BackgroundIdentification of genes responsible for medically important traits is a major challenge in human genetics. Due to the genetic heterogeneity of hearing loss, targeted DNA capture and massively parallel sequencing are ideal tools to address this challenge. Our subjects for genome analysis are Israeli Jewish and Palestinian Arab families with hearing loss that varies in mode of inheritance and severity.ResultsA custom 1.46 MB design of cRNA oligonucleotides was constructed containing 246 genes responsible for either human or mouse deafness. Paired-end libraries were prepared from 11 probands and bar-coded multiplexed samples were sequenced to high depth of coverage. Rare single base pair and indel variants were identified by filtering sequence reads against polymorphisms in dbSNP132 and the 1000 Genomes Project. We identified deleterious mutations in CDH23, MYO15A, TECTA, TMC1, and WFS1. Critical mutations of the probands co-segregated with hearing loss. Screening of additional families in a relevant population was performed. TMC1 p.S647P proved to be a founder allele, contributing to 34% of genetic hearing loss in the Moroccan Jewish population.ConclusionsCritical mutations were identified in 6 of the 11 original probands and their families, leading to the identification of causative alleles in 20 additional probands and their families. The integration of genomic analysis into early clinical diagnosis of hearing loss will enable prediction of related phenotypes and enhance rehabilitation. Characterization of the proteins encoded by these genes will enable an understanding of the biological mechanisms involved in hearing loss.

These findings describe, for the first time, variable inner ear malformations and outer ear dysplasia in the presence of constant microdontia, associated with homozygous inheritance of the p.R95W mutation in FGF3, mirroring phenotypes observed in mouse models ablating FGF3/FGFR2 signaling.

Laryngopharyngectomy followed by adjuvant radiotherapy (PORT) or primary radiochemotherapy represents the treatment of choice for locally advanced laryngeal and hypopharyngeal carcinoma. 1 Despite increasing insights into the molecular pathways and constant efforts to improve therapy regimens, the outcome of patients with advanced stage disease remains poor. 2,3 Particularly, 50%-70% of patients with stage III or IV disease will die due to disease 5 years after the diagnosis. 4 Locoregional and distant failure are the major prognostic determinants, and therefore, the primary factor of mortality in this patient population with recurrence rates ranging between 25% and 50%. 5 Regional lymph node metastases, advanced stage disease, surgical resection margin and extracapsular extension are established risk factors for locoregional recurrence or distant metastasis in laryngeal and hypopharyngeal carcinoma. [6][7][8] Nevertheless, identification of new prognostic factors for recurrence is of utmost importance as it may improve treatment strategies and post-therapeutic surveillance.Recently, the lymph node ratio (LNR) has been shown to be an important prognostic factor in bladder, oesophageal and oral squamous cell carcinomas (SCCs). 9-11 LNR is defined as the ratio of positive lymph nodes to the total number of dissected lymph nodes. Although studies have also been performed in patients with laryngeal and hypopharyngeal cancer, the prognostic value of LNR was contradictory because the prognostic power of LNR was not significant for all

POU3F4 is a POU domain transcription factor that is required for hearing. In the ear, POU3F4 is essential for mesenchymal remodeling of the bony labyrinth and is the causative gene for DFNX2 human non-syndromic deafness. Ear abnormalities underlie this form of deafness, characterized previously in multiple spontaneous, radiation-induced and transgenic mouse mutants. Here we report three novel mutations in the POU3F4 gene that result in profound hearing loss in both humans and mice. A p.Gln79* mutation was identified in a child from an Israeli family, revealed by massively parallel sequencing (MPS). This strategy demonstrates the strength of MPS for diagnosis with only one affected individual. A second mutation, p.Ile285Argfs*43, was identified by Sanger sequencing. A p.Cys300* mutation was found in an ENU-induced mutant mouse, schwindel (sdl), by positional cloning. The mutation leads to a predicted truncated protein, similar to the human mutations, providing a relevant mouse model. The p.Ile285Argfs*43 and p.Cys300* mutations lead to a shift of Pou3f4 nuclear localization to the cytoplasm, demonstrated in cellular localization studies and in the inner ears of the mutant mice. The discovery of these mutations facilitates a deeper comprehension of the molecular basis of inner ear defects due to mutations in the POU3F4 transcription factor.