NBDC Research ID: hum0005.v8
SUMMARY
Aims: To identify the causative gene mutation of hearing impairment including non-syndromic hearing loss, syndromic hearing loss, and inner, middle, outer ear malformation.
Methods: Massively Parallel DNA Sequencing was performed with an Ion Torrent Personal Genome Machine (PGM), Ion Proton or Ion S5 system using the Ion PGM 200, Proton HiQ Sequencing Kit and Ion 318 Chip or Ion P1 chip (Thermo Fisher Scientific) or 540 chip chef kit (S5) or HiSeq 2000 system (Illumina).
Participants/Materials: Usher Syndrome: 17 patients
Non-usher syndrome: 39 patients (Controlled-access) + 5 patients (Unrestricted-access) + 19 patients (Controlled-access) + 19 patients (Controlled-access) + 39 patients (Controlled-access) + 1 patient (Controlled-access) + 28 patients (Controlled-access) + 7 patient (Controlled-access) + 26 patients (Controlled-access) + 15 patients (Controlled-access) + 2969 patients (Controlled-access)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| DRA001273 | NGS (Target Capture: Nine genes) | Unrestricted-access | 2014/01/27 |
| JGAS000032 | NGS (Target Capture) | Controlled-access (Type I) | 2017/02/24 |
| DRA003791 | NGS (Target Capture) | Unrestricted-access | 2017/02/24 |
| JGAS000093 | NGS (Target Capture) | Controlled-access (Type I) | 2017/06/19 |
| JGAS000123 |
NGS (Target Capture) |
Controlled-access (Type I) | 2018/02/13 |
| JGAS000166 |
NGS (Target Capture) |
Controlled-access (Type I) | 2019/04/18 |
| JGAS000191 | NGS (Target Capture) | Controlled-access (Type I) | 2021/07/30 |
| JGAS000192 |
NGS (Target Capture) |
Controlled-access (Type I) | 2021/07/30 |
| JGAS000200 | NGS (Target Capture) | Controlled-access (Type I) | 2021/07/30 |
| JGAS000201 |
NGS (Target Capture) |
Controlled-access (Type I) | 2021/07/30 |
| JGAS000323 |
NGS (Target Capture) |
Controlled-access (Type I) | 2021/11/19 |
| JGAS000490 |
NGS (Target Capture) |
Controlled-access (Type I) | 2023/10/02 |
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*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials | 17 usher syndrome patients |
| Targets | Target Capture |
| Target Loci for Capture Methods |
Nine genes (MYO7A, USH1C, CDH23, PCDH15, SANS[USH1G], USH2A, GPR98[USH2C], DFNB31[USH2D], CLRN[USH3A]) |
| Platform | Thermo Fisher Scientific [Ion PGM] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Custom kit |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| DDBJ Sequence Read Archive ID | DRA001273 |
| Total Data Volume | 726.6 MB |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
39 non-syndromic hearing loss patients (JGAS000032) 19 non-syndromic hearing loss patients (JGAS000093) 16 non-syndromic hearing loss patients (JGAS000123) 37 non-syndromic hearing loss patients (JGAS000166) 1 non-syndromic hearing loss patient (JGAS000191) 9 non-syndromic hearing loss patients (JGAS000192) (a data from the same patient is included in JGAS000032) 7 non-syndromic hearing loss patients (JGAS000201) 3 non-syndromic hearing loss patients (JGAS000323) 1410 non-syndromic hearing loss patients (JGAS000490) (ICD10: H90) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
69 genes （ACTG1, CCDC50, CDH23, CEACAM16, CLDN14, COCH, COL11A2, CRYM, DFNA5, DFNB59, DIAPH1, ESPN, ESRRB, EYA4, GIPC3, GJB2, GJB3, GJB6, GPSM2, GRHL2, GRXCR1, HGF, ILDR1, KCNQ4, LHFPL5, LOXHD1, LRTOMT, MARVELD2, MIRN96, MSRB3, MYH14, MYH9, MYO15A, MYO1A, MYO3A, MYO6, MYO7A, OTOA, OTOF, PCDH15, POU3F4, POU4F3, PRPS1, PTPRQ, RDX, SERPINB6, SLC17A8, SLC26A4, SLC26A5, SMAC, SMPX, STRC, TECTA, TJP2, TMC1, TMIE, TMPRSS3, TPRN, TRIOBP, USH1C, USH2A, WFS1, WHRN） |
| Platform | Thermo Fisher Scientific [Ion PGM, Ion Proton] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Custom kit, Ion AmpliSeq Library Kit ver 2.0 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| DDBJ Sequence Read Archive ID | |
| Total Data Volume |
JGAD000032 : 13.73 GB (fastq) JGAD000093 : 6 GB (fastq) JGAD000134 : 18 GB (fastq) JGAD000244 : 18 GB (fastq) JGAD000274：292 MB（fastq） JGAD000275：14.3 GB（fastq） JGAD000286：57 GB（fastq） JGAD000434：8.8 GB（fastq） JGAD000607：1.1 TB（fastq） |
| Comments (Policies) | NBDC policy |
| Participants/Materials | 5 non-syndromic hearing loss patients (ICD10: H90) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
69 genes （ACTG1, CCDC50, CDH23, CEACAM16, CLDN14, COCH, COL11A2, CRYM, DFNA5, DFNB59, DIAPH1, ESPN, ESRRB, EYA4, GIPC3, GJB2, GJB3, GJB6, GPSM2, GRHL2, GRXCR1, HGF, ILDR1, KCNQ4, LHFPL5, LOXHD1, LRTOMT, MARVELD2, MIRN96, MSRB3, MYH14, MYH9, MYO15A, MYO1A, MYO3A, MYO6, MYO7A, OTOA, OTOF, PCDH15, POU3F4, POU4F3, PRPS1, PTPRQ, RDX, SERPINB6, SLC17A8, SLC26A4, SLC26A5, SMAC, SMPX, STRC, TECTA, TJP2, TMC1, TMIE, TMPRSS3, TPRN, TRIOBP, USH1C, USH2A, WFS1, WHRN） |
| Platform | Thermo Fisher Scientific [Ion PGM] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Custom Panel, Ion AmpliSeq Library Kit ver 2.0 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| DDBJ Sequence Read Archive ID | DRA003791 |
| Total Data Volume | 412.5 MB (fastq) |
| Comments (Policies) | NBDC policy |
JGAS000123, JGAS000166, JGAS000192, JGAS000201, JGAS000323
| Participants/Materials |
3 non-syndromic hearing loss patients (JGAS000123) 2 non-syndromic hearing loss patients (JGAS000166) 2 non-syndromic hearing loss patients (JGAS000192) 4 non-syndromic hearing loss patients (JGAS000201) 1 non-syndromic hearing loss patients (JGAS000323) (ICD10: H90) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
(ACTG1, AIFM1, ALMS1, ATP2B2, CABP2, CACNA1D, CATSPER2, CCDC50, CDH23, CEACAM16, CIB2, CLDN14, CLRN1, COCH, COL11A2, CRYL1, CRYM, DFNA5, DIABLO, DIAPH1, DSPP, ESPN, ESSRB, EYA1, EYA4, FOXI1, GIPC3, GJB2, GJB3, GJB6, GPR98, GPSM2, GRHL2, GRXCR1, HGF, ILDR1, KCNJ10, KCNQ1, KCNQ4, LHFPL5, LOXHD1, LRTOMT, MARVELD2, MSRB3, MYH14, MYH9, MYO15A, MYO1A, MYO3A, MYO6, MYO7A, OTOA, OTOF, OTOG, OTOGL, P2RX2, PCDH15, PDZD7, PJVK, PNPT1, POU3F4, POU4F3, PRPS1, PTPRQ, RDX, SERPINB6, SIX1, SLC17A8, SLC26A4, SLC26A5, SMPX, STRC, TECTA, TJP2, TMC1, TMIE, TMPRSS3, TPRN, TRIOBP, TSPEAR, USH1C, USH1G, USH2A, WFS1, WHRN, MIR96, MIR182, MIR183, MTRNR1, MTTS1) |
| Platform | Illumina [HiSeq 2000] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Agilent Sure Select XT |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| DDBJ Sequence Read Archive ID | |
| Total Data Volume |
JGAD000134 : 18 GB (fastq) JGAD000244 : 18 GB (fastq) JGAD000275：14.3 GB（fastq） JGAD000286：57 GB（fastq） JGAD000434：8.8 GB（fastq） |
| Comments (Policies) | NBDC policy |
JGAS000192, JGAS000200, JGAS000201, JGAS000323, JGAD000490
| Participants/Materials |
17 non-syndromic hearing loss patients (JGAS000192) 7 non-syndromic hearing loss patients (JGAS000200) 15 non-syndromic hearing loss patients (JGAS000201) 11 non-syndromic hearing loss patients (JGAS000323) 1559 non-syndromic hearing loss patients (JGAS000490) (ICD10: H90) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
63 genes (ACTG1, CCDC50, CDH23, CEACAM16, CLDN14, COCH, COL11A2, CRYM, DFNA5, DFNB59, DIAPH1, ESPN, ESRRB, EYA4, GIPC3, GJB2, GJB3, GJB6, GPSM2, GRHL2, GRXCR1, HGF, ILDR1, KCNQ4, LHFPL5, LOXHD1, LRTOMT, MARVELD2, MIRN96, MSRB3, MYH14, MYH9, MYO15A, MYO1A, MYO3A, MYO6, MYO7A, OTOA, OTOF, PCDH15, POU3F4, POU4F3, PRPS1, PTPRQ, RDX, SERPINB6, SLC17A8, SLC26A4, SLC26A5, SMAC, SMPX, STRC, TECTA, TJP2, TMC1, TMIE, TMPRSS3, TPRN, TRIOBP, USH1C, USH2A, WFS1, WHRN) |
| Platform | Thermo Fisher Scientific [Ion PGM, Ion Proton, Ion S5] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Custom kit, Ion AmpliSeq Library Kit ver 2.0 |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| DDBJ Sequence Read Archive ID | |
| Total Data Volume |
JGAD000275：14.3 GB（fastq） JGAD000285：2 GB（fastq） JGAD000286：57 GB（fastq） JGAD000434：8.8 GB（fastq） JGAD000607：1.1 TB（fastq） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shin-ichi Usami
Affiliation: Department of Hearing Implant Sciences, Shinshu University School of Medicine
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Health and Labour Sciences Research Grant for Research on Rare and Intractable Diseases | Research and Survey for Usher syndrome | H22-Nanchi-Ippan-058 |
| Health and Labour Sciences Research Grant for Research on Rare and Intractable Diseases | Research and Survey for Inherited Hearing Loss and Inner-, Middle- and Outer Ear Malfolmation | H24-Nanchi(Nan)-Ippan-032 |
| Health and Labour Sciences Research Grant for Comprehensive Research on Disability Health and Welfare | Development and Clinical Application of NGS Based Genetic Testing for Deafness | H25-Kankaku-Ippan-002 |
| Health and Labour Sciences Research Grant for Comprehensive Research on Disability Health and Welfare | Research and Survey for Intractable Hearing Loss | H26-Nanchitou(Nan)-Ippan-032 |
| Practical Research Project for Rare / Intractable Diseases, Japan Agency for Medical Research and Development | Development of evidence based treatments for inherited hearing loss | JP16ek0109114 |
| Program for an Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development | Development of unified data storage (DS) of clinical and genomic information for sensory disorders | JP16kk0205010 |
| Practical Research Project for Rare / Intractable Diseases, Japan Agency for Medical Research and Development | Development of evidence based clinical management for hereditary hearing loss. | JP18ek0109363 |
| Health and Labour Sciences Research Grant for Comprehensive Research on Disability Health and Welfare | Research and Survey for Intractable Hearing Loss | H29-Nanchitou(Nan)-Ippan-031 |
| Health and Labour Sciences Research Grant for Comprehensive Research on Disability Health and Welfare | Research and Survey for Intractable Hearing Loss | 20FC1048 |
| Research and Development Grants for Comprehensive Research for Persons with Disabilities, Japan Agency for Medical Research and Development | Research on building a treatment and rehabilitation system for childhood hearing loss based on causal diagnosis. | JP16dk0310067 |
| Practical Research Project for Rare / Intractable Diseases, Japan Agency for Medical Research and Development | Development of evidence based clinical management for syndromic hearing loss. | JP21ek0109542 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Massively parallel DNA sequencing facilitates diagnosis of patients with Usher syndrome type 1. | doi: 10.1371/journal.pone.0090688 | DRA001273 |
| 2 | An effective screening strategy for deafness in combination with a next-generation sequencing platform: a consecutive analysis. | doi: 10.1038/jhg.2015.143 | JGAD000032 |
| 3 | Frequency of Usher syndrome type 1 in deaf children by massively parallel DNA sequencing. | doi: 10.1038/jhg.2015.168 | DRA003791 |
| 4 | POU4F3 mutation screening in Japanese hearing loss patients: Massively parallel DNA sequencing-based analysis identified novel variants associated with autosomal dominant hearing loss | doi: 10.1371/journal.pone.0177636 | |
| 5 | WFS1 mutation screening in a large series of Japanese hearing loss patients: Massively parallel DNA sequencing-based analysis. | doi: 10.1371/journal.pone.0193359 | |
| 6 | OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients. | doi: 10.1371/journal.pone.0215932 | |
| 7 | Detailed Clinical Features of Deafness Caused by a Claudin-14 Variant. | doi: 10.3390/ijms20184579 | JGAD000274 |
| 8 | Mutational Spectrum and Clinical Features of Patients with LOXHD1 Variants Identified in an 8074 Hearing Loss Patient Cohort. | doi: 10.3390/genes10100735 | JGAD000275 (69 genes・63 genes・90 genes) |
| 9 | Mid-Frequency Hearing Loss Is Characteristic Clinical Feature of OTOA-Associated Hearing Loss. | doi: 10.3390/genes10090715 | JGAD000285 |
| 10 | The Prevalence and Clinical Characteristics of TECTA-Associated Autosomal Dominant Hearing Loss. | doi: 10.3390/genes10100744 | JGAD000286 (69 genes・63 genes・90 genes) |
| 11 | Prevalence and Clinical Characteristics of Hearing Loss Caused by MYH14 Variants. | doi: 10.3390/genes12101623 | JGAD000434 (69 genes・63 genes・90 genes) |
| 12 | Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel. | doi: 10.1002/mgg3.399 | JGAD000607 (69 genes・63 genes) |
| 13 | The Clinical Next-Generation Sequencing Database: A Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification. | doi: 10.1002/humu.23160 | JGAD000607 (69 genes・63 genes) |
| 14 | Frequency and clinical features of hearing loss caused by STRC deletions. | doi: 10.1038/s41598-019-40586-7 | JGAD000607 (69 genes・63 genes) |
| 15 | Diagnostic pitfalls for GJB2-related hearing loss: A novel deletion detected by Array-CGH analysis in a Japanese patient with congenital profound hearing loss. | doi: 10.1002/ccr3.1800 | JGAD000607 (69 genes・63 genes) |
| 16 | Sensorineural hearing loss and mild cardiac phenotype caused by an EYA4 mutation. | doi: 10.1038/s41439-018-0023-9 | JGAD000607 (69 genes・63 genes) |
| 17 | Frequency of the STRC-CATSPER2 deletion in STRC-associated hearing loss patients. | doi: 10.1038/s41598-021-04688-5 | JGAD000607 (69 genes・63 genes) |
| 18 | Variants in CDH23 cause a broad spectrum of hearing loss: from non-syndromic to syndromic hearing loss as well as from congenital to age-related hearing loss. | doi: 10.1007/s00439-022-02431-2 | JGAD000607 (69 genes・63 genes) |
| 19 | Genetic background in late-onset sensorineural hearing loss patients. | doi: 10.1038/s10038-021-00990-2 | JGAD000607 (69 genes・63 genes) |
| 20 | The genetic etiology of hearing loss in Japan revealed by the social health insurance-based genetic testing of 10K. | doi: 10.1007/s00439-021-02371-3 | JGAD000607 (69 genes・63 genes) |
| 21 | Detailed clinical features and genotype-phenotype correlation in an OTOF-related hearing loss cohort in Japan. | doi: 10.1007/s00439-021-02351-7 | JGAD000607 (69 genes・63 genes) |
| 22 | Prevalence and clinical features of autosomal dominant and recessive TMC1-associated hearing loss. | doi: 10.1007/s00439-021-02364-2 | JGAD000607 (69 genes・63 genes) |
| 23 | Human deafness-associated variants alter the dynamics of key molecules in hair cell stereocilia F-actin cores. | doi: 10.1007/s00439-021-02304-0 | JGAD000607 (69 genes・63 genes) |
| 24 | Identification of a Novel Copy Number Variation of EYA4 Causing Autosomal Dominant Non-syndromic Hearing Loss. | doi: 10.1097/MAO.0000000000003169 | JGAD000607 (69 genes・63 genes) |
| 25 | Novel ACTG1 mutations in patients identified by massively parallel DNA sequencing cause progressive hearing loss. | doi: 10.1038/s41598-020-63690-5 | JGAD000607 (69 genes・63 genes) |
| 26 | Clinical Characteristics and In Vitro Analysis of MYO6 Variants Causing Late-Onset Progressive Hearing Loss. | doi: 10.3390/genes11030273 | JGAD000607 (69 genes・63 genes) |
| 27 | Prevalence and clinical features of hearing loss caused by EYA4 variants. | doi: 10.1038/s41598-020-60259-0 | JGAD000607 (69 genes・63 genes) |
| 28 | Cochlear Implantation From the Perspective of Genetic Background. | doi: 10.1002/ar.24360 | JGAD000607 (69 genes・63 genes) |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Satoshi Yuhara | Bioinformatics section, SRL inc. | Japan | Validation of Rare Disease Clinical Reporting System | JGAD000032, JGAD000093, JGAD000134, JGAD000244, JGAD000274, JGAD000275, JGAD000285, JGAD000286, JGAD000434, JGAD000607 |
2024/07/01-2027/03/31 |
