NBDC Research ID: hum0005.v4

 

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 (Un-restricted Access) + 19 patients (Controlled-Access) + 19 patients (Controlled-Access)

 

Data Set IDType of DataCriteriaRelease Date
DRA001273 NGS (Target Capture: Nine genes) Un-restricted Access 2014/01/27
JGAS00000000032 NGS (Target Capture) Controlled-Access (Type I) 2017/02/24
DRA003791 NGS (Target Capture) Un-restricted Access 2017/02/24
JGAS00000000093 NGS (Target Capture) Controlled-Access (Type I) 2017/06/19
JGAS00000000123

NGS (Target Capture)

69 genes89 genes

Controlled-Access (Type I) 2018/02/13

*Release Note

 

MOLECULAR DATA

DRA001273

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

 

JGAS00000000032, JGAS00000000093, JGAS00000000123

Participants/Materials

39 non-syndromic hearing loss patients (JGAS00000000032)

19 non-syndromic hearing loss patients (JGAS00000000093)

16 non-syndromic hearing loss patients (JGAS00000000123)

(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

JGAD00000000032

JGAD00000000093

JGAD00000000123

Total Data Volume

JGAD00000000032 : 13.73 GB (fastq)

JGAD00000000093 : 6 GB (fastq)

JGAD00000000123 : 18 GB (fastq)

Comments (Policies) NBDC policy

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

DRA003791

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

*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

 

JGAS00000000123

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 JGAD00000000123
Total Data Volume 18 GB (fastq)
Comments (Policies) NBDC policy

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

DATA PROVIDER

Principal Investigator: Shin-ichi Usami

Affiliation: Department of Otorhinolaryngology, Shinshu University School of Medicine

URL: -

Funds / Grants (Research Project Number):

NameTitleProject 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 16ek0109114h0002
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 16kk0205010h0001

 

PUBLICATIONS

TitleDOIData Set 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 JGAD00000000032
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 JGAD00000000093

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use