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Background  Congenital hearing loss is one of the most common birth defects. Early identification and management play a crucial role in improving patients’ communication and language acquisition. Previous studies demonstrated that genetic screening complements newborn hearing screening in clinical settings.    Methods  We developed a multiplex PCR amplicon sequencing assay to sequence the full coding region of the  GJB2  gene, the most pathogenic variants of the  SLC26A4  gene, and hotspot variants in the  MT-RNR1  gene. The sensitivity, specificity, and reliability were validated via samples with known genotypes. Finally, a pilot study was performed on 300 anonymous dried blood samples.    Results  Of 103 samples with known genotypes, the multiplex PCR amplicon sequencing assay accurately identified all the variants, demonstrating a 100% sensitivity and specificity. The consistency is high in the analysis of the test–retest reliability and internal consistency reliability. In the pilot study, 12.3% (37/300) of the newborns were found to carry at least one pathogenic variant, including 24, 10, and 3 from the  GJB2 ,  SLC26A4 , and  MT-RNR1  gene, respectively. With an allele frequency of 2.2%, the NM_004004.6( GJB2 ):c.109G>A was the most prevalent variant in the study population.    Conclusion  The multiplex PCR amplicon sequencing assay is an accurate and reliable test to detect hearing loss variants in the  GJB2 ,  SLC26A4 , and  MT - RNR1  genes. It can be used to screen genetic hearing loss in newborns.

A multiplex PCR amplicon sequencing assay to screen genetic hearing loss variants in newborns