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 IDType of DataCriteriaRelease 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

*Release Note

*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

hum0347.v1.freq.v1

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

hum0347.v1.freq.v1

(Click the Dataset ID to download the file)

Total Data Volume 18 KB (txt)
Comments (Policies) NBDC policy

 

hum0347.v2.gwas.v1

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

hum0347.v2.gwas.v1

(Click the Dataset ID to download the file)

Dictionary 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 DOIDataset 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