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Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.

ABSTRACT: Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI), the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS), we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs) and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFT scores (>0.95) prioritized 5 indels (insertions/deletions) and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes.

SUBMITTER: Wu CC

PROVIDER: S-EPMC3579845 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.

Wu Chen-Chi CC Lin Yin-Hung YH Lu Ying-Chang YC Chen Pei-Jer PJ Yang Wei-Shiung WS Hsu Chuan-Jen CJ Chen Pei-Lung PL

PloS one 20130222 2

Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI), the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MP ...[more]

PMID: 23451214

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Project description:IntroductionTo compare inpatient treated patients with idiopathic (ISSNHL) and non-idiopathic sudden sensorineural hearing loss (NISSNHL) regarding frequency, hearing loss, treatment and outcome.MethodsAll 574 inpatient patients (51% male, median age: 60 years) with ISSNHL and NISSNHL, who were treated in federal state Thuringia in 2011 and 2012, were included retrospectively. Univariate and multivariate statistical analyses were performed.ResultsISSNHL was diagnosed in 490 patients (85%), NISSNHL in 84 patients (15%). 49% of these cases had hearing loss due to acute otitis media, 37% through varicella-zoster infection or Lyme disease, 10% through Menière disease and 7% due to other reasons. Patients with ISSNHL and NISSNHL showed no difference between age, gender, side of hearing loss, presence of tinnitus or vertigo and their comorbidities. 45% of patients with ISSNHL and 62% with NISSNHL had an outpatient treatment prior to inpatient treatment (p < 0.001). The mean interval between onset of hearing loss to inpatient treatment was shorter in ISSNHL (7.7 days) than in NISSNHL (8.9 days; p = 0.02). The initial hearing loss of the three most affected frequencies in pure-tone average (3PTAmax) scaled 72.9 dBHL ± 31.3 dBHL in ISSNHL and 67.4 dBHL ± 30.5 dBHL in NISSNHL. In the case of acute otitis media, 3PTAmax (59.7 dBHL ± 24.6 dBHL) was lower than in the case of varicella-zoster infection or Lyme disease (80.11 dBHL ± 34.19 dBHL; p = 0.015). Mean absolute hearing gain (Δ3PTAmaxabs) was 8.1 dB ± 18.8 dB in patients with ISSNHL, and not different in NISSNHL patients with 10.2 dB ± 17.6 dB. A Δ3PTAmaxabs ≥ 10 dB was reached in 34.3% of the patients with ISSNHL and to a significantly higher rate of 48.8% in NISSNHL patients (p = 0.011).ConclusionsISSNHL and NISSNHL show no relevant baseline differences. ISSNHL tends to have a higher initial hearing loss. NISSHNL shows a better outcome than ISSNHL.

Project description:ImportancePatients with idiopathic sudden sensorineural hearing loss (ISSNHL) often experience permanent hearing impairment, which could result in psychological perturbations. However, the relationship between ISSNHL and affective disorders, including depression, anxiety, and bipolar disorder, has not been fully evaluated.ObjectiveTo investigate the potential relationship between ISSNHL and affective disorders using nationwide representative cohort sample data.Design, setting, and participantsThis study used a nationwide propensity score-matched cohort sample from the Korean National Health Insurance Service database from 2002 through 2013, which comprises data from approximately 1 million patients. The study included 1425 patients with ISSNHL and 7125 individuals without ISSNHL who were matched using propensity score matching, according to sociodemographic factors and enrollment year.Main outcomes and measuresSurvival analysis, the log-rank test, and Cox proportional hazards regression models were used to calculate the incidence, survival rate, and hazard ratio (HR) of developing affective disorders (anxiety, depression, and bipolar disorder) for each group.ResultsOf the total study population of 8550 (51.5% female), 961 developed affective disorders during the 11-year follow-up: 225 in the ISSNHL group (15.8%) and 736 in the comparison group (10.3%). We examined a total of 96 885.5 person-years (81 177.4 person-years in the comparison group and 15 708.1 person-years in the ISSNHL group). The incidence of affective disorders was 14.3 per 1000 person-years in the ISSNHL group and 9.1 per 1000 person-years in the comparison group. After adjustment for other factors, individuals with ISSNHL developed affective disorders more frequently than those in the comparison group (HR, 1.50; 95% CI, 1.30-1.75). Among the affective disorders, the HR of developing depression (HR, 1.66; 95% CI, 1.44-1.91) and anxiety disorder (HR, 1.79; 95% CI, 1.56-2.05) but not bipolar disorder (HR, 0.95; 95% CI, 0.54-1.70), was significantly greater in patients with ISSNHL.Conclusions and relevanceThis cohort study suggests that ISSNHL is associated with an increased incidence of affective disorders, specifically depression and anxiety. Therefore, these findings suggest that clinicians should monitor patients with ISSNHL carefully, and take specific precautions to reduce their risk of depression and anxiety disorder.

Dataset Information

Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.

Publications

Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment.

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