Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel

Nishio, Shin‐ya; Moteki, Hideaki; Usami, Shin‐ichi

doi:10.1002/mgg3.399

Cited by 26 publications

(24 citation statements)

References 17 publications

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“…Emulsion PCR and sequencing was performed according to the manufacturer’s instructions. The detailed protocol has been described elsewhere [38,39]. MPS was performed with an Ion Proton™ system using the Ion PI™ Hi-Q™ Sequencing 200 Kit and Ion PI™ Chip (ThermoFisher Scientific, Waltham, MA, USA) according to the manufacturers’ instructions.…”

Section: Methodsmentioning

confidence: 99%

Detailed Clinical Features of Deafness Caused by a Claudin-14 Variant

Kitano

Nishio

Usami

2019

IJMS

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Tight junctions are cellular junctions that play a major role in the epithelial barrier function. In the inner ear, claudins, occludin, tricellulin, and angulins form the bicellular or tricellular binding of membrane proteins. In these, one type of claudin gene, CLDN14, was reported to be responsible for human hereditary hearing loss, DFNB29. Until now, nine pathogenic variants have been reported, and most phenotypic features remain unclear. In the present study, genetic screening for 68 previously reported deafness causative genes was carried out to identify CLDN14 variants in a large series of Japanese hearing loss patients, and to clarify the prevalence and clinical characteristics of DFNB29 in the Japanese population. One patient had a homozygous novel variant (c.241C>T: p.Arg81Cys) (0.04%: 1/2549). The patient showed progressive bilateral hearing loss, with post-lingual onset. Pure-tone audiograms indicated a high-frequency hearing loss type, and the deterioration gradually spread to other frequencies. The patient showed normal vestibular function. Cochlear implantation improved the patient’s sound field threshold levels, but not speech discrimination scores. This report indicated that claudin-14 is essential for maintaining the inner ear environment and suggested the possible phenotypic expansion of DFNB29. This is the first report of a patient with a tight junction variant receiving a cochlear implantation.

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Section: Methodsmentioning

confidence: 99%

Detailed Clinical Features of Deafness Caused by a Claudin-14 Variant

Kitano

Nishio

Usami

2019

IJMS

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“…CNV analysis was performed with NGS analysis read depth data according to the method described in a previous report 58 .…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of syndromic hearing loss patients in Japan

Ideura

Nishio

Moteki

et al. 2019

Sci Rep

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More than 400 syndromes associated with hearing loss and other symptoms have been described, corresponding to 30% of cases of hereditary hearing loss. In this study we aimed to clarify the mutation spectrum of syndromic hearing loss patients in Japan by using next-generation sequencing analysis with a multiple syndromic targeted resequencing panel (36 target genes). We analyzed single nucleotide variants, small insertions, deletions and copy number variations in the target genes. We enrolled 140 patients with any of 14 syndromes (BOR syndrome, Waardenburg syndrome, osteogenesis imperfecta, spondyloepiphyseal dysplasia congenita, Stickler syndrome, CHARGE syndrome, Jervell and Lange-Nielsen syndrome, Pendred syndrome, Klippel-Feil syndrome, Alport syndrome, Norrie disease, Treacher-Collins syndrome, Perrault syndrome and auditory neuropathy with optic atrophy) and identified the causative variants in 56% of the patients. This analysis could identify the causative variants in syndromic hearing loss patients in a short time with a high diagnostic rate. In addition, it was useful for the analysis of the cases who only partially fulfilled the diagnostic criteria.

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“…We performed a CNV detection method with Ion AmpliSeq sequencing and multiplex PCR-based targeted genome enrichment. The detailed protocol has been described elsewhere [40]. The read depth data was used for copy number analysis.…”

Section: Methodsmentioning

confidence: 99%

Mid-Frequency Hearing Loss Is Characteristic Clinical Feature of OTOA-Associated Hearing Loss

Sugiyama

Moteki

Kitano

et al. 2019

Genes

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The OTOA gene (Locus: DFNB22) is reported to be one of the causative genes for non-syndromic autosomal recessive hearing loss. The copy number variations (CNVs) identified in this gene are also known to cause hearing loss, but have not been identified in Japanese patients with hearing loss. Furthermore, the clinical features of OTOA-associated hearing loss have not yet been clarified. In this study, we performed CNV analyses of a large Japanese hearing loss cohort, and identified CNVs in 234 of 2262 (10.3%, 234/2262) patients with autosomal recessive hearing loss. Among the identified CNVs, OTOA gene-related CNVs were the second most frequent (0.6%, 14/2262). Among the 14 cases, 2 individuals carried OTOA homozygous deletions, 4 carried heterozygous deletions with single nucleotide variants (SNVs) in another allele. Additionally, 1 individual with homozygous SNVs in the OTOA gene was also identified. Finally, we identified 7 probands with OTOA-associated hearing loss, so that its prevalence in Japanese patients with autosomal recessive hearing loss was calculated to be 0.3% (7/2262). As novel clinical features identified in this study, the audiometric configurations of patients with OTOA-associated hearing loss were found to be mid-frequency. This is the first study focused on the detailed clinical features of hearing loss caused by this gene mutation and/or gene deletion.

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Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel

Cited by 26 publications

References 17 publications

Detailed Clinical Features of Deafness Caused by a Claudin-14 Variant

Detailed Clinical Features of Deafness Caused by a Claudin-14 Variant

Comprehensive analysis of syndromic hearing loss patients in Japan

Mid-Frequency Hearing Loss Is Characteristic Clinical Feature of OTOA-Associated Hearing Loss

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