Cheng-Yu Tsai

Enlarged vestibular aqueduct (EVA) is a common inner ear malformation that causes sensorineural hearing loss. It is frequently associated with pathogenic variants in the SLC26A4 gene. This study aimed to investigate the genetic basis of hearing loss in Mongolian patients with EVA. Whole-exome sequencing was performed in 19 Mongolian patients from 15 unrelated families diagnosed with EVA with or without cochlear incomplete partition type II. All patients underwent high-resolution computed tomography of the temporal bone to confirm the diagnosis. Biallelic SLC26A4 pathogenic variants were identified in all 15 families, achieving a 100% diagnostic yield. The most frequent variant was c.919-2A>G (40%), followed by c.2027T>A (23.3%) and c.1318A>T (16.7%). The spectrum of variants includes population-specific variants found in East Asians (c.919-2A>G), North Asians (c.2027T>A), and Southwest Asians (c.716T>A), suggesting a unique mutation spectrum in this Mongolian cohort characterized by variants prevalent across various Eurasian populations, which remains to be confirmed in larger studies. Furthermore, correlation analyses on multi-ethnic allele frequencies of biallelic SLC26A4 genotypes demonstrated positive correlations with deaf cohorts of East Asian, North Asian, Northeast Asian, and Western Asian groups. Digenic inheritance (with pathogenic variants in FOXI1, KCNJ10, or EPHA2) was not observed, and there was no clear genotype–phenotype correlation between specific SLC26A4 genotypes and hearing levels or inner ear malformations. This study provides a comprehensive overview of the genetic landscape of EVA in the Mongolian population. The identification of biallelic SLC26A4 pathogenic variants in all families underscores the clinical role of this gene in EVA pathogenesis. The observed pan-ethnic mutation spectrum likely reflects the genetic diversity resulting from historical migrations of Mongolians.

Artificial intelligence (AI) has been used in many areas of medicine, and large language models (LLMs) have shown potential utility for various clinical applications. However, to determine if LLMs can accelerate the pace of genetic diagnosis and discovery, we examined whether recently developed LLMs (Med‐PaLM 2 and Gemini) could assist in solving four types of genetic problems with sequentially increasing complexity. First, in response to free‐text input, Med‐PaLM 2 correctly identified murine genes with experimentally verified causative genetic factors for six previously studied murine models of biomedical traits. Second, Med‐PaLM 2 identified a novel causative murine genetic factor for spontaneous hearing loss that was validated using knock‐in mice. Third, we developed a retrieval and grounding pipeline that enabled Gemini 2.5 Pro to analyze large lists of genes, which contained genetic variants that were identified in the genomic sequences of 20 human subjects with hearing loss, and demonstrated that it can assist in identifying causative genetic factors for hearing loss. Fourth, we modified the genetic analysis pipeline to enable Gemini 2.5 Pro without any task‐specific fine‐tuning to identify causative genetic factors for six subjects with rare genetic diseases, which required 14 to 34 different terms to describe their multi‐faceted symptom complexes. These results demonstrate that an AI pipeline can facilitate genetic diagnosis and discovery in mice and humans.

Waardenburg syndrome (WS) is a rare genetic disorder that affects both hearing and pigmentation. The wide divergence of WS poses significant diagnostic and management challenges. This study investigated type 4 WS within an underrepresented Mongolian population. Whole-exome sequencing revealed that two unique heterozygous variants were identified in the SOX10 gene: c.393C>G (p.Asn131Lys) in a five-year-old female patient presenting with profound sensorineural hearing loss (SNHL), dystopia canthorum, and a white forelock; and c.535A>T (p.Lys179Ter) in a nine-year-old male patient presenting with profound SNHL, dystopia canthorum, and Hirschsprung’s disease. Temporal bone imaging revealed abnormalities in the inner ear structure in both patients. The genotypic and phenotypic characteristics were meticulously delineated, incorporating the deleterious effects of these variants, as evaluated by multiple predictive tools and the American College of Medical Genetics and Genomics (ACMG) criteria. In addition, structural characterizations were also presented using AlphaFold. The findings of this study contribute valuable genetic data to the limited literature on type 4 WS within this ethnic group and highlight the importance of genetic testing and multidisciplinary care for this rare disorder in settings with limited resources.

Objectives. State-run newborn hearing screening (NBHS) programs have limitations in identifying children with mild or late-onset sensorineural hearing impairment (SNHI). Given that over 50% of pediatric SNHI cases are linked to genetic causes, the increasing accessibility of high-throughput, low-cost genomic sequencing may help address these shortcomings. This study investigates the feasibility of integrating a next-generation sequencing (NGS)-based genomic screening protocol into conventional NBHS and examines its potential benefits and challenges.Methods. A total of 8,261 newborns underwent simultaneous NBHS and NGS-based genomic screening targeting 46 deafness genes in this prospective study. The subjects’ genotypes were determined, and those with conclusive genetic diagnoses received audiological assessments.Results. Conclusive genetic diagnoses were confirmed in 164 subjects, with 112 carrying variants in GJB2 and MTRNR1 and 52 carrying variants in other deafness genes. Notably, 126 of these subjects passed the NBHS, suggesting that an additional 1.5% (126/8,261) of children at risk for SNHI, who would have been missed by conventional physiological screening, can be identified through targeted genomic screening in the general population. Furthermore, one subject’s father, who carried a COL4A5 variant, and three paternal relatives of another subject carrying an EDNRB variant (previously undiagnosed) were identified with Alport and Waardenburg syndromes, respectively, underscoring the familial benefits of this approach.Conclusion. Targeted genomic sequencing in newborns may serve as a valuable complement to conventional NBHS by identifying children at risk for SNHI and enabling early diagnosis in families with non-syndromic mimics.

Recessive variants of SLC26A4 are a common cause of hereditary hearing impairment and are responsible for non-syndromic enlarged vestibular aqueducts and Pendred syndrome. Patients with bi-allelic SLC26A4 variants often suffer from fluctuating hearing loss and recurrent vertigo, ultimately leading to severe to profound hearing impairment. However, there are currently no satisfactory prevention or treatment options for this condition. The CRISPR/Cas9 genome-editing technique is a well-known tool for correcting point mutations or manipulating genes and shows potential therapeutic applications for hereditary disorders. In this study, we used the homology-independent targeted integration (HITI) strategy to correct the SLC26A4 c.919-2A>G variant, the most common SLC26A4 variant in the Han Chinese population. Next-generation sequencing was performed to evaluate the editing efficiency of the HITI strategy. The results showed that only 0.15% of the reads successfully exhibited HITI integration, indicating that the c.919-2 region may not be a suitable region for HITI selection. This suggests that other site selection or insertion strategies may be needed to improve the efficiency of correcting the SLC26A4 c.919-2A>G variant. This experience may serve as a valuable reference for other researchers considering CRISPR target design in this region.

Background: Pathogenic variants in OTOF are a major cause of auditory synaptopathy. However, challenges remain in interpreting OTOF variants, including difficulties in confirming haplotype phasing using traditional short-read sequencing (SRS) due to the large gene size, the potential incomplete penetrance of certain variants, and difficulties in assessing variants at non-canonical splice sites. This study aims to revisit the genetic landscape of OTOF variants in a Taiwanese non-syndromic auditory neuropathy spectrum disorder (ANSD) cohort using a combination of sequencing technologies, predictive tools, and experimental validations. Methods: We performed SRS to analyze OTOF variants in 65 unrelated Taiwanese patients diagnosed with non-syndromic ANSD, complemented by long-read sequencing (LRS) for haplotype phasing. A prediction-to-validation pipeline was implemented to assess the pathogenicity of cryptic variants using SpliceAI software and minigene assays. Results: Biallelic pathogenic OTOF variants were identified in 33 patients (50.8%), while monoallelic variants were found in five patients. Three novel variants, c.3864G > A (p.Ala1288 =), c.4501G > A (p.Ala1501Thr), and c.5813 + 2T > C, were detected. The pathogenicity of two non-canonical mis-splicing variants, c.3894 + 5G > C and c.3864G > A (p.Ala1288 =), was confirmed by minigene assays. LRS-based haplotype phasing revealed that the common missense variant c.5098G > C (p.Glu1700Gln) and the novel variant c.5975A > G (p.Lys1992Arg) are in cis and form a founder pathogenic allele in the Taiwanese population. Conclusions: Our study highlights the genetic heterogeneity of DFNB9 and emphasizes the importance of population-specific variant interpretation. The integration of advanced sequencing technologies, predictive algorithms, and functional validation assays will improve the accuracy of molecular diagnosis and inform personalized treatment strategies for individuals with DFNB9. Graphical

Background: Enlarged vestibular aqueduct (EVA) is a common inner ear malformation that can cause sensorineural hearing loss. It is frequently associated with mutations in the SLC26A4 gene. This study aimed to investigate the genetic basis of hearing loss in Mongolian patients with EVA. Methods: Whole exome sequencing was performed in 19 Mongolian patients from 15 unrelated families diagnosed with EVA with/without cochlear incomplete partition type II. All patients underwent high-resolution computed tomography of the temporal bone to confirm the diagnosis. Results: Biallelic SLC26A4 pathogenic variants were identified in all 15 families (100%). The most frequent variant was c.919-2A>G (40%), followed by c.2027T>A (23.3%) and c.1318A>T (16.7%). Population-specific variants in East Asians (c.919-2A>G), North Asians (c.2027T>A), and Southwest Asians (c.716T>A) were all present in Mongolian patients, demonstrating a panethnic mutation spectrum. Digenic inheritance was not observed. There was no clear genotype-phenotype correlation between specific SLC26A4 genotypes and hearing levels or inner ear malformations. Conclusions: This study provides a comprehensive overview of the genetic landscape of EVA in the Mongolian population. The identification of biallelic SLC26A4 pathogenic variants in all families highlights the importance of this gene in the pathogenesis of EVA. The unique mutation spectrum observed in this study may reflect the genetic diversity resulting from historical migrations of Mongolians.

Background: Sensorineural hearing impairment (SNHI) is a common disorder with a significant genetic component. Genetic testing for SNHI often involves next-generation sequencing (NGS), but SNHI-related pathogenic STRC variants cannot be directly addressed by conventional NGS due to the complex genomic scenario derived from large genomic rearrangements and a highly homologous pseudogene. Long-read sequencing (LRS) offers an unprecedented resolution to these challenges. Methods: We developed a comprehensive workflow that integrates the PacBio-based LRS approach with marker-mediated refinements to effectively address pseudogene contamination. This methodology was applied to analyze the STRC gene in a cohort of 100 unrelated Taiwanese patients diagnosed with SNHI of unknown genetic cause after first-tier NGS testing. Results: We identified bi-allelic STRC variants in 11 patients (11% diagnostic yield), including homozygous deletions, compound heterozygous deletions and conversions, and compound heterozygous SNVs and CNVs. In total, we detected STRC variants in 27 patients, with 81.6% of these variants occurring in patients with mild to moderate SNHI. Conclusions: This study represents the first large-scale clinical investigation utilizing LRS technology for the genetic diagnosis of SNHI. Our study highlights the diagnostic capabilities of LRS in detecting complex variants within the STRC and advancing our understanding of the genetic etiology of SNHI that remains unresolved by conventional NGS.

Background/Objective: The genetic landscape of sensorineural hearing impairment (SNHI) varies across populations. In Mongolia, previous studies have shown a lower prevalence of GJB2 mutations and a higher frequency of variants in other deafness-related genes. This study aimed to investigate the genetic variants associated with idiopathic SNHI in Mongolian patients. Methods: We utilized the next-generation sequencing for investigating the causative mutations in 99 Mongolian patients with SNHI. Results: We identified pathogenic variants in 53 of the 99 SNHI patients (54%), with SLC26A4 being the most frequently mutated gene. The c.919-2A>G variant in SLC26A4 was the most prevalent, accounting for 46.2% of the mutant alleles. In addition, we identified 19 other known and 21 novel mutations in a total of 21 SNHI genes in autosomal recessive or dominant inheritance patterns. Conclusions: Our findings expand the understanding of the genetic landscape of SNHI in Mongolia and highlight the importance of considering population-specific variations in genetic testing and counseling for SNHI.

Sensorineural hearing impairment (SNHI), a common childhood disorder with heterogeneous genetic causes, can lead to delayed language development and psychosocial problems. Next-generation sequencing (NGS) offers high-throughput screening and high-sensitivity detection of genetic etiologies of SNHI, enabling clinicians to make informed medical decisions, provide tailored treatments, and improve prognostic outcomes. This review covers the diverse etiologies of HHI and the utility of different NGS modalities (targeted sequencing and whole exome/genome sequencing), and includes HHI-related studies on newborn screening, genetic counseling, prognostic prediction, and personalized treatment. Challenges such as the trade-off between cost and diagnostic yield, detection of structural variants, and exploration of the non-coding genome are also highlighted. In the current landscape of NGS-based diagnostics for HHI, there are both challenges (e.g. detection of structural variants and non-coding genome variants) and opportunities (e.g. the emergence of medical artificial intelligence tools). The authors advocate the use of technological advances such as long-read sequencing for structural variant detection, multi-omics analysis for non-coding variant exploration, and medical artificial intelligence for pathogenicity assessment and outcome prediction. By integrating these innovations into clinical practice, precision medicine in the diagnosis and management of HHI can be further improved.