Massively Parallel DNA Sequencing Successfully Identifies New Causative Mutations in Deafness Genes in Patients with Cochlear Implantation and EAS

Miyagawa, Maiko; Nishio, Shin‐ya; Ikeda, Takuo; Fukushima, Kunihiro; Usami, Shin‐ichi

doi:10.1371/journal.pone.0075793

Cited by 82 publications

(131 citation statements)

References 20 publications

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“…The detailed protocol was described elsewhere [5]. After preparation, the amplicon libraries were diluted to 20pM and equal amounts of 6 libraries for 6 patients were pooled for one sequence reaction.…”

Section: Methodsmentioning

confidence: 99%

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Mutations in LOXHD1 Gene Cause Various Types and Severities of Hearing Loss

Mori

Moteki

Kobayashi

et al. 2015

Ann Otol Rhinol Laryngol

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Objective We present two families that were identified with novel mutations in LOXHD1, as a cause of non-progressive hearing loss. Methods One thousand three hundred fourteen (1,314) Japanese subjects with sensorineural hearing loss from unrelated families were enrolled in the study. Targeted genomic enrichment and massively parallel sequencing of all known non-syndromic hearing loss genes were performed to identify the genetic cause of hearing loss. Results Two patients in one family affected with homozygous mutation; c.879+1G>A in LOXHD1, showed profound congenital hearing loss, whereas two patients in the other family with compound heterozygous mutations; c.5869G>T (p.E1957X) and c.4480C>T (p.R1494X) showed moderate to severe hearing loss. Conclusion Mutations in LOXHD1 are extremely rare, and these cases are the first identified in a Japanese population. The genotype-phenotype correlation in LOXHD1 is still unclear. The differences of phenotypes in each patient might be the result of the nature of the mutations, or the location at the gene, or be influenced by genetic modifier.

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Section: Methodsmentioning

confidence: 99%

“…The detailed protocol was described elsewhere [5]. MPS was performed with an Ion Torrent Personal Genome Machine (PGM) system using the Ion PGM ™ 200 Sequencing Kit and Ion 318 ™ Chip (Life Technologies).…”

Section: Methodsmentioning

confidence: 99%

Mutations in LOXHD1 Gene Cause Various Types and Severities of Hearing Loss

Mori

Moteki

Kobayashi

et al. 2015

Ann Otol Rhinol Laryngol

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show abstract

“…The detailed protocol was described elsewhere (Miyagawa et al, 2013 The sequence data were processed with standard Ion Torrent SuiteÔ Software ver 4.0 and the Torrent Server was used to successively map the human genome sequence (build GRCh37/hg19) with a Torrent Mapping Alignment Program optimized to Ion TorrentÔ data. After the sequence mapping, the DNA variant regions were piled up with Torrent Variant Caller plug-in software set to run at high stringency.…”

Section: Amplicon Library Preparationmentioning

confidence: 99%

“…In our previous study, MPS analysis using an Ion PGMÔ system and Ion AmpliSeqÔ for the known 63 deafnesscausing genes was able to identify rare gene mutations responsible for hearing loss in patients with cochlea implantation (Miyagawa et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Clinical Application of a Custom AmpliSeq Library and Ion Torrent PGM Sequencing to Comprehensive Mutation Screening for Deafness Genes

Nishio

Hayashi²,

Watanabe³

et al. 2015

Genetic Testing and Molecular Biomarkers

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Background: Congenital hearing loss is one of the most common sensory disorders, with 50-70% of cases attributable to genetic causes. Although recent advances in the identification of deafness genes have resulted in more accurate molecular diagnosis, leading to the better determination of suitable clinical interventions, difficulties remain with regard to clinical applications due to the extreme genetic heterogeneity of deafness. Aim: Toward more effective genetic testing, we adopted Massively Parallel DNA Sequencing (MPS) of target genes using an Ion PGMÔ system and an Ion AmpliSeqÔ panel to diagnose common mutations responsible for deafness and discover rare causative gene mutations. Before its clinical application, we investigated the accuracy of MPS-based genetic testing. Results: We compared the results of Invader assay-based genetic screening, the accuracy of which has already been verified in previous studies, with those of MPS-based genetic testing for a large population of Japanese deafness patients and revealed that over 99.98% of the results were the same for each genetic testing system. Conclusion: The Ion Personal Genome Machine system had sufficient uniformity and accuracy for application to the clinical diagnosis of common causative mutations and efficiently identified rare causative mutations and/or mutation candidates.

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“…We performed comprehensive next-generation sequencing analysis for 68 genes reported to cause hearing impairment as described previously [6]. As a result, we identified compound heterozygous mutations, GJB2:NM004004.5:c. 223C > T:p.R75W and GJB2:NM004004.5:c.235delC: p.L79fs, in the proband.…”

Section: Introductionmentioning

confidence: 99%

Massively Parallel DNA Sequencing Successfully Identifies New Causative Mutations in Deafness Genes in Patients with Cochlear Implantation and EAS

Cited by 82 publications

References 20 publications

Mutations in LOXHD1 Gene Cause Various Types and Severities of Hearing Loss

Mutations in LOXHD1 Gene Cause Various Types and Severities of Hearing Loss

Clinical Application of a Custom AmpliSeq Library and Ion Torrent PGM Sequencing to Comprehensive Mutation Screening for Deafness Genes

Compound heterozygous dominant and recessiveGJB2mutations cause deafness with palmoplantar keratoderma

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