NBDC Research ID: hum0347.v2
SUMMARY
Aims: The objective of our study is that explore susceptibility genes for acute encephalopathy (AE). The ultimate purpose of our research is to elucidate the pathology of AE and to establish early diagnosis and specific treatment.
Methods: Peripheral blood samples were collected from the AE with biphasic seizures and late reduced diffusion (AESD) patients. DNA extraction and PCR were conducted, then PCR amplicons were subjected to the sequencing analysis by the Sanger method or performed a genome-wide association study using genotyping data obtained from SNP chip.
Participants/Materials: Sequencing analysis: 283 AESD patients
GWAS: 254 AESD patients and 799 healthy adult controls
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| hum0347.v1.freq.v1 | rs16944 genotype of AESD patients | Unrestricted-access | 2022/05/23 |
| hum0347.v2.gwas.v1 | GWAS for AESD | Unrestricted-access | 2022/07/15 |
*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 them in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials | AESD (ICD-10: G934) : 283 cases |
| Targets | rs16944 (IL1B) |
| Target Loci for Capture Methods | - |
| Platform | 310 Genetic Analyzer, 3100 Genetic Analyzer, 3130xl Genetic Analyzer (Life Technologies) |
| Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) |
AmpliTaq PCR kits, the Big Dye Terminator FS ready-reaction kit (Applied Biosystems) PCR product presequencing kit (Amersham Biosciences) |
| Genotype Call Methods (software) | Applied Biosystems™ Sequence Scanner Software v2.0 |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 18 KB (txt) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
AESD (ICD-10: G934): 254 cases healthy adult controls: 799 individuals |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Japonica Array v.2] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Reagents (Kit, Version) | Axiom 2.0 Reagent Kit |
| Genotype Call Methods (software) | Affymetrix Power Tools ver. 1.18.2 |
| Filtering |
Exclude the following conditions: Sample QCs: (1) overall call rates < 0.97 (2) relatives (PI_HAT > 0.1875) (3) outliers from Japanese cluster by principal component analysis SNP QCs: (1) SNP call rate < 0.99 (2) HWE P < 0.0001 (3) MAF < 0.05 (4) located in sex chromosomes or mitochondria |
| Marker Number (after QC) | 445,917 SNPs (ref: hg19) |
| Analysis Method (software) | PLINK (v1.9) |
| NBDC Dataset ID |
(Click the Dataset ID to download the file) |
| Total Data Volume | 35 MB (csv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Masashi Mizuguchi
Affiliation: Graduate School of Medicine, Department of Developmental Medical Sciences, The University of Tokyo
Project / Group Name: Comprehensive genetic analysis of acute encephalopathy
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Grant-in-Aid for Scientific Research (B) | Interface of neural activity, immunity and metabolism in acute encephalopathy | 15H04872 |
| Grant-in-aid for Policy Research for Intractable Diseases | Establishment of therapeutic guidelines of acute encephalopathy and status epilepticus in children | H30-Nanji-Ippan-007 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Association of IL-1B rs16944 polymorphism with acute encephalopathy with biphasic seizures and late reduced diffusion is opposite to that with febrile seizures. | doi: 10.3389/fneur.2022.891721 | hum0347.v1.freq.v1 |
| 2 | GWAS identifies candidate susceptibility loci and microRNA biomarkers for acute encephalopathy with biphasic seizures and late reduced diffusion | doi: 10.1038/s41598-021-04576-y | hum0347.v2.gwas.v1 |
