Yongchuan Chai

Genetic etiology study of the non-syndromic deafness in Chinese Hans by targeted next-generation sequencing

BackgroundAlthough over 60 non-syndromic deafness genes have been identified to date, the etiologic contribution of most deafness genes remained elusive. In this study, we addressed this issue by targeted next-generation sequencing of a large cohort of non-syndromic deaf probands.MethodsProbands with mutations in commonly screened deafness genes GJB2, SLC26A4 and MT-RNR1 were pre-excluded by Sanger sequencing. The remaining 125 deaf probands proceeded through targeted exon capturing of 79 known deafness genes and Illumina HiSeq2000 sequencing.ResultsBi-allelic mutations in 15 less commonly screened deafness genes were identified in 28 deaf probands, with mutations in MYO15A, GPR98, TMC1, USH2A and PCDH15 being relatively more frequent (≥3 probands each). Dominant mutations in MYO6, TECTA, POU4F3 and COCH were identified in 4 deaf families. A mitochondrial MTTS1 mutation was identified in one maternally inherited deaf family. No pathogenic mutations were identified in three dominant deaf families and two consanguineous families.ConclusionsMutations in the less commonly screened deafness genes were heterogeneous and contributed to a significant percentage (17.4%) of causes for non-syndromic deafness. Targeted next-generation sequencing provided a comprehensive and efficient diagnosis for known deafness genes. Complementary to linkage analysis or whole-exome sequencing of deaf families, pre-exclusion of known deafness genes by this strategy may facilitate the discovery of novel deafness genes.

Screening for delayed-onset hearing loss in preschool children who previously passed the newborn hearing screening

OBJECTIVE The goal of this study was to investigate the prevalence of delayed-onset hearing loss in preschool children who previously passed newborn hearing screening in Shanghai, China. METHODS Between October 2009 and September 2010, 21,427 preschool children were enrolled from five areas of Shanghai, who had passed newborn hearing screening. Children were screened for delayed-onset hearing loss with pediatric audiometers. Children with positive results in initial and re-screening tests were assessed audiologically and for risk indicators according to the Year 2007 Statement of the American Joint Committee on Infant Hearing (JCIH). RESULTS During the study period, 445 children (2.08%) were referred for audiologic assessment; 16 (0.75/1000, 95% CI 0.38-1.12) had permanent delayed-onset hearing loss. Of these, five (0.23/1000) had bilateral moderate hearing loss; seven (0.33/1000) had mild bilateral hearing loss; and four (0.19/1000) had unilateral moderate or mild hearing loss. JCIH risk indicators were established for six children (6/16, 37.5%), including parental concern regarding speech and language developmental delay, neonatal intensive care unit with assisted ventilation or hyperbilirubinemia, recurrent otitis media with effusion, craniofacial malformation, and family history (n=1 for each). The remaining ten (62.5%) had no related risk factors. CONCLUSIONS A significant proportion of preschool children have undiagnosed delayed-onset hearing loss. Hearing screening in preschool is recommended for an early detection.

The p.V37I exclusive genotype of GJB2: a genetic risk-indicator of postnatal permanent childhood hearing impairment.

Postnatal permanent childhood hearing impairment (PCHI) is frequent (0.25%–0.99%) and difficult to detect in the early stage, which may impede the speech, language and cognitive development of affected children. Genetic tests of common variants associated with postnatal PCHI in newborns may provide an efficient way to identify those at risk. In this study, we detected a strong association of the p.V37I exclusive genotype of GJB2 with postnatal PCHI in Chinese Hans (P = 1.4×10−10; OR 62.92, 95% CI 21.27–186.12). This common genotype in Eastern Asians was present in a substantial percentage (20%) of postnatal PCHI subjects, and its prevalence was significantly increased in normal-hearing newborns who failed at least one newborn hearing screen. Our results indicated that the p.V37I exclusive genotype of GJB2 may cause subclinical hearing impairment at birth and increases risk for postnatal PCHI. Genetic testing of GJB2 in East Asian newborns will facilitate prompt detection and intervention of postnatal PCHI.

A dominant mutation in the stereocilia-expressing gene TBC1D24 is a probable cause for nonsyndromic hearing impairment.

Mutations in TBC1D24 have been linked to a variety of epileptic syndromes and recently to syndromic hearing impairment DOORS syndrome and nonsyndromic hearing impairment DFNB86. All TBC1D24 mutations reported so far were inherited in the recessive mode. In a dominant family segregated with late‐onset, progressive, nonsyndromic hearing impairment, linkage analysis revealed a 2.07 Mb candidate region on chromosome 16p13.3 that contains TBC1D24. Whole‐exome sequencing identified a heterozygous p.Ser178Leu variant of TBC1D24 as the only candidate mutation segregating with the hearing loss within the family. In perinatal mouse cochlea, we detected a restricted expression of Tbc1d24 in the stereocilia of the hair cells as well as in the spiral ganglion neurons. Our study suggested that the p.Ser178Leu mutation of TBC1D24 is a probable cause for dominant, nonsyndromic hearing impairment. Identification of TBC1D24 as the stereocilia‐expressing gene may shed new light on its specific function in the inner ear.

Molecular etiology of hearing impairment associated with nonsyndromic enlarged vestibular aqueduct in East China

Recessive mutations in SLC26A4 and in rarer cases double heterozygous mutations of FOXI1/SLC26A4 and KCNJ10/SLC26A4 lead to hearing impairment associated with enlarged vestibular aqueduct (EVA), the most common inner ear malformation. In our large cohort study, we addressed several important questions to the molecular etiology of this disorder. The overall prevalence of SLC26A4 mutations in nonsyndromic childhood sensorineural hearing loss (11.2%, 37/330) were determined by sequencing of SLC26A4 in 330 hearing impaired children who did not undergo inner ear radiologic imaging prior to their genetic test. The penetrance of EVA in bi‐allelic SLC26A4 mutation carriers (100%, 37/37) was determined by follow‐up computed tomography scanning. Combined with the study of 140 additional probands diagnosed with nonsyndromic EVA, we characterized the mutation spectrum of SLC26A4 in East China, which consisted of 19 novel SLC26A4 mutations and differed from those reported in other regions of China.

The homozygous p.V37I variant of GJB2 is associated with diverse hearing phenotypes

The homozygous p.V37I variant of GJB2 is frequent in East Asians and has been reported to have a pathogenic role in mild‐to‐moderate hearing impairment (HI). In this study, we investigated the prevalence and phenotypic spectrum of homozygous p.V37I in three Chinese Han cohorts with severe‐to‐profound HI (n = 857, Cohort S), mild‐to‐moderate HI (n = 88, Cohort M) and normal hearing (n = 1550, Cohort N). Sequencing of GJB2 showed that homozygous p.V37I was detected in 1.63% (14/857), 12.5% (11/88) and 0.32% (5/1550) of subjects in Cohorts S, M and N, respectively. It was strongly associated with both mild‐to‐moderate (p = 2.0 × 10−11) and severe‐to‐profound (p = 0.001) HI, but was estimated to have a rather low penetrance (17%). Among the hearing impaired subjects with homozygous p.V37I, the onset of HI was congenital in 65% (11/17) and delayed in 35% (6/17). By targeted next‐generation sequencing of 79 known deafness genes, we identified an additional homozygous pathogenic mutation of CDH23 in 1 of 14 p.V37I homozygous subjects from Cohort S. Our study suggested that homozygous p.V37I is associated with a broader spectrum of hearing phenotypes than previously revealed. Data presented in this study can be effectively applied to clinical evaluation and genetic counseling of people carrying this variant.

Targeted next-generation sequencing in Uyghur families with non-syndromic sensorineural hearing loss.

The mutation spectrum of deafness genes may vary in different ethnical groups. In this study, we investigated the genetic etiology of nonsyndromic deafness in four consanguineous and two multiplex Uyghur families in which mutations in common deafness genes GJB2, SLC26A4 and MT-RNR1 were excluded. Targeted next-generation sequencing of 97 deafness genes was performed in the probands of each family. Novel pathogenic mutations were identified in four probands including the p.L416R/p.A438T compound heterozygous mutations in TMC1, the homozygous p.V1880E mutation in MYO7A, c.1238delT frameshifting deletion in PCDH15 and c.9690+1G>A splice site mutation in MYO15A. Co-segregation of the mutations and the deafness were confirmed within each family by Sanger sequencing. No pathogenic mutations were identified in one multiplex family and one consanguineous family. Our study provided a useful piece of information for the genetic etiology of deafness in Uyghurs.

Association of GRM7 variants with different phenotype patterns of age-related hearing impairment in an elderly male Han Chinese population.

Several single nucleotide polymorphisms (SNPs) of the Glutamate metabotrophic receptor 7 gene (GRM7) have recently been identified by the genome-wide association study (GWAS) as potentially playing a role in susceptibility to age-related hearing impairment (ARHI), however this has not been validated in the Han Chinese population. The aim of this study was to determine if these SNPs are also associated with ARHI in an elderly male Han Chinese population. In this case-control candidate genes association study, a total of 982 men with ARHI and 324 normal-hearing controls subjects were studied. Using K-means cluster analysis, four audiogram shape subtypes of ARHI were identified in the case group: ‘‘flat shape (FL)’’, ‘‘sloping shape (SL)’’, ‘‘2-4 kHz abrupt loss (AL) shape’’ and ‘‘8 kHz dip (8D) shape’’. Results suggested that the SNP rs11928865 (A>T) of GRM7 was significantly associated with ARHI after adjusting for non-genetic factors (p= 0.000472, OR= 1.599, 95%CI= 1.229~2.081). Furthermore, frequency of TT genotype (rs11928865) were significant higher in the SL subgroup and AL subgroup with compared to controls group (p= 9.41E-05, OR= 1.945, 95%CI= 1.393~2.715; p= 0.000109, OR= 1.915, 95%CI= 1.378~2.661 adjusted, respectively) after Bonferroni correction. However, there wasn’t significant difference in the frequency of the TT genotype between cases in the FL subgroup or the 8D subgroup with when compared with controls. Results of the current study suggest that, in an elderly male Han Chinese population, GRM7 SNP rs11928865 (TT) occurs more frequently in ARHI patients with SL and AL phenotype patterns.

Clinical characterization of a novel COCH mutation G87V in a Chinese DFNA9 family

OBJECTIVES To characterize the clinical features of a Chinese DFNA9 family associated with a novel COCH mutation and to confirm the proposed genotype-phenotype correlation of COCH. METHODS Mutation screening of 79 deafness genes was performed in the proband by targeted next-generation sequencing. Co-segregation of the disease phenotype and the detected variants was confirmed in all family members by PCR amplification and Sanger sequencing. The progression of hearing impairment in affected family members was followed and the concomitant vestibular dysfunction was verified by the caloric vestibulo-ocular reflex test. RESULTS A novel COCH mutation p.G87V was identified in the family segregating with late-onset, progressive sensorineural hearing impairment and consistent vestibular dysfunction. CONCLUSION The p.G87V mutation leads to a very similar phenotype as a previously reported p.G87W mutation of COCH. Our study suggested that the G87 residue is critical for function of COCH and further confirms a previously proposed genotype-phenotype correlation for DFNA9.

Double heterozygous mutations of MITF and PAX3 result in Waardenburg syndrome with increased penetrance in pigmentary defects

Yang T, Li X, Huang Q, Li L, Chai Y, Sun L, Wang X, Zhu Y, Wang Z, Huang Z, Li Y, Wu H. Double heterozygous mutations of MITF and PAX3 result in Waardenburg syndrome with increased penetrance in pigmentary defects.