1. A next-generation sequencing gene panel (MiamiOtoGenes) for comprehensive analysis of deafness genes
- Author
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Guney Bademci, Denise Yan, Joseph Foster, Shengru Guo, Yong Feng, Susan H. Blanton, Xuezhong Liu, Demet Tekin, and Mustafa Tekin
- Subjects
Genetic Markers ,0301 basic medicine ,Heredity ,Nuclear gene ,Hearing loss ,Deafness ,Biology ,Article ,DNA sequencing ,03 medical and health sciences ,Exon ,0302 clinical medicine ,Hearing ,Untranslated Regions ,Databases, Genetic ,otorhinolaryngologic diseases ,OMIM : Online Mendelian Inheritance in Man ,medicine ,Humans ,Genetic Predisposition to Disease ,Gene ,Genetic Association Studies ,Genetics ,Genetic heterogeneity ,Computational Biology ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Exons ,Sensory Systems ,Pedigree ,Phenotype ,030104 developmental biology ,Human genome ,medicine.symptom ,030217 neurology & neurosurgery - Abstract
Extreme genetic heterogeneity along with remarkable variation in the distribution of causative variants across in different ethnicities makes single gene testing inefficient for hearing loss. We developed a custom capture/next-generation sequencing gene panel of 146 known deafness genes with a total target size of approximately 1 MB. The genes were identified by searching databases including Hereditary Hearing Loss Homepage, the Human Genome Mutation Database (HGMD), Online Mendelian Inheritance in Man (OMIM) and most recent peer-reviewed publications related to the genetics of deafness. The design covered all coding exons, UTRs and 25 bases of intronic flanking sequences for each exon. To validate our panel, we used 6 positive controls with variants in known deafness genes and 8 unsolved samples from individuals with hearing loss. Mean coverage of the targeted exons was 697X. On average, each sample had 99.8%, 96.2% and 92.7% of the targeted region coverage of 1X, 50X and 100X reads, respectively. Analysis detected all known variants in nuclear genes. These results prove the accuracy and reliability of the custom capture experiment.
- Published
- 2016
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