Five novel loci for inherited hearing loss mapped by SNP-based homozygosity profiles in Palestinian families

Abstract

In communities with high rates of consanguinity and consequently high prevalence of recessive phenotypes, homozygosity mapping with SNP arrays is an effective approach for gene discovery. In 20 Palestinian kindreds with prelingual nonsyndromic hearing loss, we generated homozygosity profiles reflecting linkage to the phenotype. Family sizes ranged from small nuclear families with two affected children, one unaffected sibling, and parents to multigenerational kindreds with 12 affected relatives. By including unaffected parents and siblings and screening 250 K SNP arrays, even small nuclear families yielded informative profiles. In 14 families, we identified the allele responsible for hearing loss by screening a single candidate gene in the longest homozygous region. Novel alleles included missense, nonsense, and splice site mutations of CDH23, MYO7A, MYO15A, OTOF, PJVK, Pendrin/SLC26A4, TECTA, TMHS, and TMPRSS3, and a large genomic deletion of Otoancorin (OTOA). All point mutations were rare in the Palestinian population (zero carriers in 288 unrelated controls); the carrier frequency of the OTOA genomic deletion was 1%. In six families, we identified five genomic regions likely to harbor novel genes for human hearing loss on chromosomes 1p13.3 (DFNB82), 9p23-p21.2/p13.3-q21.13 (DFNB83), 12q14.3-q21.2 (DFNB84; two families), 14q23.1-q31.1, and 17p12-q11.2 (DFNB85).

Figure 1

Inherited prelingual hearing loss in Palestinian families. Hearing loss in affected individuals (filled symbols) is prelingual with thresholds >90 dB. Double bars between parents indicate marriages within the same hamula, or clan. Only enrolled individuals and their parents are shown. Based on complete pedigree information, segregation of hearing loss is consistent with recessive inheritance in each family.

Figure 2

Genomic regions of homozygosity associated with hearing loss. Each colored bar represents a genomic region homozygous for the same haplotype in all deaf individuals in a family, and heterozygous or homozygous for the alternate allele among unaffected parents or siblings in the same family. Chromosome arms are indicated on X-axes; lengths in Mb of the homozygous regions are indicated on Y-axes. Green bars represent homozygous regions with a deleterious mutation in a known deafness gene, as indicated in Table 1. Red bars represent homozygous regions likely to harbor novel deafness genes as indicated in Table 2. Blue bars indicate other regions of homozygosity.

Figure 3

Genomic deletion of Otoancorin (OTOA). (a) Family DO pedigree and PCR amplification of a unique STS in OTOA intron 17 at chr16: 21 645 309. The STS is present in the unaffected mother and sibling and absent from all affected siblings. (b) Presence (+) or absence (−) of multiple STSs within and flanking OTOA in genomic DNA from unaffected mother DO1 and deaf child DO5. (c) High-resolution arrayCGH of 16p12.2 (chr16: 21 200 000–22 000 000) in genomic DNA from Palestinian control individuals HGDP4921 and HGDP5043 and from family DO unaffected mother DO1 and deaf child DO5. Deviations from zero of log₂ ratios of probe intensities are depicted by vertical lines, with ratios >1.5 SDs from the mean ratio colored red and green to represent relative losses and gains, respectively. Segmental duplications of increasing similarity (90–98, 98–99, and >99%) are represented by gray, yellow, and orange bars, respectively. The size of the OTOA locus (black bar) is 82 kb; the size of the deletion is 320–550 kb. In the Palestinian hearing population, the carrier frequency of the deletion is 1% (3/288 controls).