ID
45413
Description
Principal Investigator: Edwin van den Oord, PhD, Virginia Commonwealth University, VA, USA MeSH: Schizophrenia https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000608 Schizophrenia (SCZ) is a devastating psychiatric disorder. The aim of this study was to detect DNA methylation (5meC) profiles in whole blood associated with SCZ. The sample consisted of schizophrenia cases and controls selected from national population registers in Sweden. We employed MBD protein-based enrichment of the methylated DNA fraction, followed by single end sequencing (50 bp reads) on the SOLiD platform. To improve methylome-wide coverage we used an existing protocol variant, which increases the relative number of fragments from CpG poor regions. To analyze the data, we used an analysis pipeline described elsewhere7, that was designed specifically for MBD-seq and included alignment, quality control (QC) of reads and samples, coverage calculations for the 26,752,702 autosomal CpGs in the reference genome using a non-parametric estimate of the fragment size distribution, an in silico experiment to identify CpGs in loci with alignment problems, a 2-stage adaptive algorithm to combine data from correlated adjacent CpG sites in "blocks", principal component analysis (PCA), association testing, bioinformatics annotation and network analysis. After QC, 1459 subjects with on average 32.4 million high quality reads remained. Association testing was performed on 4.3 million high quality blocks after regressing out possible assay related technical artifacts, sex/age, and unmeasured confounders through the PCA components.
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Versions (1)
- 20/11/2022 20/11/2022 - Chiara Middel
Détendeur de droits
Edwin van den Oord, PhD, Virginia Commonwealth University, VA, USA
Téléchargé le
20 novembre 2022
DOI
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Licence
Creative Commons BY 4.0
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dbGaP phs000608 Whole Genome Profiling to Detect Schizophrenia Methylation Markers
Subject ID, consent group, subject source, subject source ID, and affection status of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- StudyEvent: SEV1
- Subject ID, consent group, subject source, subject source ID, and affection status of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- Sample ID, sample source, sample source ID, and subject ID of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- Subject ID, case or control, age, gender, PCA, initial starting material for MBD-seq, total mass captured after MethyMiner enrichment, batch ID, whether sample was done in duplicate, whether sample was rerun because of low read count of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- Sample ID, body site where sample was obtained, analyte type, histological type of sample, and tumor status of samples of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
Similar models
Subject ID, consent group, subject source, subject source ID, and affection status of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- StudyEvent: SEV1
- Subject ID, consent group, subject source, subject source ID, and affection status of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- Sample ID, sample source, sample source ID, and subject ID of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- Subject ID, case or control, age, gender, PCA, initial starting material for MBD-seq, total mass captured after MethyMiner enrichment, batch ID, whether sample was done in duplicate, whether sample was rerun because of low read count of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
- Sample ID, body site where sample was obtained, analyte type, histological type of sample, and tumor status of samples of participants with or without schizophrenia and involved in the "Whole Genome Profiling to Detect Schizophrenia Methylation Markers" project.
C0242481 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,2])
C0681850 (UMLS CUI [1,3])
C3847505 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])