NBDC Research ID: hum0005.v4
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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) system using the Ion PGM 200 Sequencing Kit and Ion 318 Chip or Ion P1 chip (Life Technologies) or HiSeq2000 system (Illumina).
Participants/Materials: Usher Syndrome: 17 patients
Non-usher syndrome: 39 patients (Controlled-access (Type I)) + 5 patients (Unrestricted-access) + 19 patients (Controlled-access) + 19 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 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
*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 | Life technologies [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 |
*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
JGAS000032, JGAS000093, JGAS000123
| Participants/Materials |
39 non-syndromic hearing loss patients (JGAS000032) 19 non-syndromic hearing loss patients (JGAS000093) 16 non-syndromic hearing loss patients (JGAS000123) (ICD10: H90) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
69 genes (ACTG1, CCDC50, CDH23, CEACAM16, CLDN14, COCH, COL11A2, CRYM, DFNA5, 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, DFNB59, POU3F4, POU4F3, PRPS1, PTPRQ, RDX, SERPINB6, SLC17A8, SLC26A4, SLC26A5, SMAC, SMPX, STRC, TECTA, TJP2, TMC1, TMIE, TMPRSS3, TPRN, TRIOBP, USH1C, USH2A, WFS1, WHRN) |
| Platform | Life technologies [Ion PGM/IonProton] |
| 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) |
| 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, 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, DFNB59, POU3F4, POU4F3, PRPS1, PTPRQ, RDX, SERPINB6, SLC17A8, SLC26A4, SLC26A5, SMAC, SMPX, STRC, TECTA, TJP2, TMC1, TMIE, TMPRSS3, TPRN, TRIOBP, USH1C, USH2A, WFS1, WHRN) |
| Platform | Life technologies [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 |
| Participants/Materials | 3 non-syndromic hearing loss patients (ICD10: H90) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
89 genes (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, DFNB59, POU3F4, POU4F3, PRPS1, PTPRQ, RDX, SERPINB6, 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) |
| 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 | JGAD000134 |
| Total Data Volume | 18 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shin-ichi Usami
Affiliation: Department of Otorhinolaryngology, Shinshu University School of Medicine
URL: -
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 |
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 | JGAD000093 |
| 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 | JGAD000134 (69 genes・89 genes) |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
