Mapping And Identification The Pathogenic Gene In A Family With Nonsyndromic Hereditary Hearing Loss

Background Hearing loss (HL) is the most common sensory disorder worldwide. Approximately1/1000infants are affected by severe or profound deafness at birth or during early childhood, i.e. the prelingual period. The etiology of hearing loss is extraordinarily complex. It can be due to genetic or environmental causes or a combination of both. Researches of the genetic basis of hearing loss are very important because more than50%of profound hearing loss patients are caused by genetic factors. Hereditary hearing loss (HHL) may occur as part of a multisystem disease (syndromic hereditary hearing loss, SHHL) or as disorder restricted to the ear and vestibular system (nonsyndromic hereditary hearing loss, NSHHL). Nonsyndromic hearing loss is the most common form of genetic deafness. Approximately70%of hereditary hearing loss is nonsyndromic. Nonsyndromic hereditary hearing loss can be inherited as an autosomal dominant (20%), autosomal recessive (75%), X-linked and mitochondrial (maternally inherited) condition (1%-5%).Hereditary hearing loss is characterized by a high degree of genetic heterogeneity. More than140genetic loci associated with nonsyndromic hearing loss have been mapped, with no less than64responsible genes identified to date. With the development of medical genetics and molecular biology, genetic testing is a powerful tool for the etiologic establishment of hearing loss, and establishing a genetic diagnosis of hereditary hearing loss is a critical component of the clinical,evaluation for hearing loss persons and their families. The identification of genes responsible for the disease is one of the preconditions for molecular diagnosis of patients, as well as testing gene carriers and prenatal testing. Gene identification also represents the first step to a better understanding of the physiological role of the underlying protein and disease pathways, which in turn serves as a starting point for developing therapeutic interventions.The genes underlying Mendelian disorders have for the past several decades been predominantly identified through positional mapping approach and candidate genes Sanger-sequencing. However, the mapping approaches commonly do not reduce the number of candidate genes sufficiently for follow-up by Sanger-sequencing, when the disease locus remains very large. It is sometimes a formidable bottleneck for identification of the causative genes. In addition, candidate gene selection is however critically dependent on prior knowledge and only few disease genes have been identified by specifically using these bioinformatics tools. Recent advances in next generation sequencing technologies have dramatically changed the process of disease gene identification, in particular by using exome sequencing in which the protein-coding part of the genome. Over the past seveal years, experimental and analytical approaches relating to exome sequencing have established a rich framework for discovering the genes underlying unsolved Mendelian disorders. It is therefore likely that exome sequencing will become the most commonly used tool for Mendelian disease gene identification in the next few years.To identify the causative gene, we performed genome-wide scan and linkage analysis on24members of the family, combined with whole-exome sequencing in four individuals from the family.Objective The aim of the present study was to identify the underlying disease-causing genes of a family with autosomal dominant nonsyndromic hearing loss.Methods We investigated a five generation family from Hunan province of China with autosomal dominant sensorineural hearing loss. The detailed medical history informations of the participants from the large family were collected. Otoscopy, physical examination, and pure-tone audiometry were performed. After excluding pathogenic mutations in the candidate genes of GJB2, GJB3, COCH, EYA4and KCNQ4, which are commonly associated with DFNA, via Sanger-sequencing technique, we performed genome-wide linkage analysis on24members, combined with whole-exome sequencing in3affected individuals and1unaffected subject from the family. Finally, Sanger sequencing was used to confirm co-segregation of the mutation with deafness in the family and carry out mutation screening of unrelated controls. Results The family showed that this is an autosomal dominant non-syndromic deafness pedigree. Clinical features were remarkably similar among affected individuals. All of them showed a progressive sensorineural hearing impairment that begins in the first to the second decade and leads to severe to profound hearing loss in the fourth to the fifth decade of their lives, progressing first at high frequencies and ultimately becoming severe to profound at all frequencies. High-frequency tinnitus was reported in the majority of affected members at the onset of hearing loss. We have completed mutation screening of the GJB2, GJB3, COCH, EYA4and KCNQ4genes; however, no disease-causing mutations were identified. Two-point linkage analysis was conducted on MERLIN. This analysis identified a region on chromosome19:q13.31-q13.42, linked to disease with a maximum two-point LOD score of4.448at rs2041975. This region is flanked by rs887392and rs9788, and spans approximately20Mb. No significant LOD scores were obtained for any other regions of the genome. Exome sequencing and candidate genes Sanger-sequencing resulted in the identification of a c.505G>A (p.G169R) mutation in exon4of the CEACAM16gene. This mutation was not present in200controls (400alleles).Conclusion (1) The studies have identified the pathogenic gene CEACAM16, which located in DFNA4locus, in a large nonsyndromic hearing loss family from China;(2) This is the first report of a novel mutation c.505G>A (p.G169R) in the CEACAM16gene that causes sensorineural hearing loss, which contributes to the wide spectrum of CEACAM16;(3) The results of this research may be useful to genetic counseling of the affected family. It may effectively prevent deafness occurs through prenatal diagnosis and intervention. In addition, there has been an important reference for genetic test of the other DFNA patients.