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To the Editor:
We identified linkage of recessive pre-lingual deafness to a new locus, designated DFNB86. This linkage was identified in a large consanguineous family PKDF799 with eleven affected individuals (Fig. 1a). Family PKDF799 was recruited in Pakistan after obtaining Institutional Review Board (IRB) approvals from the National Center of Excellence in Molecular Biology, Lahore (FWA00001758), the Combined Neuroscience IRB at the National Institutes of Health (OH-93-N-016), and the IRB Committee at the Cincinnati Children’s Hospital Research Foundation (2009-0684). Written informed consent was obtained from all participating individuals and parents of minor subjects. The proband was V:6 (Fig. 1a). Four affected individuals and three unaffected siblings from this family were tested for hearing ability using pure-tone air and bone conduction audiometry. All of the affected individuals evaluated showed profound sensorineural hearing loss across all tested frequencies (Fig. 1b). There was no history of vestibular difficulties among the deaf individuals in this family, but we were not able to perform sophisticated tests of the status of their vestibular system using posturography or a rotary chair, for example. We tentatively concluded that hearing loss segregating in family PKDF799 is nonsyndromic.
We initially observed that deafness in family PKDF799 did not co-segregate with short tandem repeat (STR) markers for 63 of the reported recessive nonsyndromic deafness loci (data not shown). A genome wide linkage analysis using 388 fluorescently labeled microsatellite (STR) markers determined that the phenotype showed significant evidence of linkage to STR markers on chromosome 16p13.3. In addition to the chromosome 16p13.3 locus, two point LOD scores of 1.54 for marker D11S1338 and 1.48 for marker D17S1852 were also found. However, genotyping additional DNA samples from family PKDF799 excluded linkage to both chromosomes 11 and 17. Additional STRs on 16p were then genotyped, and haplotype analysis revealed a 3.09 Mb linkage interval extending from the telomere of chromosome 16p to marker D16S3070 (Fig. 1a). Under a model with a disease allele frequency of 0.001 and a fully penetrant disorder, a maximum two-point LOD score of 8.54 (θ=0) was obtained for the marker D16S3024. These results define and delimit DFNB86 (HUGO approved locus symbol), a novel recessive deafness locus on chromosome 16p13.3.
There are few possible interpretations of the haplotype data (Fig. 1a) as to the number of mutant alleles segregating in family PKDF799. If there is a single mutant allele, then all affected individuals are likely to be homozygous for a region of the disease haplotype. Under this model, the causative gene resides in a 1.44 Mb interval between markers D16S3024 and D16S3070. The proximal meiotic recombination at marker D16S3024 occurred in individuals IV:5 and IV:6, while the distal recombination at marker D16S3070 is observed in normal hearing individual V:8 (Fig. 1a) However, if there are two different mutant alleles of the same deafness gene segregating in this family, the DFNB86 gene is located telomeric to marker D16S3395, and affected individuals IV:5 and IV:6 are compound heterozygotes (Fig. 1a). Under this assumption, a linkage region of 3.09 Mb extends from the telomere of chromosome 16p to marker D16S3070. Although unusual, consanguineous families segregating two different mutant alleles have been reported (1, 2). Other possibilities for the haplotype data are that individuals IV:5 and IV:6 have hearing loss due to a mutation at different locus, or are phenocopies. We will be able to distinguish between these various interpretations of the haplotype data once we have identified the DFNB86 gene.
The DFNB86 locus does not overlap with any published mutated gene associated with a hearing phenotype or other reported deafness loci on chromosome 16. There are 167 candidate genes in the 3.09 Mb DFNB86 linkage interval including MSRB1, NTN3, GFER, SYNGR3, CLDN6, and CLDN9. Methionine Sulfoxide Reductases (MSRs) are enzymes involved in repair of proteins damaged by oxidative stress. We recently reported that mutations of Methionine Sulfoxide Reductase B3 cause nonsyndromic deafness DFNB74 (3). Therefore, MSRB1 was sequenced using genomic DNA of an affected individual from family PKDF799. We did not find a causative variant in the coding exons, 3’ and 5’ untranslated regions (UTR) as well as several conserved intronic regions of MSRB1. Similarly, a likely causative variant was not found in SYNGR3, NTN3, and GFER encoding a synaptic vesicle protein, an axon guidance protein, and a growth factor, respectively. CLDN6 and CLDN9 are also located in the DFNB86 interval. Since claudins 9, 11 and 14 have been shown to be necessary for inner ear function (4–8), we sequenced the coding exons of CLDN6 and CLDN9, but did not find a potential pathogenic mutation. When we sequenced these six genes using genomic DNA from affected individuals from family PKDF799, the only variants we found were known SNPs. Rather than continue hierarchical sequencing of candidate genes based on function or expression in the inner ear, future studies will employ massively parallel sequencing of genomic DNA (9) enriched for the entire DFNB86 critical interval.
The authors are grateful to the family for contributing to this study. We thank Alejandro Schaffer for suggestions regarding statistical analysis of our linkage data. We also thank Dennis Drayna and Changsoo Kang for their critiques. This study was supported by Cincinnati Children’s Hospital Research Foundation intramural research funds to SiR and ZA, the National Institute on Deafness and Other Communication Disorders (NIDCD/NIH) research grant R00-DC009287-03 to ZA. ZA is also a recipient of RPB Career Development Award. Work in Pakistan was supported by the Higher Education Commission, Islamabad, EMRO/WHO-COMSTECH, Ministry of Science and Technology, Islamabad and the International Center for Genetic Engineering and Biotechnology, Trieste, Italy under project CRP/PAK08-01 Contract no. 08/009 to ShR. This study was also supported by intramural funds from the NIDCD/NIH DC00039-14 to TBF.
Conflict of interest statement
Authors declare no conflict of interest