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Diverse spectrum of rare deafness genes underlies early-childhood hearing loss in Japanese patients: a cross-sectional, multi-center next-generation sequencing study.

Mutai H, Suzuki N, Shimizu A, Torii C, Namba K, Morimoto N, Kudoh J, Kaga K, Kosaki K, Matsunaga T - Orphanet J Rare Dis (2013)

Bottom Line: Candidate genes were identified in 7 of the 15 families.Mutations in Usher syndrome-related genes were detected in three families, including one double heterozygous mutation of CDH23 and PCDH15.Targeted NGS analysis revealed a diverse spectrum of rare deafness genes in Japanese subjects and underscores implications for efficient genetic testing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan. matsunagatatsuo@kankakuki.go.jp.

ABSTRACT

Background: Genetic tests for hereditary hearing loss inform clinical management of patients and can provide the first step in the development of therapeutics. However, comprehensive genetic tests for deafness genes by Sanger sequencing is extremely expensive and time-consuming. Next-generation sequencing (NGS) technology is advantageous for genetic diagnosis of heterogeneous diseases that involve numerous causative genes.

Methods: Genomic DNA samples from 58 subjects with hearing loss from 15 unrelated Japanese families were subjected to NGS to identify the genetic causes of hearing loss. Subjects did not have pathogenic GJB2 mutations (the gene most often associated with inherited hearing loss), mitochondrial m.1555A>G or 3243A>G mutations, enlarged vestibular aqueduct, or auditory neuropathy. Clinical features of subjects were obtained from medical records. Genomic DNA was subjected to a custom-designed SureSelect Target Enrichment System to capture coding exons and proximal flanking intronic sequences of 84 genes responsible for nonsyndromic or syndromic hearing loss, and DNA was sequenced by Illumina GAIIx (paired-end read). The sequences were mapped and quality-checked using the programs BWA, Novoalign, Picard, and GATK, and analyzed by Avadis NGS.

Results: Candidate genes were identified in 7 of the 15 families. These genes were ACTG1, DFNA5, POU4F3, SLC26A5, SIX1, MYO7A, CDH23, PCDH15, and USH2A, suggesting that a variety of genes underlie early-childhood hearing loss in Japanese patients. Mutations in Usher syndrome-related genes were detected in three families, including one double heterozygous mutation of CDH23 and PCDH15.

Conclusion: Targeted NGS analysis revealed a diverse spectrum of rare deafness genes in Japanese subjects and underscores implications for efficient genetic testing.

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Related in: MedlinePlus

Molecular modeling of ACTG containing the p.G268S mutation. (A) Ribbon model of filamentous actin gamma 1. (B) Magnified ribbon model of filamentous actin gamma 1. Glycine residue 268 is shown in red and indicated by an arrow. Regions in yellow and green indicate the hydrophobic loop (262–274; a) and the corresponding interactive residues (281–289; b), respectively. (C and D) Vertical views of the regions a and b superimposed with predicted surface hydrophobicity in the wild type (C) and the p.G268S mutant (D).
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Figure 2: Molecular modeling of ACTG containing the p.G268S mutation. (A) Ribbon model of filamentous actin gamma 1. (B) Magnified ribbon model of filamentous actin gamma 1. Glycine residue 268 is shown in red and indicated by an arrow. Regions in yellow and green indicate the hydrophobic loop (262–274; a) and the corresponding interactive residues (281–289; b), respectively. (C and D) Vertical views of the regions a and b superimposed with predicted surface hydrophobicity in the wild type (C) and the p.G268S mutant (D).

Mentions: In family 1 (Figure 1A), subjects III:3 and IV:2 with hearing loss had a unique heterozygous missense mutation of ACTG1 (c.802G >A; p.G268S), whereas subject III:4 with normal hearing did not. ACTG1 encodes actin gamma 1 and is responsible for DFNA20/26 (OMIM 604717) [28]. The glycine residue at 268 of actin gamma 1 is located on a hydrophobic loop that has been suggested to be critical for polymerization of the actin monomers into a filament (Figures 2A and 2B) [29]. Molecular modeling predicted that the p.G268S mutation would disrupt the hydrophobic interactions that are important for polymerization of actin gamma 1 (Figures 2C and Figure 2D). The p.G268S mutant would weaken polymerization of actin gamma 1, which could result in destabilized cytoskeletal structure of stereocilia and dysfunction of the sensory hair cells.


Diverse spectrum of rare deafness genes underlies early-childhood hearing loss in Japanese patients: a cross-sectional, multi-center next-generation sequencing study.

Mutai H, Suzuki N, Shimizu A, Torii C, Namba K, Morimoto N, Kudoh J, Kaga K, Kosaki K, Matsunaga T - Orphanet J Rare Dis (2013)

Molecular modeling of ACTG containing the p.G268S mutation. (A) Ribbon model of filamentous actin gamma 1. (B) Magnified ribbon model of filamentous actin gamma 1. Glycine residue 268 is shown in red and indicated by an arrow. Regions in yellow and green indicate the hydrophobic loop (262–274; a) and the corresponding interactive residues (281–289; b), respectively. (C and D) Vertical views of the regions a and b superimposed with predicted surface hydrophobicity in the wild type (C) and the p.G268S mutant (D).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231469&req=5

Figure 2: Molecular modeling of ACTG containing the p.G268S mutation. (A) Ribbon model of filamentous actin gamma 1. (B) Magnified ribbon model of filamentous actin gamma 1. Glycine residue 268 is shown in red and indicated by an arrow. Regions in yellow and green indicate the hydrophobic loop (262–274; a) and the corresponding interactive residues (281–289; b), respectively. (C and D) Vertical views of the regions a and b superimposed with predicted surface hydrophobicity in the wild type (C) and the p.G268S mutant (D).
Mentions: In family 1 (Figure 1A), subjects III:3 and IV:2 with hearing loss had a unique heterozygous missense mutation of ACTG1 (c.802G >A; p.G268S), whereas subject III:4 with normal hearing did not. ACTG1 encodes actin gamma 1 and is responsible for DFNA20/26 (OMIM 604717) [28]. The glycine residue at 268 of actin gamma 1 is located on a hydrophobic loop that has been suggested to be critical for polymerization of the actin monomers into a filament (Figures 2A and 2B) [29]. Molecular modeling predicted that the p.G268S mutation would disrupt the hydrophobic interactions that are important for polymerization of actin gamma 1 (Figures 2C and Figure 2D). The p.G268S mutant would weaken polymerization of actin gamma 1, which could result in destabilized cytoskeletal structure of stereocilia and dysfunction of the sensory hair cells.

Bottom Line: Candidate genes were identified in 7 of the 15 families.Mutations in Usher syndrome-related genes were detected in three families, including one double heterozygous mutation of CDH23 and PCDH15.Targeted NGS analysis revealed a diverse spectrum of rare deafness genes in Japanese subjects and underscores implications for efficient genetic testing.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan. matsunagatatsuo@kankakuki.go.jp.

ABSTRACT

Background: Genetic tests for hereditary hearing loss inform clinical management of patients and can provide the first step in the development of therapeutics. However, comprehensive genetic tests for deafness genes by Sanger sequencing is extremely expensive and time-consuming. Next-generation sequencing (NGS) technology is advantageous for genetic diagnosis of heterogeneous diseases that involve numerous causative genes.

Methods: Genomic DNA samples from 58 subjects with hearing loss from 15 unrelated Japanese families were subjected to NGS to identify the genetic causes of hearing loss. Subjects did not have pathogenic GJB2 mutations (the gene most often associated with inherited hearing loss), mitochondrial m.1555A>G or 3243A>G mutations, enlarged vestibular aqueduct, or auditory neuropathy. Clinical features of subjects were obtained from medical records. Genomic DNA was subjected to a custom-designed SureSelect Target Enrichment System to capture coding exons and proximal flanking intronic sequences of 84 genes responsible for nonsyndromic or syndromic hearing loss, and DNA was sequenced by Illumina GAIIx (paired-end read). The sequences were mapped and quality-checked using the programs BWA, Novoalign, Picard, and GATK, and analyzed by Avadis NGS.

Results: Candidate genes were identified in 7 of the 15 families. These genes were ACTG1, DFNA5, POU4F3, SLC26A5, SIX1, MYO7A, CDH23, PCDH15, and USH2A, suggesting that a variety of genes underlie early-childhood hearing loss in Japanese patients. Mutations in Usher syndrome-related genes were detected in three families, including one double heterozygous mutation of CDH23 and PCDH15.

Conclusion: Targeted NGS analysis revealed a diverse spectrum of rare deafness genes in Japanese subjects and underscores implications for efficient genetic testing.

Show MeSH
Related in: MedlinePlus