Dataset Information

AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening.

ABSTRACT: Autosomal dominant nonsyndromic hearing loss (ADNSHL) is a common and often progressive sensory deficit. ADNSHL displays a high degree of genetic heterogeneity and varying rates of progression. Accurate, comprehensive, and cost-effective genetic testing facilitates genetic counseling and provides valuable prognostic information to affected individuals. In this article, we describe the algorithm underlying AudioGene, a software system employing machine-learning techniques that utilizes phenotypic information derived from audiograms to predict the genetic cause of hearing loss in persons segregating ADNSHL. Our data show that AudioGene has an accuracy of 68% in predicting the causative gene within its top three predictions, as compared with 44% for a majority classifier. We also show that AudioGene remains effective for audiograms with high levels of clinical measurement noise. We identify audiometric outliers for each genetic locus and hypothesize that outliers may reflect modifying genetic effects. As personalized genomic medicine becomes more common, AudioGene will be increasingly useful as a phenotypic filter to assess pathogenicity of variants identified by massively parallel sequencing.

SUBMITTER: Taylor KR

PROVIDER: S-EPMC3753227 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature

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AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening.

Taylor Kyle R KR Deluca Adam P AP Shearer A Eliot AE Hildebrand Michael S MS Black-Ziegelbein E Ann EA Anand V Nikhil VN Sloan Christina M CM Eppsteiner Robert W RW Scheetz Todd E TE Huygen Patrick L M PL Smith Richard J H RJ Braun Terry A TA Casavant Thomas L TL

Human mutation 20130219 4

Autosomal dominant nonsyndromic hearing loss (ADNSHL) is a common and often progressive sensory deficit. ADNSHL displays a high degree of genetic heterogeneity and varying rates of progression. Accurate, comprehensive, and cost-effective genetic testing facilitates genetic counseling and provides valuable prognostic information to affected individuals. In this article, we describe the algorithm underlying AudioGene, a software system employing machine-learning techniques that utilizes phenotypic ...[more]

PMID: 23280582

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Project description:BackgroundRecent advances in molecular genetics have enabled to determine the genetic causes of non-syndromic hearing loss, and more than 100 genes have been related to the phenotype. Due to this extraordinary genetic heterogeneity, a large percentage of patients remain without any molecular diagnosis. This condition imply the need for new methodological strategies in order to detect a greater number of mutations in multiple genes. In this work, we optimized and tested a panel of 86 mutations in 17 different genes screened using a high-throughput genotyping technology to determine the molecular etiology of hearing loss.MethodsThe technology used in this work was the MassARRAY iPLEX® platform. This technology uses silicon chips and DNA amplification products for accurate genotyping by mass spectrometry of previous reported mutations. The generated results were validated using conventional techniques, as direct sequencing, multiplex PCR and RFLP-PCR.ResultsAn initial genotyping of control subjects, showed failures in 20 % of the selected alterations. To optimize these results, the failed tests were re-designed and new primers were synthesized. Then, the specificity and sensitivity of the panel demonstrated values above 97 %. Additionally, a group of 180 individuals with NSHL without a molecular diagnosis was screened to test the diagnostic value of our panel, and mutations were identified in 30 % of the cases. In 20 % of the individuals, it was possible to explain the etiology of the HL. Mutations in GJB2 gene were the most prevalent, followed by other mutations in in SLC26A4, CDH23, MT-RNR1, MYO15A, and OTOF genes.ConclusionsThe MassARRAY technology has the potential for high-throughput identification of genetic variations. However, we demonstrated that optimization is required to increase the genotyping success and accuracy. The developed panel proved to be efficient and cost-effective, being suitable for applications involving the molecular diagnosis of hearing loss.

Project description:Presbyacusis, or age-related hearing loss, can be characterized in humans as metabolic and sensory phenotypes, based on patterns of audiometric thresholds that were established in animal models. The metabolic phenotype is thought to result from deterioration of the cochlear lateral wall and reduced endocochlear potential that decreases cochlear amplification and produces a mild, flat hearing loss at lower frequencies coupled with a gradually sloping hearing loss at higher frequencies. The sensory phenotype, resulting from environmental exposures such as excessive noise or ototoxic drugs, involves damage to sensory and non-sensory cells and loss of the cochlear amplifier, which produces a 50-70 dB threshold shift at higher frequencies. The mixed metabolic + sensory phenotype exhibits a mix of lower frequency, sloping hearing loss similar to the metabolic phenotype, and steep, higher frequency hearing loss similar to the sensory phenotype. The current study examined audiograms collected longitudinally from 343 adults 50-93 years old (n = 686 ears) to test the hypothesis that metabolic phenotypes increase with increasing age, in contrast with the sensory phenotype. A Quadratic Discriminant Analysis (QDA) was used to classify audiograms from each of these ears as (1) Older-Normal, (2) Metabolic, (3) Sensory, or (4) Metabolic + Sensory phenotypes. Although hearing loss increased systematically with increasing age, audiometric phenotypes remained stable for the majority of ears (61.5 %) over an average of 5.5 years. Most of the participants with stable phenotypes demonstrated matching phenotypes for the left and right ears. Audiograms were collected over an average period of 8.2 years for ears with changing audiometric phenotypes, and the majority of those ears transitioned to a Metabolic or Metabolic + Sensory phenotype. These results are consistent with the conclusion that the likelihood of metabolic presbyacusis increases with increasing age in middle to older adulthood.

Project description:Background and aimsConcurrent hearing and genetic screening of newborns have been widely adopted as an effective strategy in early diagnosis and intervention for hearing loss in many cities in China. Here, we aimed to firstly explore the efficacy of combining conventional hearing screening with genetic screening among the large-scale newborns in Jiangxi Province.MethodsA total of 24,349 newborns from Jiangxi Maternal and Child Health Hospital were enrolled in our study from April 2021 to June 2022. Newborn hearing screening was conducted using otoacoustic emission (OAE) and automated auditory brainstem response (AABR). Meanwhile, newborn dried blood spots were collected and twenty common variants in four genes, including GJB2, SLC26A4, MT-RNR1(12SrRNA), and GJB3, were screened using a BGISEQ-500 next generation sequencing platform. Whole coding regions sequencing of GJB2 and SLC26A4 were performed by Sanger sequencing and NGS, respectively. Following up of hearing for the newborns was undertaken by phone interviews.ResultsAmong the 24,349 newborns, 7.00% (1,704/24,349) were bilaterally or unilaterally referred in their initial hearing screening, whereas 1.30% (316/24,349) exhibited bilateral or unilateral hearing loss in the repeated screening. Genetic screening revealed that 4.813% (1,172/24,349) of the screened newborns were positive for at least one mutant allele (heterozygote, homozygote, or compound heterozygote in one gene, mtDNA homoplasmy or heteroplasmy and combined variants in different genes). A total of 1,146 individuals were identified with mutant allele in one gene, including 525 of GJB2, 371 of SLC26A4, 189 as homoplasmic or heteroplasmic of MT-RNR1, and 61 of GJB3, indicating that GJB2 and SLC26A4 are the most common endemic deafness-associated genes among newborns in Jiangxi Province. Nineteen newborns were detected with combined heterozygous variants in different genes, with "c.235delC heterozygous and c.919-2A > G heterozygous" as the most prevalent genotype. Additionally, seven newborns were screened as homozygotes or compound heterozygotes responsible for congenital or late-onset prelingual hearing loss, including three cases with GJB2 c.235delC homozygous and one with SLC26A4 c.919-2A > G homozygous variant, one case with compound heterozygous variants for GJB2 and two with compound heterozygous variants for SLC26A4. Coding regions sequencing of GJB2 or SLC26A4 for overall 265 infants revealed that 14 individuals were identified as compound heterozygote with a second pathogenic variant not screened by our genetic panel.ConclusionsHerein our study firstly investigated the efficacy of concurrent hearing screening and genetic screening of common hearing impairment variants among large-scale newborns in Jiangxi Province. Concurrent screening provides a more comprehensive approach for management of congenital or delayed onset prelingual hearing loss and prevention of drug-induced hearing impairment for newborns at risk as well as their maternal relatives. An insight into the molecular epidemiology for hearing loss genes among Jiangxi population will also be beneficial to the genetic counseling and birth defect prevention.

Dataset Information

AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening.

Publications

AudioGene: predicting hearing loss genotypes from phenotypes to guide genetic screening.

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