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
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000111 | Methylation array | Controlled-access (Type I) | 2017/06/26 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| 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 Methylation analysis: Infinium® Human Methylation 450K BeadChip kit |
| Algorithms for Calculating Methylation-rate (software) | iScan system and GenomeStudio Software |
| 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 Dataset ID | JGAD000120 |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Epigenome-wide association study of DNA methylation in panic disorder | doi: 10.1186/s13148-016-0307-1 | JGAD000120 |
| 2 | - | - | - |
USERS (Controlled-access Data)
| Principal Investigator: | Affiliation: | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|
| Brock Christensen | Geisel School of Medicine at Dartmouth - Department of Epidemiology | JGAD000120 | 2018/08/06-2020/09/28 |
