Copy number variants are a common cause of non-syndromic hearing loss

Abstract

Background: Copy number variants (CNVs) are a well-recognized cause of genetic disease; however, methods for their identification are often gene-specific, excluded as 'routine' in screens of genetically heterogeneous disorders, and not implemented in most next-generation sequencing pipelines. For this reason, the contribution of CNVs to non-syndromic hearing loss (NSHL) is most likely under-recognized. We aimed to incorporate a method for CNV identification as part of our standard analysis pipeline and to determine the contribution of CNVs to genetic hearing loss.

Methods: We used targeted genomic enrichment and massively parallel sequencing to isolate and sequence all exons of all genes known to cause NSHL. We completed testing on 686 patients with hearing loss with no exclusions based on type of hearing loss or any other clinical features. For analysis we used an integrated method for detection of single nucleotide changes, indels and CNVs. CNVs were identified using a previously published method that utilizes median read-depth ratios and a sliding-window approach.

Results: Of 686 patients tested, 15.2% (104) carried at least one CNV within a known deafness gene. Of the 38.9% (267) of individuals for whom we were able to determine a genetic cause of hearing loss, a CNV was implicated in 18.7% (50). We identified CNVs in 16 different genes including 7 genes for which no CNVs have been previously reported. CNVs of STRC were most common (73% of CNVs identified) followed by CNVs of OTOA (13% of CNVs identified).

Conclusion: CNVs are an important cause of NSHL and their detection must be included in comprehensive genetic testing for hearing loss.

Figure 1

A biallelic gene-pseudogene conversion of STRC is the causative mutation in patient 45. (a) Ratio plots showing apparent homozygous deletion of first 11 exons of STRC and duplication of first 11 exons of ψSTRC. (b) Hypothesized mechanism of gene-pseudo-gene conversion (non-allelic gene conversion in trans) and depiction of the biallelic change in the patient.

Figure 2

Ratio depth-of-coverage plot showing homozygous deletion of OTOA as the causative mutation in patient 14. The last 10 exons appear to be only heterozygous deletion, but this is an artifact due to segmental duplication of these exons (see text for details).

Figure 3

A two-exon deletion of TMC1 is responsible for deafness in patient 100. (a) Ratio depth-of-coverage plot showing a two-exon heterozygous deletion. This deletion was found in trans with a missense change predicted to be pathogenic (c.1276G > A, p.Ala426Thr). (b) Highlighted region from UCSC genome browser RepeatMasker track demonstrates multiple short interspersed elements (SINEs; primarily Alu repeats), long interspersed elements (LINEs; including L1 repeats), and long terminal repeats (LTR) in this region. The two deleted exons are marked with asterisks. The hypothesized mechanism for this deletion involves these repeat elements and NAHR.