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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

Pedigrees of the seven families with hearing loss. Double horizontal bars above a symbol indicate individuals who underwent genetic analysis by targeted next-generation sequencing. Single horizontal bars above a symbol indicate individuals who underwent analysis by Sanger sequencing. A-G denote pedigrees of family 1-7, respectively.
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Figure 1: Pedigrees of the seven families with hearing loss. Double horizontal bars above a symbol indicate individuals who underwent genetic analysis by targeted next-generation sequencing. Single horizontal bars above a symbol indicate individuals who underwent analysis by Sanger sequencing. A-G denote pedigrees of family 1-7, respectively.

Mentions: Pedigrees of the seven families are shown in Figure 1; clinical features are described in Table 1 and supplemental materials [Additional file 2 and Additional file 3]. In this targeted NGS study, the mean read depth of the target regions was more than 100× for all subjects (data not shown). Table 2 summarizes the number of variants detected from the 61 or 84 targeted genes for each subject. The number of variants was consistent across subjects (339–435 variants per subject for 61 genes, 539–607 variants per subject for 84 genes), which supported the reproducibility and reliability of our technical procedures and analytical pipeline. After excluding frequent variants (>1%) in public databases, 12 variants of 9 genes co-segregated with symptoms and were selected as possible pathogenic mutations (Table 3) or variants with uncertain pathogenicity in 7 families (Table 4).


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)

Pedigrees of the seven families with hearing loss. Double horizontal bars above a symbol indicate individuals who underwent genetic analysis by targeted next-generation sequencing. Single horizontal bars above a symbol indicate individuals who underwent analysis by Sanger sequencing. A-G denote pedigrees of family 1-7, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Pedigrees of the seven families with hearing loss. Double horizontal bars above a symbol indicate individuals who underwent genetic analysis by targeted next-generation sequencing. Single horizontal bars above a symbol indicate individuals who underwent analysis by Sanger sequencing. A-G denote pedigrees of family 1-7, respectively.
Mentions: Pedigrees of the seven families are shown in Figure 1; clinical features are described in Table 1 and supplemental materials [Additional file 2 and Additional file 3]. In this targeted NGS study, the mean read depth of the target regions was more than 100× for all subjects (data not shown). Table 2 summarizes the number of variants detected from the 61 or 84 targeted genes for each subject. The number of variants was consistent across subjects (339–435 variants per subject for 61 genes, 539–607 variants per subject for 84 genes), which supported the reproducibility and reliability of our technical procedures and analytical pipeline. After excluding frequent variants (>1%) in public databases, 12 variants of 9 genes co-segregated with symptoms and were selected as possible pathogenic mutations (Table 3) or variants with uncertain pathogenicity in 7 families (Table 4).

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