Hereditary Hearing Loss and Deafness Panel

Hearing loss (HL) or deafness is the most common sensory deficit in humans, affecting an estimated 5% of the world's population. HL may be caused by environmental or genetic factors (Azaiez et al. 2018. PubMed ID: 30245029). Hereditary hearing loss and deafness (HHLD) is classified by type (conductive, sensorineural, or mixed), age at onset (congenital, pre-lingual, post-lingual, or age-related), audiological characteristics (severity and affected frequencies), associated clinical features (syndromic or nonsyndromic), and mode of inheritance (autosomal dominant, autosomal recessive, X-linked, or mitochondrial).

Molecular genetic testing is available for many types of HHLD and plays a prominent role in diagnosis and genetic counseling (Hilgert et al. 2009. PubMed ID: 18804553; Shearer and Smith. 2012. PubMed ID: 23042251; Shearer et al. 2017. PubMed ID: 20301607; Smith et al. 2005. PubMed ID: 15752533).

This comprehensive panel consists of genes that have been associated with all types of HHLD. Importantly, both syndromic and nonsyndromic HL genes are included in this panel due to the variable or mild features associated with some syndromic HL genes.

In developed countries, HL is primarily caused by genetic factors and is nonsyndromic (Sloan-Heggen et al. 2016. PubMed ID: 26969326). The majority of HHLD is monogenic, with the exception of age-related HL, which is typically a complex genetic disorder (Azaiez et al. 2018. PubMed ID: 30245029). Congenital or pre-lingual HL is 80% genetic as compared to 20% acquired or environmental. Of pre-lingual genetic HL, 20% is syndromic and 80% nonsyndromic. Of pre-lingual genetic nonsyndromic hearing loss (NSHL), 80% is recessive, 19% is dominant, and the remainder is X-linked or mitochondrial (Shearer et al. 2017. PubMed ID: 20301607). To our knowledge, although de novo variants causing hearing loss have been documented, they are not a common cause of disease for the genes in this panel.

The gene most commonly associated with NSHL is GJB2 (also known as connexin 26), which accounts for 50% of congenital severe-to-profound autosomal recessive NSHL cases (Smith et al. 2016. PubMed ID: 20301449). The most prevalent pathogenic GJB2 variant is c.35delG, having a global population frequency of 0.62%, and a frequency of 0.96% in European populations (gnomAD population database).

The most common types of syndromic HL are Usher, Waardenburg, and Pendred syndromes (Koffler et al. 2015. PubMed ID: 26443487). Other less common syndromic causes of HL are also included in this panel (Perrault, Treacher Collins, Stickler, Jervell and Lange-Nielsen, branchio-oto-renal (BOR), Wolfram, Heimler, and Alport syndromes).

Copy number variant (CNV) detection is an important component of clinical genetic testing for HHLD, with CNVs contributing 18.7% of all positive genetic diagnoses in a large cohort of NSHL patients. The majority of CNVs detected in this study were in two genes: STRC (73%) and OTOA (13%). The carrier frequency of STRC CNVs was estimated at 1.1-1.6% in individuals without HL, indicating that STRC CNVs may be an equal or potentially larger contributor to autosomal recessive NSHL than GJB2 in some populations (Shearer et al. 2014. PubMed ID: 24963352). STRC CNVs often include the nearby CATSPER2 gene. Although CATSPER2 is not known to directly cause hearing loss, it is included in this panel because together with STRC, these two genes are associated with deafness-infertility syndrome. This test is able to detect CNVs in STRC, CATSPER2, and OTOA.

This test includes probes for CNV detection that cover all known GJB2 cis-regulatory element deletions associated with hearing loss, previously associated with digenic GJB2/GJB6 hearing loss and spanning from GJB6 to CRYL1. This includes the 309 kb GJB6-D13S1830 and 232 kb GJB6-D13S1854 deletions reported to be most common (del Castillo et al. 2003. PubMed ID: 14571368; del Castillo. 2005. PubMed ID: 15994881). The 95 kb region included in all published GJB2 regulatory element deletions has been especially targeted with CNV probes in this test (Tayoun et al. 2016. PubMed ID: 26444186). Additionally, a targeted test for the GJB6-D13S1830 and GJB6-D13S1854 deletions is available separately (see Related Test section for more information).

This panel also includes syndromic causes of HL affecting the external structure of the ear such as microtia (HOXA2) and aural atresia (TSHZ1). Genes that cause hearing loss as an early occurring feature (FITM2) and genes with new or rarely reported associations with HL are also included (AP1B1, ASIC5, ATOH1, CLDN9, DE1C, DMXL2, GRAP, IFNLR1, MAFB, MAP1B, MPZL2, REST, TBX1, TMEM126A, TMEM43, TRRAP, SLC44A4, NOG, PLS1, REEP6).

In a study of 1,119 individuals with any type of hearing loss, 82% of positive diagnoses were due to 15 genes (GJB2, STRC, SLC26A4, TECTA, MYO15A, MYO7A, USH2A, CDH23, ADGRV1, TMC1, PCDH15, OTOF, TMPRSS3, LOXHD1, and OTOA) (Sloan-Heggen et al. 2016. PubMed ID: 26969326).

See individual gene summaries for detailed information about molecular biology of gene products and spectra of pathogenic variants.

Clinical sensitivity of similar panels has been reported to be 33-40% overall, but can be as low as 1% in patients with unilateral hearing loss and as high as 72% in patients of Middle Eastern ethnicity (Shearer et al. 2014. PubMed ID: 24963352; Sloan-Heggen et al. 2016. PubMed ID: 26969326; Zazo Seco et al. 2017. PubMed ID: 28000701; Azaiez et al. 2018. PubMed ID: 30245029).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 97.9% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Paralogous regions of the genome exhibit high levels of sequence similarity to one or more additional genomic regions. Inherent limitations of short-read based NGS technology reduces coverage of paralogous regions via low read mapping quality scores. Reduced coverage may result in reduced ability to detect sequence variants or CNVs in paralogous regions.

In this panel, the genes with substantial paralogy and the coverage we are able to obtain for sequence variant detection via NGS are: STRC (52.8%), CATSPER2 (97.8%), and OTOA (76.1%). Despite high paralogy, we are able to detect large deletions and duplications via NGS based CNV analysis in these three genes. Long-range PCR assays designed with appropriate paralogy considerations and ability to detect gene/pseudogene conversions are used to confirm sequence variants in these genes. MLPA is used to confirm all CNVs originally detected via NGS for these high paralogy genes.

CATSPER2 is included only for CNV detection; sequence variants will not be reported. This test includes analysis of CATSPER2 due to deletion of both STRC and CATSPER2 together being associated with autosomal recessive deafness and male infertility (OMIM #611102). However, CATSPER2 copy number variants in patients with normal STRC copy number will not be reported due to lack of an established disease association without STRC involvement.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).