Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran

Abstract

Background: Countries with culturally accepted consanguinity provide a unique resource for the study of rare recessively inherited genetic diseases. Although hereditary hearing loss (HHL) is not uncommon, it is genetically heterogeneous, with over 85 genes causally implicated in non-syndromic hearing loss (NSHL). This heterogeneity makes many gene-specific types of NSHL exceedingly rare. We sought to define the spectrum of autosomal recessive HHL in Iran by investigating both common and rarely diagnosed deafness-causing genes.

Design: Using a custom targeted genomic enrichment (TGE) panel, we simultaneously interrogated all known genetic causes of NSHL in a cohort of 302 GJB2-negative Iranian families.

Results: We established a genetic diagnosis for 67% of probands and their families, with over half of all diagnoses attributable to variants in five genes: SLC26A4, MYO15A, MYO7A, CDH23 and PCDH15. As a reflection of the power of consanguinity mapping, 26 genes were identified as causative for NSHL in the Iranian population for the first time. In total, 179 deafness-causing variants were identified in 40 genes in 201 probands, including 110 novel single nucleotide or small insertion-deletion variants and three novel CNV. Several variants represent founder mutations.

Conclusion: This study attests to the power of TGE and massively parallel sequencing as a diagnostic tool for the evaluation of hearing loss in Iran, and expands on our understanding of the genetics of HHL in this country. Families negative for variants in the genes represented on this panel represent an excellent cohort for novel gene discovery.

Keywords: Copy-number; Diagnostics tests; Molecular genetics; Neurosciences.

Figure 1. Phenotypic characteristics of Iranian individuals with hearing loss

Amongst the 302 Iranian probands with hearing loss 267 had complete phenotypic data available. The inner ring indicates the severity of hearing loss, separated by color (red, yellow, and blue for mild to moderate, moderate to severe, and severe to profound, respectively); the middle ring indicates the onset, prelingual or postlingual; and the outer ring denotes the presence of additional phenotypes, Pendred syndrome (Pendred), Usher syndrome (Usher), or another suspected syndrome (other). White segments in the outer ring represent individuals with non-syndromic hearing loss.

Figure 2. Proportions of causative mutation types in 201 Iranian families

A. Proportional identification of homozygous versus compound heterozygous, X-linked, or mitochondrial variants within 201 diagnosed families. B. Causative mutation type as a portion of all causative alleles: missense, nonsense, splice-site, indel, and CNV’s. X-linked autosomal recessive, mitochondrial, and heterozygous variants are each assigned a count of one, while homozygous calls are counted as two, one for each allele (n=398). Causative variant type varied very slightly in individuals from consanguineous (C) or non-consanguineous (D) families, n=319 and 79 alleles, respectively.

Figure 3. Selected representative CNVs identified within a population of 302 Iranians

Homozygous whole gene deletion of OTOA gene (A), homozygous duplication of exons 7–10 of TMPRSS3 gene (B), and partial deletion of USH2A are shown below gene diagrams, indicating the structure of each gene and its exons. X-axis indicates chromosomal position. Y-axis shows the number of reads, represented as a ratio; 1.0 indicates the normal level of 2 alleles (black lines), 0.5 indicates a heterozygous deletion, 0 implies a homozygous deletion (both indicated by red lines), 1.5 indicates a heterozygous duplication and 2.0 corresponds to homozygous duplication (both indicated by blue lines).

Figure 4. Commonly diagnosed genes in Iranian families exhibit unique patterns for different mutation types

Mutation types: missense, nonsense, splice-site, indel, and CNV’s are displayed based upon allele count for all diagnosed patients, SLC26A4, MYO15A, MYO7A, CDH23, and PCHD15 with an n = 398, 74, 58, 30, 28, and 18, respectively.

Figure 5. Founder effects are associated with particular PCDH15, MYO15A, and SLC26A4 variants

Genotype and location for 14, 14, or 9 SNPs (green arrows) surrounding the causative variants in individuals segregating PCDH15 p.Gln1576Stop (A), MYO15A p. Tyr1392Stop (B), or SLC26A4 p.Leu445Trp (C) (red arrows) used to construct haplotypes.