Rapid screening of copy number variations in STR C by droplet digital PCR in patients with mild-to-moderate hearing loss

Copy number variations (CNVs) are commonly reported in STRC, the causal gene for DFNB16. Various techniques are used clinically for CNV detection, and droplet digital PCR (ddPCR) provides highly precise absolute quantification of DNA copy number. We aimed to validate the feasibility and efficiency of ddPCR in combination with long-range PCR (LR-PCR) in identifying CNVs and mutations in STRC. Additionally, we determined the frequency of CNVs and mutations in STRC in Japanese patients with mild-to-moderate hearing loss. We evaluated 84 unrelated Japanese patients with mild-to-moderate bilateral idiopathic or autosomal recessive nonsyndromic sensorineural hearing loss. The ratio of STRC copy number to the copy number of the internal control RPP30 ranged from 0.949 to 1.009 (0.989 ± 0.017) in 77 patients; it ranged from 0.484 to 0.538 (0.509 ± 0.024) in five patients and was 0.000 in two patients, indicating heterozygous and homozygous deletions, respectively. The copy number deletion prevalence rates were 7.7% and 0.9% in the patients and healthy controls, respectively. In combination with LR-PCR, ddPCR revealed that at least three patients (3.6%) had STRC-related hearing loss. Detecting STRC CNVs by ddPCR was rapid, precise, and cost-effective and facilitated the identification of STRC CNVs. Detecting a common genetic cause of hearing loss is now easier, thanks to a new method. Loss of one or both copies of STRC, a gene required for function of the sound-detecting hairs in the inner ear, can cause hearing loss. Compared to detecting mutations, counting gene copies had been very challenging. Taku Ito at Tokyo Medical and Dental University, Japan, and colleagues applied a new technology that divides samples into thousands of droplets, then measures the genetic information in each droplet, allowing precise gene copy counting. Studying samples from nearly 100 Japanese patients with hearing loss, they were able to determine that hearing loss in several patients was caused by deletion of one or both copies of STRC. This method will speed diagnosis of STRC-related hearing loss, and has potential for application to other disorders.