NBDC Research ID: hum0474.v1
SUMMARY
Aims: Autism Spectrum Disorders (ASDs) are psychiatric disorders with a high prevalence and a significant genetic component. The aetiology is still unknown and there are still no fundamental treatments. The aim of this study was to investigate the presence or absence of variants (mutations or polymorphisms) in genes associated with the onset and transition of the condition in children with autistic spectrum disorder and their families, to examine the relationship between genetic variants and the clinical phenotype (clinical condition), and to use this information for diagnosis, treatment and support.
Methods: Based on the SFARI gene database, 16 highly confident ASD-associated genes, one promoter region, and 20 intergenic regions containing ASD-associated SNPs were selected for the biotinylated oligonucleotide probe design. For sequencing, buccal mucosa was collected using a swab. Genomic DNA extracted from the buccal mucosa samples were used for Target Capture Sequencing analysis.
Participants/Materials: 32 children with ASD, 8 children with low birth weight, 3 children with sub-threshold ASD, 36 typically developing children
URL: https://kodomokokoro.w3.kanazawa-u.ac.jp/en/
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000731 | NGS (Target Capture) | Controlled-access (Type I) | 2024/08/22 |
* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| Participants/Materials |
32 children with ASD (ICD10: F849) 8 children with low birth weight 3 children with sub-threshold ASD 36 typically developing children buccal mucosa: each 1 sample (total 79 samples) |
| Targets | Target Capture |
| Target Loci for Capture Methods |
ASD-associated genes: POGZ, SCN1A, SCN2A, FOXP1, SLC6A1, ARID1B, SYNGAP1, CNTNAP2, KCNQ3, PTEN, SUV420H1, GRIN2B, CHD8, ADNP, DYRK1A, SHANK3 Promoter region: HTTLPR SNPs in intergenic regions: rs1620977, rs34213746, rs1452075, rs16854048 , rs325506, rs2388334, rs111931861, rs7794745, rs10099100, rs11787216, rs2094530, rs10149470, rs113877277, rs6035856, rs6035857, rs6047381, rs6137325, rs6137326, rs71190156, rs910805 |
| Platform | Illumina [iSeq 100] |
| Library Source | DNAs extracted from buccal mucosa samples |
| Cell Lines | - |
| Library Construction (kit name) | KAPA HyperPlus Kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | Burrows-Wheeler Aligner v0.7.17 |
| Mapping Quality | - |
| Reference Genome Sequence | GRCh38 |
| Coverage (Depth) | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000864 |
| Total Data Volume | 4.5 GB (fastq, vcf) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shigeru Yokoyama
Affiliation: Research Center for Child Mental Development, Kanazawa University
Project / Group Name: Bambi Plan
URL: https://kodomokokoro.w3.kanazawa-u.ac.jp/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for JSPS Fellows | Establishment of diagnostic indices of sub-threshold autism spectrum disorder by brain function imaging and genomic analyses | 22J14602 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | A study of symptom variability corresponding to functional features of brain activity in children with autism spectrum disorder | 20H03599 |
| KAKENHI Grant-in-Aid for Scientific Research (B) | study of biological investigation of autism spectrum disorder including sub-threshold | 23K27526 |
PUBLICATIONS
USRES (Controlled-access Data)
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Association of Genetic Variants with Autism Spectrum Disorder in Japanese Children Revealed by Targeted Sequencing | doi: 10.3389/fgene.2024.1352480 | JGAD000864 |
| 2 |
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
