Targeted sequencing identifies novel variants involved in autosomal recessive hereditary hearing loss in Qatari families

Targeted sequencing identifies novel variants involved in autosomal recessive hereditary hearing loss in Qatari families

Mutat Res Fund Mol Mech Mutagen 800–802 (2017) 29–36 Contents lists available at ScienceDirect Mutat Res Fund Mol Mech Mutagen journal homepage: www...

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Mutat Res Fund Mol Mech Mutagen 800–802 (2017) 29–36

Contents lists available at ScienceDirect

Mutat Res Fund Mol Mech Mutagen journal homepage: www.elsevier.com/locate/mut

Targeted sequencing identifies novel variants involved in autosomal recessive hereditary hearing loss in Qatari families

MARK

Moza K. Alkowaria, Diego Vozzib, Shruti Bhagatc, Navaneethakrishnan Krishnamoorthya,d, Anna Morganb,e, Yousra Hayderf, Barathy Logendrac, Nehal Najjarf, Ilaria Gandinb, ⁎ Paolo Gasparinib,e, Ramin Badiic, Giorgia Girottob,e, , Khalid Abdulhadif a

Division of Experimental Genetics, Sidra Medical and Research Centre, Doha, Qatar Medical Genetics, Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”, Trieste, Italy c Molecular Genetics Laboratory, HMC, Doha, Qatar d Heart Science Centre, National Heart and Lung Institute, Imperial College London, United Kingdom e Medical Sciences, Chirurgical and Health Department, University of Trieste, Trieste, Italy f Audiology and Balance Unit, HMC, Doha, Qatar b

A B S T R A C T Hereditary hearing loss is characterized by a very high genetic heterogeneity. In the Qatari population the role of GJB2, the worldwide HHL major player, seems to be quite limited compared to Caucasian populations. In this study we analysed 18 Qatari families affected by non-syndromic hearing loss using a targeted sequencing approach that allowed us to analyse 81 genes simultaneously. Thanks to this approach, 50% of these families (9 out of 18) resulted positive for the presence of likely causative alleles in 6 different genes: CDH23, MYO6, GJB6, OTOF, TMC1 and OTOA. In particular, 4 novel alleles were detected while the remaining ones were already described to be associated to HHL in other ethnic groups. Molecular modelling has been used to further investigate the role of novel alleles identified in CDH23 and TMC1 genes demonstrating their crucial role in Ca2+ binding and therefore possible functional role in proteins. Present study showed that an accurate molecular diagnosis based on next generation sequencing technologies might largely improve molecular diagnostics outcome leading to benefits for both genetic counseling and definition of recurrence risk.

1. Introduction Hearing loss (HL) is a remarkably complex and heterogeneous disease presenting with various phenotypes as a result of both genetic and environmental factors. Approximately 70% of cases affected by hereditary hearing loss (HHL) can be classified as non-syndromic hearing loss (NSHL) (i.e. with the absence of abnormalities in other organs), whereas the remaining 30% are classified as syndromic [1]. The vast majority of NSHL cases (70–80%) are transmitted as autosomal recessive traits (ARNSHL) with 64 known genes. The remaining 15–20% show an autosomal dominant pattern of inheritance (ADNSHL, 36 known genes) while a small proportion is X-linked (4 known genes) or mitochondrial (8 known mutations) (Hereditary Hearing Loss Homepage; http://hereditaryhearingloss.org/). Neonates belonging to inbred populations, such as the Qatari one, might have a higher risk of developing ARNSHL [2] and other autosomal recessive diseases as well [3]. Through the Qatar’s national

program aimed to hearing loss early detection, the 5.2% of newborns have been diagnosed as affected by hearing impairment and 60.5% of them are born from consanguineous mating [4]. Previous studies have shown that mutations in GJB2 are the leading cause of HHL in the Caucasian population [5] however within the Qatari population GJB2 seems to play a less relevant role [6]. In this light, there is the strong need to investigate several Qatari families to look for new causative alleles/genes such as BDP1 gene, recently identified in a consanguineous family [7]. Given the high genetic heterogeneity of HHL, high throughput approaches such as next generation sequencing (NGS) are the most appropriate and reliable tools to dissect the complexity of HHL [8,9]. In this light, here we report the data, obtained from a series of Qatari families affected by HHL and analysed by targeted re-sequencing for the presence of possible causative mutations in 81 different HHL genes.

⁎ Corresponding author at: Medical Sciences, Chirurgical and Health Department, University of Trieste/Medical Genetics, Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”, Trieste, Italy. E-mail address: [email protected] (G. Girotto).

http://dx.doi.org/10.1016/j.mrfmmm.2017.05.001 Received 16 February 2017; Received in revised form 11 April 2017; Accepted 3 May 2017 Available online 04 May 2017 0027-5107/ © 2017 Elsevier B.V. All rights reserved.

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2. Materials and methods

nucleotide substitutions and variants with minor allele frequencies (MAF) > 0.03. In particular, the following databases were used: NCBI dbSNP build142 (http://www.ncbi.nlm.nih.gov/SNP/), 1000 Genomes Project (http://www.1000genomes.org/), NHLBI Exome Sequencing Project (ESP) Exome Variant Server (http://evs.gs.washington.edu/ EVS/), ExAC browser (http://exac.broadinstitute.org/). The pathogenicity of known variants was evaluated using ClinVar (http://www.ncbi. nlm.nih.gov/clinvar/), Deafness Variation Database (http:// deafnessvariationdatabase.org/) and The Human Gene Mutation Database (http://www.hgmd.cf.ac.uk/ac/index.php). For novel variants several in silico tools, such as PolyPhen-2 [10], SIFT [11], MutationTaster [12], PhyloP [13], GERP++ [14] and CADD score [15] were used, in order to consider both the effects on protein structure and the conservation of the affected residues. A schematic representation of the analytical workflow is reported in Supplementary Fig. S1. The Coverage Analysis Report, a collection of summary statistics and graphical representations of the reads coverage available for the Ion Torrent Suite™ (Life Technologies, USA), was used for the identification of any inconsistencies, including coverage falls due to the presence of homozygous deletions. On a patient-by-patient base, the candidate variants were discussed in the context of phenotypic data at weekly interdisciplinary meetings by a team of experts including clinicians, scientists, geneticists, genetic counselors, and bioinformaticians. Finally, Sanger sequencing analysis to confirm the mutations and to check the segregation was carried out.

2.1. Ethical statement Eighteen families were recruited for this study. A written informed consent was obtained from all participants; in case of minors, their next of kin provided written informed consent. The study was approved either by the Institutional Review Board of Hamad Medical Corporation, Doha, Qatar and the Institutional Review Board of IRCCS Burlo Garofolo, Trieste, Italy. 2.2. Patients: clinical evaluation and sample collection Subjects affected by sensorineural NSHL were recruited at the ENT Department, Hamad Medical Corporation (HMC), Doha, Qatar. A total of 18 families (80 individuals including 27 probands) were enrolled in the study. Probands’ age was ranging from 1 to 13 years, 14 of them were males and 13 were females. An accurate anamnestic history (clinical and instrumental) was collected for all of them. A complete medical evaluation was performed on each family to exclude hearing loss due to infections, trauma, or other non-genetic causes. The presence of a syndromic deafness was also excluded. All participants underwent pure tone audiometric testing (PTA) or auditory brainstem response (ABR) (depending on the probands’ age) in order to characterise the severity of HL according to the following guidelines [1]:

• Slight: 16-25 dB (dB) • Mild: 26–40 dB • Moderate: 41–55 dB • Moderately severe: 56–70 dB • Severe: 71–90 dB • Profound: 91 dB or more

2.5. Molecular modelling and structural analysis The most frequent mutations detected in our families were further investigated at protein level. Briefly, the structural consequences of the missense mutations in CDH23 and TMC1 were analysed by molecular modelling (CDH23 UniProt: Q9H251 and TMC1 UniProt: Q8TDI8 respectively). In both cases, for CDH23 (cadherin domains 20–21) and TMC1 (residues 402–652) there were no 3D structures available. Thus, for CDH23, the crystal structure of mouse N-cadherin ectodomain protein (PDB ID: 3Q2W) [16] sharing 42% similarity with human CDH23 was used, while, for TMC1, the crystal structure of a calcium (Ca 2 + ) channel protein (PDB ID: 4WIS) from the fungus (Nectria haematococca) [17], that shares 26% similarity with human TMC1, was considered. The quality of the models was evaluated as previously described [18], showing that structures were biologically reliable. The constructed wild type structures were used for building mutational models (p.P2205L in CDH23 and p.R445H & p.L603H in TMC1) in the discovery studio (Accelrys Inc., San Diego, CA, USA) as previously described [19] and to identify functional (Ca2+ binding) sites and the key residues involved. Pymol was used to visualize the proteins and to prepare model representations (www.pymol.org).

All probands were completely negative for mutations in both GJB2 and MTRNR1 genes. Blood samples were taken from 77 participants, while saliva samples from the remaining ones. Genomic DNA was extracted using Promega Maxwell® 16 Blood DNA purification kit and Norgen Biotek’s Saliva DNA Collection Preservation and Isolation Kit, from whole blood and saliva respectively. Quality and quantity of DNA was checked using NanoDrop 1000 spectrophotometer and Qubit 2.0 Fluorometer respectively. At least 3 individuals (both affected and unaffected) from each family were sequenced and included in the genetic co-segregation analysis. 2.3. Hereditary hearing loss panel A panel of 81 genes was designed using the Ion AmpliSeq™ Designer v1.2 (Life Technologies, CA, USA). The genes were selected on the basis of the most updated literature survey and the most comprehensive HHL databases such as Deafness Variation Database (http://deafnessvariationdatabase.org/) and Hereditary Hearing Loss Database (http:// hereditaryhearingloss.org/). The sequencing panel includes 25 known ARNSHL genes, 18 known ADNSHL genes, 6 genes for both ARNSHL and ADNSHL and 1 gene known to cause X-linked NSHL. The remaining 31 genes are known to be involved in hearing function or to be expressed in mouse inner ear. A complete list of genes is provided in Supplementary Table S1. Targeted regions include coding regions (CCDS) plus 50 bp flanking exons of each gene. The overall coverage is approximately 95% accounting for 317 kb.

3. Results On average 95.48% of the targeted region was covered by sequencing data at least 20-folds, while 270-folds mean-depth total coverage was reached. An overall amount of 763 genetic variations was identified (i.e. 170 synonymous, 178 non-synonymous, 43 frameshift/ 3 non-frameshift INDELs and the remaining ones intronic and within UTRs). After the filtering process, six point mutations in 5 HHL genes (CDH23, MYO6, GJB6, OTOF, TMC1) and a large deletion in OTOA were identified thus characterizing 50% of families investigated (9 out of 18) (Table 1). As expected, being consanguineous families, the possible causative variants were found at the homozygous state while healthy relatives were WT or heterozygous. Clinical and instrumental details of patients carrying these alleles and belonging to the 9 families characterized are reported in Supplementary Table S2.

2.4. Targeted Re-Sequencing (TRS) and data analysis Sequencing was performed using the Ion Torrent™ platform (Life Technologies, USA) and libraries prepared as described in Supplementary S1. Among all the identified genetic variants, we filtered out those with quality score (QUAL) < 30, synonymous 30

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Table 1 List of mutations identified in the analyzed families. ID

Locus

Gene

cDNA change

aa change

Frequency ExAC

1000g

GERP++

PhyloP

Poly phen-2

SIFT

MT

CADD

REF

PHEN

1

DFNB12

CDH23 (NM_022124)

c.6614C > T

p.P2205L

NA

NA

5.06

7.786

0.999

0.06

1

26.7

NA

S/P

9 22 23 4

DFNB1B DFNB37

GJB6 (NM_006783) MYO6 (NM_001300899) OTOF (NM_194248) TMC1 (NM_138691)

c.209C > T c.178G > C

p.P70L p.E60Q

0.00001651 0.00006059

NA NA

5.38 5.92

9.807 9.444

1 0.994

0 0.01

1 1

21.6 32

NA NA

S/P S/P

c.2239G > T c.1334G > A

p.E747X p.R445H

NA 0.00000823

NA NA

4.83 5.93

7.637 9.789

. 0.998

0.91 0

1 1

43 32

[39] [42,44]

S P

c.1808T > A Deletion chr16:21,689,51421,747,721

p.L603H

NA

NA

5.72

6.263

1

0

0.988

27

NA [45]

S

28 12 13 15

DFNB9 DFNB7/ DFNB11 DFNB22

OTOA (NM_144672)

ID: family ID; aa change: amino acid change; Frequency: frequency of ExAC and 1000 g databases is reported for each mutation. Predictor tools: GERP++ (higher number is more conserved, > 0 is generally conserved), PhyloP (Pathogenicity score: conserved > 0.95, not conserved < 0.95), Polyphen-2 (Pathogenicity score: probably damaging > 0.85, possibly damaging 0.85-0.15, benign < 0.15), SIFT (Pathogenicity score: closer to 0 is more damaging), MT: MutationTaster (Pathogenicity score: closer to 1 is more likely to be damaging), CADD (Pathogenicity score: > 10 predicted to be deleterious), REF: References; PHEN: Phenotypes (S/P: severe to profound, S: severe) NA: not available.

haplotype thus supporting the presence of a common ancestor or of a founder effect. Patients carrying this allele showed pre-lingual bilateral severe to profound sensorineural hearing loss. ABR test of patient, II:2, from Family 1 showed no response up to 90nHL in both ears by click and tone burst in all frequencies. As regards the proband, II:5, of Family 22, ABR click showed no response up to 90 ndBHL in both ears while the tone burst traced wave V at 90 dBnHL. Finally, in Family 9, ABR click testing on patient, II:2, displayed wave V at 50 dBnHL in both ear while Otoacoustic Emissions (OAEs) showed positive response at 500 Hz to 2 KHz in the left ear while it was absent in the right ear. On the other hand, ABR test on twins, II:4 and II:5, indicated no response until

3.1. CDH23 So far, several CDH23 mutations have been described as causative of ARNSHL [20–23]. Here, we identified a new CDH23 homozygous missense mutation, c.6614C > T; p.P2205L (NM_022124) in three families (Families 1,9 and 22) (Table 1) (Figs. 1 and 2). This allele was never described as associated with hearing phenotype nor it is present in ExAC database (http://exac.broadinstitute.org/). It involves a highly evolutionary conserved amino acid and it is predicted to be pathogenic by several in silico tools (see Table 1). Interestingly, the analysis of haplotypes (defined using 18 SNPs spanning 70 kb of sequence flanking the p.P2205L mutation) revealed that all the patients carry the same

Fig. 1. Pedigrees of HHL Qatari families included in the study.

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Fig. 2. Sanger sequencing electropherograms showing nucleotide variants identified in CDH23, GJB6, MYO6 and TMC1 genes.

heterozygous state in the ExAC South Asian and African population database in one individual out of 60.706 (Table 1). Pure tone audiometry showed severe to profound hearing loss in both patients (Supplementary Fig. S2A).

90 dBnHL and the tympanometry test showed bilateral type A. Since this allele characterizes a significant number of Qatari families in our cohort (∼17%), we further investigated its role by analysing the impact on the protein structure through molecular modelling. The 3D protein model of CHD23 domains 20 and 21 (Fig. 4) demonstrated that p.P2205 is located next to the functional site of Ca2+ binding. This site is highly packed with five negatively charged residues (four aspartic acids (D) and a glutamic acid (E)) and it is also present in between these domains (20 and 21) (Fig. 4B). Significantly, p.P2205 is positioned at the same structural loop where the P2202 is located and it is directly involved in the formation of the functional site. Thus, our CHD23 modelling provides further evidence that the previously reported mutational position p.D2202 (p.D2202N) [24] is directly involved in the Ca2+ binding (Fig. 4B). As regards p.P2205L mutation, the change of the side chain from a cyclic p.P2205 to a linear p.L2205 on the loop region makes potential structural interference (Fig. 4C). These results suggest that the location of p.P2205 can play a key role in the organization of the structural domains and the function of CDH23.

3.4. OTOF Mutations in OTOF have been associated with autosomal recessive (DFNB89) hearing loss [35] in several populations coming from Lebanon, Middle East and Europe [36–39]. In Family 28 (Fig. 1) we identified a nonsense mutation c.2239G > T (NM_194322), predicted to be pathogenic, and leading to an early truncated Otoferlin protein (p.E747X) (Table 1). This variant has been already described as causative of NSHL in a patient of Arabic origin (i.e. coming from Libya), showing prelingual profound NSHL [39]. Our patient, II:2, showed early onset bilateral severe sensorineural hearing loss. OAEs indicated a “refer” response (negative) on both ears, tympanometry test showed bilateral type B pattern while ABR showed no wave traced to 80–90 dBnHL by click and tone burst in all frequencies (Supplementary Table S2).

3.2. GJB6 Mutations in GJB6 are associated with autosomal dominant (DFNA3B) and recessive (DFNB1B) HHL. So far, several mutations (including large deletions) have been described in patients from Syria, France, Spain, Israel, United Kingdom and Italy [25–29]. In Family 23 (Fig. 1) we identified a homozygous missense mutation c.209C > T (NM_006783) leading to the amino acid substitution p.P70L in a highly conserved region of the protein (Table 1, Fig. 2). The variant, predicted to be damaging, was never associated to the hearing phenotype but it is present at a very low frequency (0.00001651) in the ExAC South Asian and African population database. The proband (II:1) was diagnosed with early onset bilateral profound sensorineural hearing loss without any family history. ABR showed no wave traced till 90dBnHL by click stimuli and Tone Burst in both ear, Tympanogram showed type A, while X-ray CT scan showed congenital bilateral common cavity malformation.

3.5. TMC1 To date, different mutations in TMC1 have been associated with both autosomal dominant (DFNA36) and recessive (DFNB7/11) forms of hearing loss [40,41] in patients from Turkey, Pakistan and China [41–43]. Here, we describe two missense mutations in TMC1 gene in Families 12 and 13 (Fig. 1). In Family 13, the affected child, II:1, showing an early onset profound sensorineural hearing loss, carries a novel missense mutation c.1808T > A (NM_138691) (Table 1 and Fig. 2). The mutation, predicted as damaging by several in silico tools, leads to the substitution p.L603H. This residue is located in the protein cytoplasmic domain and it is highly conserved across species (Table 1). ABR and AOE showed no response up to 80dbHL. Patients from Family 12, II:1 and II:2, diagnosed with pre-lingual profound sensorineural hearing loss, carry the missense mutation c.1334G > A (NM_138691) (Table 1) previously reported as damaging in Turkish and Pakistani HHL families [42,44]. Taking into consideration the potential role of TMC1 in the Qatari population (i.e. mutated twice in our cohort), we further investigated the pathogenic effect of the two alleles by molecular modelling. The modelled segment of TMC1 (residues 402–652) provided structural details of the calcium channel, Ca2+ binding site and positions of the mutations (p.R445 and p.L603) that are on both the sides of the Ca2+ binding site (Fig. 5). This functional site contains amino acids with polar (S, N and Q) and hydrophobic (A and I) side chains (Fig. 5B). The structural positions and the side chains of the mutations p.R445H and p.L603H are adjacent to the residues p.S608, p.N576 and p.A579 of the

3.3. MYO6 Mutations in MYO6 have been associated with autosomal dominant (DFNA22) and recessive (DFNB37) hearing loss [30,31] and, to date, different mutations have been described in several European and Asiatic populations [32–34]. A homozygous missense mutation c.178G > C (NM_001300899) leading to the amino acid substitution p.E60Q (Table 1, Fig. 2) was detected in the two affected siblings, II:1 and II:2, from Family 4 (Fig. 1). This residue is located within a highly conserved region of the Myosin VI protein. The variant, predicted to be damaging, was never associated so far to the hearing phenotype and, it is present only at the 32

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Fig. 3. Coverage Overview for the 3 siblings of family 15 extracted from the Ion Torrent Suite™ Coverage Analysis Report. X-axis: the genomic regions ordered by position; Y-axis: the base coverage expressed in the log10 scale. Chromosome 16: a clear fall in the coverage (red shape) that corresponds to a homozygous deletion is highlighted.

mutations were reported in HHL families of Middle Eastern populations (Jewish-Algerian, Palestinian, Turkish, Iranian and Pakistani [22,24,46–48]. The mutation here described (p.P2205) is located within the same protein domain of p.D2202N, a previously described allele [22,24]. Results from protein modelling analysis revealed a strong relationship between p.D2202 and p.P2205. As a matter of facts, they both share the same structural loop directly involved in the formation of the functional Ca2+ binding site. In the case of the mutation here described, the change from a Proline (cyclic structured side chain) to a Leucine (linear structured side chain) affects the loop structure and the negatively charged Ca2+ binding site, and therefore the regular function of the protein itself (Fig. 4). Interestingly, all patients carry the same haplotype suggesting the presence of a common ancestor or of a founder effect. As regards to TMC1, characterizing two families in our cohort (i.e. 11%), approximately 50 mutations have been already described in this gene. Here, we showed a novel variant (p.L603H) located in a highly conserved protein region as well as a mutation previously described (p.R445H) in Turkey [42], Pakistani [44] and Chinese [49] families. In both cases, protein modelling supported the pathogenic role of these alleles through a structural destabilization affecting the nearby Ca2+ binding residues and thus leading to malfunction of TMC1. Interestingly, a missense variant located very close to p.L603 (i.e. p.R604G) was recently classified as pathogenic after a 3D modelling approach [50] (Fig. 5). As regards to the other genes, we detected the first GJB6 allele in the Qatari population and in a broader sense in the Arabic peninsula and Gulf region. This allele, is located in the highly conserved CNX domain that, most likely, should play an essential role for the protein structure itself. Regarding MYO6 gene, the missense mutation identified is located in a known ATPase domain named MYSc in which other pathogenic mutations have been already described [51].

binding site (Fig. 5C). The mutations replace the linear residues R and L with ring structured H. This arrangement indicates the importance of the mutational spots p.R445 and p.L603 in maintaining the structure and regular functionality of the protein. 3.6. Otoa As regards to OTOA, Shahin H et al. identified a large deletion encompassing most of the OTOA genomic region (chr16: 21,678,51421,760,729) in a Palestinian family affected by NSHL [45]. Very interestingly, all the affected siblings of Family 15 (Fig. 1) carry a similar large homozygous deletion spanning at least 58.016 bp (from chr16: 21,689,514 to 21,747,721) which partially overlaps with that previously described [45] (Fig. 3). In our patients the hearing phenotype is characterized by the presence of a moderate hearing loss as shown by pure tone audiometry (Supplementary Fig. S2B). 4. Discussion In this study, we report the molecular characterization of 18 Qatari families affected by NSHL and negative for the presence of mutations in GJB2, the major worldwide player. These families are highly valuable for the identification of recessive genes involved in hearing impairment since they belong to an inbreed population. Moreover, the limited pathogenic role of GJB2 gene in the Qatari population [4] makes these families even more precious to define the whole molecular epidemiology picture of NSHL in Qatar, and more broadly in the Gulf area. Using our TRS panel, we characterized 50% of the families under investigation identifying both novel and known causative alleles in the following genes: CDH23, GJB6, MYO6, OTOF, TMC1 and OTOA. Interestingly, CDH23 and TMC1 genes showed a higher prevalence of mutated alleles being involved in three and two families respectively. As regards CDH23, affecting ∼17% of our families, 14 missense 33

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Fig. 4. Molecular models of CDH23. (A) Schematic diagram of CDH23: the red arrow indicates the mutational region. 3D model structures are given for P2205 (B) and P2205L (C). Functional site residues are highlighted in orange sticks around the Ca2+ which is represented as a grey sphere.

\deletions (Table 2), some of them being novel while others previously described. In particular, 14 families (13% of the cohort) carry mutations in GJB2 while 3 families carry the same CDH23 mutation. Four different mutations (28% of the total) have been detected in GJB2, being so far the gene with the highest allele heterogeneity in our Qatari cohort. Additional studies and the use of whole exome sequencing technology in the negative families would be useful to discover novel NSHL Qatari genes and to draw a complete molecular epidemiology picture. In conclusion, in this study, we confirmed the usefulness of the NGS technology to screen families that have been waiting many years to get a precise molecular diagnosis and to define the molecular picture of the prevalence and frequency of HHL genes in the Qatari population. Furthermore, an effective molecular diagnosis is a real benefit for genetic counseling, for the definition of the recurrence risk, prognosis

A nonsense mutation was also identified in OTOF gene. The same allele was already described in a patient from Libya showing a very similar clinical phenotype detected in our family [39]. It could be interesting to check if these two cases share any common haplotype. Being a known homozygous nonsense mutation, leading to the loss of more than half of the protein, it will heavily damage the protein folding and function. Finally, we detected a deletion in OTOA gene, similar to that reported by Shahin H et al. [45] in a family from Palestine. Most likely, the presence of such deletion, which involves most of the gene, should be further investigated in different Arabic populations to define its final molecular epidemiology picture. During the last decade we have analysed 108 Qatari HHL families publishing the corresponding results [6–8]. Pooling the data together, 26 ARNSHL cases can be explained by likely causative mutations

Fig. 5. Molecular models of TMC1. (A) Schematic representation of TMC1: the red arrows show the location of the mutations, with molecular models of wild type (B) and mutant (C). Functional site residues are in orange sticks around the Ca2+ that is represented as a grey sphere.

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Table 2 Whole list of mutations detected in our cohort of Qatari families since 2012. Gene

Locus

N°families

c.DNA changes

aa changes

References

GJB2(NM_004004)

DFNB1A

DFNB1B DFNB77 DFNB7/DFNB11

OTOF(NM_194322) MYO15A(NM_016239) MYO6(NM_001300899) BDP1(NM_018429) CDH23(NM_022124) OTOA(NM_144672)

DFNB9 DFNB3 DFNB37

c.G506A c.35delG c.T299C c.IVSI + 1G > A c.C209T c.G1588T c.G1334A c.T1808A c.G2239T c.453_455delCGAinsTGGACGCCTGGTCGGGCAGTGG c.G178C c.T7873G c.C6614T Deletion chr16:21,689,514-21,747,721

p.C169Y Frameshift mutation p.W77R Splice site mutation p.P70L p.E530X p.R445H p.L603H p.E747X p.E152GfsX81 p.E60Q p.*2625Eext*11 p.P2205L

[6]

GJB6(NM_006783) LOXHD1 (NM_144612) TMC1(NM_138691)

6 3 1 4 1 1 1 1 1 1 1 1 3 1

DFNB12 DFNB22

and eventually therapeutic options. [12]

Acknowledgement [13]

We gratefully acknowledge the Qatar National Research Fund for sponsoring this study through a grant from the National Priorities Research Program (NPRP No.: 7-583-3-156).

[14]

[15]

Appendix A. Supplementary data [16]

Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.mrfmmm.2017.05.001. [17]

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