preference, insurance coverage, timeliness, and readability
of reports. Examples of commonly used NGS panels include the OtoGenome Test (performed at Harvard Partners Laboratory for
Molecular Medicine) and the OtoScope Test (performed at the Molecular Otolaryngology and Renal Research Laboratories,
University of Iowa). Additional laboratories oer targeted NGS
tests as well.
Pearl
Genetic testing by targeted NGS has become the standard of care for children with hearing loss. A panel of hearing loss genes (approximately 100) should be tested at one time rather than sequential testing of single genes. Dominant and recessive genes as well as genes for syndromic and nonsyndromic hearing loss should be tested.
Negative
No variants were identified in the genes that were tested/
sequenced. This does not rule out a genetic cause for an indi­vidual’s hearing loss. Additional testing can be considered in the f
uture as new hearing loss genes are discovered and added to
testing panels.
3.10.2 Genetic Testing for Hearing Loss: Standard of Care and Cost-
Eective
Positive
A likely pathogenic or known pathogenic variant is identified.
This gives the individual a genetic or molecular diagnosis and
answers the question of “how did this happen?” Identification
of a pathogenic variant also determines whether the hearing
Genetic evaluation, genetic testing, and genetic counseling are
standard of care for children who are deaf or hard of hearing. The
emerging standard is to perform NGS as a first-line test.2 Studies
are showing that a hearing loss diagnosis can be made, on aver-
age, 41% of the time depending on the populations studied and
37
I Hearing Loss: Essential Information
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
the family structure.66 It has recently been shown that genetic
testing for hearing loss has value and is a cost-eective tool in
providing care for children who are deaf or hard of hearing.
67
3.11 Genetic Counseling for Hearing Loss
At the initial visit, t he genetic counselor will meet with the fa mily to review the family medical history and to construct a three- to four-generation pedig ree, discuss genetic testing options (includ-
ing the benefits and limitations of testing), and obtain informed
consent for testing. After the results return from a child’s testing, the genetic counselor provides interpretation and explanations to the family. This potentially leads to a review of a new diag­nosis, combined with a discussion of inheritance and associated
recurrence chance for future children. If a VUS is identified on
testing, the genetic counselor will coordinate parental testing when necessary. If there is a negative/normal result, a genetic cause for a child’s hearing loss has not been ruled out. Therefore, posttest counseling could include a discussion of further testing in the future as new hearing loss genes are discovered.
Constructing a pedigree is an ecient way to record the family
medical history information and can illustrate a possible mode of inheritance for the hearing loss. When obtaining this information, the genetic counselor will focus on hearing loss history in the family as well as additional history of vision loss, kidney disease, cardiac disease (or sudden death), developmental disabilities, and
birth defects. Once a genetic cause for hearing loss is identified in
a family, the genetic counselor can facilitate testing for relatives who are at risk for hearing loss or for relatives that could be carri­ers of a pathogenic variant.
3.12 Incorporating Genetic Testing as Part of Newborn Hearing Screening Programs
The cost of genetic testing has decreased considerably through
the use of NGS panels, and it is feasible to consider oering
genetic testing following initial referral on a newborn hearing screening rather than later in life.
While newborn hearing screening programs can identify hearing loss caused by a number of genetic variants at birth, if hearing loss is not present at birth or if it presents as a sub-
clinical finding (not detected by newborn hearing screening),
the cause of the hearing loss will continue to be unknown until genetic testing is completed. It is estimated that if a newborn can be screened for sequence variants in GJB2, SLC26A4, and
the mitochondrial allele m.A1555G, in addition to being tested for congenital cytomegalovirus (cCMV), up to 60% of all infants who will be aected by late-onset, prelingual hearing loss can be identified at birth.
34
Special Consideration
Genetic testing is not an attempt to change an individual’s Deaf
identity or self-identication with the Deaf community.
3.13 Future Perspectives and Hope for the Future of Genetic Medicine
To date, there have been a number of ex amples where investigators have taken a gene that is missing or defective in mouse models of human deafness and have restored hearing by reintroducing the gene via inserting a functioning copy of the gene into the inner ear through a viral vector. This technique of replacing a variant gene copy with a functioning copy to restore hearing is called
gene therapy. Present research findings provide hope that in the
future, genetic testing will be used to identify the cause of hearing loss and, thus, enable selection of the precise therapies that may restore hearing in individuals who are deaf or hard of hearing.
Pearl
Ongoing follow-up is needed for individuals with hearing loss as technologies for genetic testing improve and new genomic dis­coveries are made. If, for example, an individual was initially tested only for GJB2 and no pathogenic variation was identied, an audiol­ogist can suggest additional follow-up with genetics professionals to further investigate the etiology of the hearing loss.
3.14 Conclusion
Audiologists are often among the first professionals to discuss
the importance of a genetics referral to a family whose child has a hearing loss, and interprofessional collaboration between audiologists and genetics professionals is key to serving families. As the knowledge surrounding the genetics of hearing loss grows over time, well-informed audiologists will provide the link
between new applications of scientific breakthroughs and the individual who might benefit from such discoveries.
Pitfall
If genetic testing comes back negative, never assume that that there is not a genetic cause behind an individual’s hearing loss. The pathogenic variant associated with hearing loss may not
yet be identied, or multiple gene interactions that are not yet
understood may produce hearing loss.
Discussion Questions
1. What information from the audiology case history can be
used by genetics professionals?
2. What is the recurrence rate for a recessive hearing loss with each birth? What is the recurrence rate for a dominant hear­ing loss with each birth?
3. What other medical evaluations or tests are typically recom-
mended following a hearing loss identication, and how do these
sults help in determining the genetic cause of hearing loss?
re
4. A child has a normal/negative genetic test result. Has this ruled out a genetic cause for the child’s hearing loss?
38
3 Genetics of Hearing Loss
Madell et al., Pediatric Audiology: Diagnosis, Technology, and Management, 3rd Ed. (ISBN 978-1-62623-401-7), copyright © 2019 Thieme Medical Publishers. All rights reserved. Usage subject to terms and conditions of license.
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