Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes

Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES)...

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Published inOrphanet journal of rare diseases Vol. 17; no. 1; p. 114
Main Authors Mutai, Hideki, Momozawa, Yukihide, Kamatani, Yoichiro, Nakano, Atsuko, Sakamoto, Hirokazu, Takiguchi, Tetsuya, Nara, Kiyomitsu, Kubo, Michiaki, Matsunaga, Tatsuo
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 05.03.2022
BioMed Central
BMC
Subjects
Deafness - genetics
Deafness - pathology
Deafness genes
Development and progression
Exome - genetics
Genetic aspects
Genetic susceptibility
GTP-Binding Proteins - genetics
Health aspects
Hearing loss
Hearing Loss - genetics
Humans
Intercellular Signaling Peptides and Proteins - genetics
Japan
Mutation
Nuclear Proteins - genetics
Pedigree
Risk factors
Solute Carrier Family 12, Member 2 - genetics
Whole Exome Sequencing
Whole exome sequencing analysis
Japan
Whole exome sequencing analysis
Deafness genes
Hearing loss
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Abstract Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. Trios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. Our findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes.
AbstractList Abstract Background Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. Results Trios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. Conclusions Our findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes.
Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. Trios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. Our findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes.
Background Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. Results Trios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. Conclusions Our findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes. Keywords: Whole exome sequencing analysis, Hearing loss, Deafness genes
Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. Trios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. Our findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes.
BACKGROUNDHeterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect pathogenic variants in multiple deafness genes, in addition to novel candidate genes associated with hearing loss, whole exome sequencing (WES), followed by analysis prioritizing genes categorized in four tiers, were applied. RESULTSTrios from families with non-syndromic or syndromic hearing loss (n = 72) were subjected to WES. After segregation analysis and interpretation according to American College of Medical Genetics and Genomics guidelines, candidate pathogenic variants in 11 previously reported deafness genes (STRC, MYO15A, CDH23, PDZD7, PTPN11, SOX10, EYA1, MYO6, OTOF, OTOG, and ZNF335) were identified in 21 families. Discrepancy between pedigree inheritance and genetic inheritance was present in one family. In addition, eight genes (SLC12A2, BAIAP2L2, HKDC1, SVEP1, CACNG1, GTPBP4, PCNX2, and TBC1D8) were screened as single candidate genes in 10 families. CONCLUSIONSOur findings demonstrate that four-tier assessment of WES data is efficient and can detect novel candidate genes associated with hearing loss, in addition to pathogenic variants of known deafness genes.
ArticleNumber 114
Audience Academic
Author Kubo, Michiaki
Mutai, Hideki
Sakamoto, Hirokazu
Matsunaga, Tatsuo
Momozawa, Yukihide
Nakano, Atsuko
Kamatani, Yoichiro
Takiguchi, Tetsuya
Nara, Kiyomitsu
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  fullname: Momozawa, Yukihide
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  givenname: Yoichiro
  surname: Kamatani
  fullname: Kamatani, Yoichiro
  organization: Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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  surname: Nakano
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  givenname: Hirokazu
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  fullname: Sakamoto, Hirokazu
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  givenname: Tetsuya
  surname: Takiguchi
  fullname: Takiguchi, Tetsuya
  organization: Department of Otolaryngology, National Hospital Organization Kanazawa Medical Center, 1-1 Shimoishibiki-machi, Kanazawa-shi, Ishikawa, 920-8650, Japan
– sequence: 7
  givenname: Kiyomitsu
  surname: Nara
  fullname: Nara, Kiyomitsu
  organization: Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan
– sequence: 8
  givenname: Michiaki
  surname: Kubo
  fullname: Kubo, Michiaki
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  givenname: Tatsuo
  orcidid: 0000-0001-9647-1496
  surname: Matsunaga
  fullname: Matsunaga, Tatsuo
  email: tatsuo.matsunaga@kankakuki.jp, tatsuo.matsunaga@kankakuki.jp
  organization: Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan. tatsuo.matsunaga@kankakuki.jp
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Issue 1
Keywords Whole exome sequencing analysis
Deafness genes
Hearing loss
Language English
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Snippet Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To detect...
Background Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing....
BACKGROUNDHeterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is increasing. To...
Abstract Background Heterogeneous genetic loci contribute to hereditary hearing loss; more than 100 deafness genes have been identified, and the number is...
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StartPage 114
SubjectTerms Deafness - genetics
Deafness - pathology
Deafness genes
Development and progression
Exome - genetics
Genetic aspects
Genetic susceptibility
GTP-Binding Proteins - genetics
Health aspects
Hearing loss
Hearing Loss - genetics
Humans
Intercellular Signaling Peptides and Proteins - genetics
Japan
Mutation
Nuclear Proteins - genetics
Pedigree
Risk factors
Solute Carrier Family 12, Member 2 - genetics
Whole Exome Sequencing
Whole exome sequencing analysis
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Title Whole exome analysis of patients in Japan with hearing loss reveals high heterogeneity among responsible and novel candidate genes
URI https://www.ncbi.nlm.nih.gov/pubmed/35248088
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https://pubmed.ncbi.nlm.nih.gov/PMC8898489
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