NBDC Research ID: hum0108.v1

 

SUMMARY

Aims: Searching for DNA methylation sites associated with panic disorder

Methods: Epigenome-wide DNA methylation analysis using array technology and case-control analysis

Participants/Materials: Patients of panic disorder and healthy controls

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000111 Methylation array Controlled Access (Type I) 2017/06/26

*Release Note

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

 

MOLECULAR DATA

JGAS00000000111

Participants/Materials

Panic disorder (ICD10: F410) : 48 cases

Healthy controls: 48 samples

(including a pair of discordant monozygotic twins)

Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina Infinium® Human Methylation 450K BeadChip
Library Source DNAs extracted from peripheral blood cells
Cell Lines -
Library Construction (kit name)

Bisulfite Conversion: EZ DNA Methylation™ Kit (Zymo Research)

Methylation analysis: Infinium® Human Methylation 450K BeadChip kit (Illumina)

Algorithms for Calculating Methylation-rate (software) iScan system and GenomeStudio Software (Illumina)
Filtering Methods

(1) detection p value of each probe ≥ 0.01 

(2) probe call rate >95%

(3) on autosomal chromosomes

(4) does not include SNP which minor allele frequency is greater than or equal to 5%

(5) hybridizes to a specific sequence*1

Normalization of microarray

(1) Lumi: quantile normalizationbeta mixture quantile*2

(2) BMIQ normalization*3

(3) ComBat*4

Probe Number (after QC) 376,602 methylation sites (reference: hg19)
Japanese Genotype-phenotype Archive Data set ID JGAD00000000120
Total Data Volume 485 MB (xlsx)
Comments (Policies) NBDC policy

*1:Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, Weksberg R: Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics 2013, 8(2):203-209

*2:Du P, Kibbe WA, Lin SM: lumi: a pipeline for processing Illumina microarray. Bioinformatics 2008, 24(13):1547-1548

*3:Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S: A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 2013, 29(2):189-196

*4:Johnson WE, Li C, Rabinovic A: Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8(1):118-127

 

DATA PROVIDER

Principal Investigator: Katsushi Tokunaga

Affiliation: Department of Human Genetics, Graduate School of Medicine, the University of Tokyo

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for JSPS Research Fellows Search for new susceptibility genetic factors associated with panic disorder 15J04964
KAKENHI Grant-in-Aid for Scientific Research (C) Search for genetic factors associated with panic disorder by a combination analysis of GWAS and DNA methylation analysis 26461712
KAKENHI Grant-in-Aid for Scientific Research (C) An interaction analysis between ‘Parental Care’ and genetic or epigenetic factors associated with depression 25461723
Takeda Science Foundation Genome-wide association analysis to identify new candidate genomic loci associated with panic disorder -

 

PUBLICATIONS

TitleDOIData Set ID
1 Epigenome-wide association study of DNA methylation in panic disorder doi: 10.1186/s13148-016-0307-1 JGAD00000000120
2 - - -

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Brock Christensen Geisel School of Medicine at Dartmouth - Department of Epidemiology JGAD00000000120 2018/08/06-2019/07/06