NBDC Research ID: hum0018.v2
SUMMARY
Aims: Identify causative genes or susceptible genes in neurodegenerative diseases
Methods: Whole exome sequencing, whole genome sequencing and RNA sequencing analyses using Illumina HiSeq 2000/2500
Participants/Materials:
14 patients with multiple system atrophy and 7 healthy control subjects
69 patients with Charcot-Marie-Tooth disease (CMT)
21 patients with Frontotemporal dementia (FTD)
121 patients with Familial amyotrophic lateral sclerosis (Familial ALS)
85 patients with Myopathy
490 patients with Sporadic amyotrophic lateral sclerosis (Sporadic ALS)
9 patients with Motor neuron disease (MND)
465 patients with Spastic paraplegia
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000009 | NGS (Exome) | Controlled-access (Type I) | 2015/02/03 |
| JGAS000337 | NGS (Exome) | Controlled-access (Type I) | 2025/07/16 |
| JGAS000374 | NGS (Exome) | Controlled-access (Type I) | 2025/07/16 |
| JGAS000358 | NGS (WGS, Exome, RNA-seq) | Controlled-access (Type I) | 2025/07/16 |
| JGAS000365 | NGS (WGS, Exome) | Controlled-access (Type I) | 2025/07/16 |
| JGAS000393 | NGS (WGS, Exome, RNA-seq) | Controlled-access (Type I) | 2025/07/16 |
| JGAS000422 | NGS (Exome) | Controlled-access (Type I) | 2025/07/16 |
| JGAS000494 | NGS (WGS, Exome) | Controlled-access (Type I) | 2025/07/16 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
[JGAS000009] multiple system atrophy (ICD10: G70.9) 14 cases and 7 healthy control subjects [JGAS000337] CMT (ICD10: G60.0): 69 cases 72 samples [JGAS000374] FTD (ICD10: G31.0): 21 cases 22 samples [JGAS000358] Familial ALS (ICD10: G12.2): 119 cases 125 samples [JGAS000365] Myopathy (IC510: G72.9): 82 cases 85 samples [JGAS000393] Sporadic ALS (ICD10：G82.1): 482 cases 484 samples [JGAS000422] MND (ICD10: G122): 9 cases 9 samples [JGAS000494] Spastic paraplegia (ICD10: G82.1): 464 cases 469 samples |
| Targets | Exome |
| Target Loci for Capture Methods |
- |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | gDNA extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) |
SureSelect Human All Exon 50 Mb Kit SureSelect Human All Exon V4 Kit SureSelect Human All Exon V5 Kit SureSelect Human All Exon V6 Kit SureSelect Human All Exon V7 Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000009: multiple system atrophy and healthy control subjects JGAD000448: CMT JGAD000488: FTD JGAD000472: Familial ALS JGAD000479: Myopathy JGAD000510: Sporadic ALS JGAD000539: MND JGAD000611: Spastic paraplegia |
| Total Data Volume |
JGAD000009: 260 GB (fastq) JGAD000448: 9.7 GB (fastq) JGAD000488: 27.7 GB (fastq) JGAD000472: 17.2 TB (fastq) JGAD000479: 22.1 TB (fastq) JGAD000510: 33.2 TB (fastq) JGAD000539: 55.6 GB (fastq) JGAD000611: 116.5 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
[JGAS000358] Familial ALS (ICD10: G12.2): 1 case 1 sample [JGAS000365] Myopathy (ICD10: G72.9): 3 cases 3 samples [JGAS000393] Sporadic ALS (ICD10: G122): 1 case 1 sample (brain tissues) [JGAS000494] Spastic paraplegia (ICD10: G82.1): 2 cases 2 samples (blood) |
| Targets | WGS |
| Target Loci for Capture Methods |
- |
| Platform | Illumina [HiSeq 2500] |
| Library Source | gDNA extracted from peripheral blood cells or brain tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free Sample Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000472: Familial ALS JGAD000479: Myopathy JGAD000510: Sporadic ALS JGAD000611: Spastic paraplegia |
| Total Data Volume |
JGAD000472: 17.2 TB (fastq) JGAD000479: 22.1 TB (fastq) JGAD000510: 33.2 TB (fastq) JGAD000611: 116.5 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
[JGAS000358] Familial ALS (ICD10: G12.2): 1 case 1 sample (cerebellum tissue) [JGAS000393] Sporadic ALS (ICD10: G122): 8 cases 22 samples (brain tissues) |
| Targets | RNA-seq |
| Target Loci for Capture Methods |
- |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNA extracted from brain tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Library Prep Kit v2 |
| Fragmentation Methods | Heat treatment (TruSeq RNA Library Prep Kit v2) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
JGAD000472: Familial ALS JGAD000510: Sporadic ALS |
| Total Data Volume | JGAD000472: 17.2 TB (fastq)
JGAD000510: 33.2 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shoji Tsuji
Affiliation: Department of Neurology, Graduate School of Medicine, The University of Tokyo
Project / Group Name:
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Ministry of Education, Culture, Sports, Science and Technology Japan (MEXT) KAKENHI | Genome Science | 211S0002 |
| Practical Research Project for Rare/Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | Elucidation of the Etiology and Pathogenesis of Adult-Onset Neurodegenerative Diseases Based on Whole Genome Analysis | JP20ek0109491 |
| Practical Research Project for Rare/Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | Elucidation of the Pathogenesis of Rare and Intractable Neurological Diseases Based on Omics Analysis | JP17ek0109279 |
| Program for an Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED) | Development of Clinical Genomic Information Integrated Database for Rare and Intractable Diseases | JP16kk0205001 |
| Practical Research Project for Rare/Intractable Diseases, Japan Agency for Medical Research and Development (AMED) | Comprehensive Genetic Analysis Study for Neurological Diseases of Unknown Cause | JP14ek0109065 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Multiple-System Atrophy Research Collaboration. Mutations in COQ2 in familial and sporadic multiple-system atrophy. | doi:10.1056/NEJMoa1212115 | JGAD000009 |
| 2 | Loss-of-function variants in NEK1 are associated with an increased risk of sporadic ALS in the Japanese population | doi:10.1038/s10038-020-00830-9 | JGAD000472 JGAD000510 |
| 3 | Juvenile amyotrophic lateral sclerosis with complex phenotypes associated with novel SYNE1 mutations | doi:110.1080/21678421.2020.1813312 | JGAD000472 |
| 4 | Splice-site mutations in KIF5A in the Japanese case series of amyotrophic lateral sclerosis | doi:10.1007/s10048-020-00626-1 | JGAD000472 |
| 5 | Atypical Familial Amyotrophic Lateral Sclerosis with Slowly Progressing Lower Extremities-predominant Late-onset Muscular Weakness and Atrophy | doi:10.2169/internalmedicine.2222-18 | JGAD000472 JGAD000539 |
| 6 | Association of ATXN2 intermediate-length CAG repeats with amyotrophic lateral sclerosis correlates with the distributions of normal CAG repeat alleles among individual ethnic populations | doi:10.1007/s10048-019-00570-9 | JGAD000472 JGAD000510 |
| 7 | Burden of rare variants in causative genes for amyotrophic lateral sclerosis (ALS) accelerates age at onset of ALS | doi:10.1136/jnnp-2018-318568 | JGAD000472 JGAD000510 |
| 8 | Frequency and characteristics of the TBK1 gene variants in Japanese patients with sporadic amyotrophic lateral sclerosis | doi:10.1016/j.neurobiolaging.2017.12.005 | JGAD000472 JGAD000510 |
| 9 | Molecular epidemiological study of familial amyotrophic lateral sclerosis in Japanese population by whole-exome sequencing and identification of novel HNRNPA1 mutation | doi:10.1016/j.neurobiolaging.2017.08.030 | JGAD000472 |
| 10 | ERBB4 Mutations that Disrupt the Neuregulin-ErbB4 Pathway Cause Amyotrophic Lateral Sclerosis Type 19 | doi:10.1016/j.ajhg.2013.09.008 | JGAD000472 |
| 11 | Mutational analysis of familial and sporadic amyotrophic lateral sclerosis with OPTN mutations in Japanese population | doi:10.3109/17482968.2012.684213 | JGAD000472 JGAD000510 |
| 12 | C9ORF72 Repeat Expansion in Amyotrophic Lateral Sclerosis in the Kii Peninsula of Japan | doi:10.1001/archneurol.2012.1219 | JGAD000472 |
| 13 | A mutation database for amyotrophic lateral sclerosis | doi:10.1002/humu.21306 | JGAD000472 |
| 14 | Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease | doi:10.1038/s41588-019-0458-z | JGAD000479 |
| 15 | Tubular aggregate myopathy caused by a novel mutation in the cytoplasmic domain of STIM1 | doi:10.1212/NXG.0000000000000050 | JGAD000479 |
| 16 | Clinicopathological features of the first Asian family having vocal cord and pharyngeal weakness with distal myopathy due to a MATR3 mutation | doi:10.1111/nan.12179 | JGAD000479 |
| 17 | Chédiak-Higashi syndrome presenting as a hereditary spastic paraplegia | doi:10.1038/s10038-021-00977-z | JGAD000611 |
| 18 | Biallelic variants in HPDL cause pure and complicated hereditary spastic paraplegia | doi:10.1093/brain/awab041 | JGAD000611 |
| 19 | SPG9A with the new occurrence of an ALDH18A1 mutation in a CMT1A family with PMP22 duplication: case report | doi:10.1186/s12883-021-02087-x | JGAD000611 |
| 20 | Identification of a novel mutation in ATP13A2 associated with a complicated form of hereditary spastic paraplegia | doi:10.1212/NXG.0000000000000514 | JGAD000611 |
| 21 | A novel mutation in the GBA2 gene in a Japanese patient with SPG46: A case report | doi:10.1016/j.ensci.2020.100238 | JGAD000611 |
| 22 | Clinical features of inherited neuropathy with BSCL2 mutations in Japan | doi:10.1111/jns.12369 | JGAD000611 |
| 23 | VPS13D-related disorders presenting as a pure and complicated form of hereditary spastic paraplegia | doi:10.1002/mgg3.1108 | JGAD000611 |
| 24 | A Novel de novo KIF1A Mutation in a Patient with Autism, Hyperactivity, Epilepsy, Sensory Disturbance, and Spastic Paraplegia | doi:10.2169/internalmedicine.3661-19 | JGAD000611 |
| 25 | UBAP1 mutations cause juvenile-onset hereditary spastic paraplegias (SPG80) and impair UBAP1 targeting to endosomes | doi:10.1038/s10038-019-0670-9 | JGAD000611 |
| 26 | Spastic Paraplegia Accompanied by Extrapyramidal Sign and Frontal Cognitive Dysfunction | doi:10.2169/internalmedicine.2765-19 | JGAD000611 |
| 27 | The novel de novo mutation of KIF1A gene as the cause for Spastic paraplegia 30 in a Japanese case | doi:10.1016/j.ensci.2018.11.026 | JGAD000611 |
| 28 | A novel homozygous mutation of the TFG gene in a patient with early onset spastic paraplegia and later onset sensorimotor polyneuropathy | doi:10.1038/s10038-018-0538-4 | JGAD000611 |
| 29 | PLA2G6-associated neurodegeneration presenting as a complicated form of hereditary spastic paraplegia | doi:10.1038/s10038-018-0519-7 | JGAD000611 |
| 30 | Novel mutations in the ALDH18A1 gene in complicated hereditary spastic paraplegia with cerebellar ataxia and cognitive impairment | doi:10.1038/s10038-018-0477-0 | JGAD000611 |
| 31 | Molecular epidemiology and clinical spectrum of hereditary spastic paraplegia in the Japanese population based on comprehensive mutational analyses | doi:10.1038/jhg.2015.159 | JGAD000611 |
| 32 | Exome sequencing reveals a novel missense mutation in the KIAA0196 gene in a Japanese patient with SPG8 | doi:10.1016/j.clineuro.2016.02.031 | JGAD000611 |
| 33 | Novel mutations in the PNPLA6 gene in Boucher-Neuhäuser syndrome | doi:10.1038/jhg.2015.3 | JGAD000611 |
| 34 | Late-onset spastic ataxia phenotype in a patient with a homozygous DDHD2 mutation | doi:10.1038/srep07132 | JGAD000611 |
| 35 | Autosomal-recessive complicated spastic paraplegia with a novel lysosomal trafficking regulator gene mutation | doi:10.1136/jnnp-2013-306981 | JGAD000611 |
| 36 | Molecular epidemiology and clinical spectrum of hereditary spastic paraplegia in the Japanese population based on comprehensive mutational analyses | doi:10.1038/jhg.2013.139 | JGAD000611 |
| 37 | Hereditary spastic paraplegia type 43 (SPG43) is caused by mutation in C19orf12 | doi:10.1002/humu.22378 | JGAD000611 |
| 38 | A homozygous mutation of C12orf65 causes spastic paraplegia with optic atrophy and neuropathy (SPG55) | doi:10.1136/jmedgenet-2012-101212 | JGAD000611 |
USERS (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 | JGAD000009 | 2024/07/01-2027/03/31 |
