Ontology highlight
ABSTRACT:
PROVIDER: PRJNA672174 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12903783_1.fastq.gz | Fastqsanger.gz | |||
| SRR12903783_2.fastq.gz | Fastqsanger.gz |
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Project description:Next-Generation Sequencing techniques (i.e, targeted re-sequencing and whole exome sequencing) have been employed for the study of two Italian patients affected by age-related hearing loss and of an Italian family affected by hereditary hearing loss. Data analysis led to the identification of three variants in SPATC1L, associated with the clinical phenotype.
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Project description:Hereditary hearing loss (HHL) exhibits significant genetic heterogeneity, with mutations in LMX1A related to autosomal dominant non-syndromic hearing loss (DFNA7). Here, we report a novel heterozygous frameshift variant, LMX1A c.405delT (p. Phe135LeufsTer3) in a three-generation Chinese family with progressive and asymmetric sensorineural hearing loss (ASNHL). Clinical evaluations revealed variable severity (mild-to-profound) and onset (infancy to mid-adulthood), with cochlear aperture stenosis observed in the proband. Whole exon sequencing (WES), Sanger sequencing and segregation analysis confirmed the novel mutation and its cosegregation with the phenotype. Structural modeling predicted that truncation within the conserved LIM2 domain disrupts protein function. Functional studies demonstrated reduced transcriptional activity, supporting haploinsufficiency as the pathogenic mechanism. RNA sequencing (RNA-seq) of HEI-OC1 cells revealed dysregulation of neurodevelopmental, synaptic and mitochondrial pathways, implicating neurodegeneration and metabolic dysfunction in LMX1A-related hearing loss. This study highlights the role of LMX1A in auditory homeostasis, provides insights into genotype-phenotype correlations and underscores structural cochlear anomalies as potential contributors to ASNHL.
2026-06-11 | GSE299979 | GEO
Project description:Background The genetic diversity of loci and mutations underlying hereditary hearing loss is an active area of investigation. To identify loci associated with predominantly non-syndromic sensorineural hearing loss, we performed exome sequencing of families and of single probands, as well as copy number variation (CNV) mapping in a case-control cohort. Results Analysis of three distinct families revealed several candidate loci in two families and a single strong candidate gene, MYH7B, for hearing loss in one family. MYH7B encodes a Type II myosin, consistent with a role for cytoskeletal proteins in hearing. High-resolution genome-wide CNV analysis of 150 cases and 157 controls revealed deletions in genes known to be involved in hearing (e.g. GJB6, OTOA, and STRC, encoding connexin 30, otoancorin, and stereocilin, respectively), supporting CNV contributions to hearing loss phenotypes. Additionally, a novel region on chromosome 16 containing part of the PDXDC1 gene was found to be frequently deleted in hearing loss patients (OR = 3.91, 95% CI: 1.62-9.40, p = 1.45 x 10-7). Conclusions We conclude that many known as well as novel loci and distinct types of mutations not typically tested in clinical settings can contribute to the etiology of hearing loss. Our study also demonstrates the challenges of exome sequencing and genome-wide CNV mapping for direct clinical application, and illustrates the need for functional and clinical follow-up as well as curated open-access databases. Single replicates of 151 non-syndromic hereditary hearing loss cases and 157 controls with normal hearing were analyzed.
2014-12-19 | E-GEOD-64088 | biostudies-arrayexpress
Project description:Next Generation Sequencing in cancer: a feasibility study in France to assess sample circuit and to perform analyzes within a limited time.
| 2274538 | ecrin-mdr-crc
Project description:Objectives: Despite recent advancements in diagnostic tools, the genomic landscape of hereditary hearing loss remains largely uncharacterized. One strategy to understand genome-wide aberrations includes the analysis of copy number variation that can be mapped using SNP-microarray technology. A growing collection of literature has begun to uncover the importance of copy number variation in hereditary hearing loss. This pilot study underpins a larger effort that involves the stage-wise analysis of hearing loss patients, many of whom have advanced to high-throughput sequencing analysis. Data description: Our data originate from Infinium HumanOmni1-Quad v1.0 SNP-microarrays (Illumina) that provide useful markers for genome-wide association studies and copy number variation analysis. This dataset comprises a cohort of 108 individuals (99 with hearing loss, 9 normal hearing family members) for the purpose of understanding the genetic contribution of copy number variations to hereditary hearing loss.
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Project description:Background The genetic diversity of loci and mutations underlying hereditary hearing loss is an active area of investigation. To identify loci associated with predominantly non-syndromic sensorineural hearing loss, we performed exome sequencing of families and of single probands, as well as copy number variation (CNV) mapping in a case-control cohort. Results Analysis of three distinct families revealed several candidate loci in two families and a single strong candidate gene, MYH7B, for hearing loss in one family. MYH7B encodes a Type II myosin, consistent with a role for cytoskeletal proteins in hearing. High-resolution genome-wide CNV analysis of 150 cases and 157 controls revealed deletions in genes known to be involved in hearing (e.g. GJB6, OTOA, and STRC, encoding connexin 30, otoancorin, and stereocilin, respectively), supporting CNV contributions to hearing loss phenotypes. Additionally, a novel region on chromosome 16 containing part of the PDXDC1 gene was found to be frequently deleted in hearing loss patients (OR = 3.91, 95% CI: 1.62-9.40, p = 1.45 x 10-7). Conclusions We conclude that many known as well as novel loci and distinct types of mutations not typically tested in clinical settings can contribute to the etiology of hearing loss. Our study also demonstrates the challenges of exome sequencing and genome-wide CNV mapping for direct clinical application, and illustrates the need for functional and clinical follow-up as well as curated open-access databases.
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