Genome-wide SNP and DNA Methylation Analysis

Human CytoSNP-12 Infinium HD BeadChips and GenomeStudio software (Illumina) were used for genome-wide single nucleotide polymorphism (SNP) genotyping and for data filtering and analysis, respectively. Copy number variation (CNV) analysis was performed using CNVPartition version 2.4.4 with a confidence threshold set at 50 and a minimum of 10 SNP probes per CNV region [26 (link)]. Specific PEX gene exons were sequenced using described protocols [27 (link)]. 450K Infinium Methylation BeadChips (Illumina) and GenomeStudio software were used for global DNA methylation analysis, as described [28 (link), 29 (link)]. DNA methylation levels were summarized as β-values ranging from 0 (unmethylated) to 1 (fully methylated). Scaled DNA methylation scores and .idat files are available at the NCBI GEO repository [25 ] under Series Accession Number GSE68134. Confirmatory bisulfite DNA sequencing was conducted as described [28 (link), 29 (link)].

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Wang X.M., Yik W.Y., Zhang P., Lu W., Huang N., Kim B.R., Shibata D., Zitting M., Chow R.H., Moser A.B., Steinberg S.J, & Hacia J.G. (2015). Induced pluripotent stem cell models of Zellweger spectrum disorder show impaired peroxisome assembly and cell type-specific lipid abnormalities. Stem Cell Research & Therapy, 6, 158.

Publication 2015

Human CytoSNP-12 Infinium HD BeadChips GenomeStudio

Bisulfite Copy number variation Dna methylation Exons Gene Genome Human Methylation Single nucleotide polymorphism

Corresponding Organization :

Other organizations : University of Southern California, Kennedy Krieger Institute

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Variable analysis

independent variables

Copy number variation (CNV) analysis using CNVPartition version 2.4.4 with a confidence threshold set at 50 and a minimum of 10 SNP probes per CNV region
Sequencing of specific PEX gene exons using described protocols
Global DNA methylation analysis using 450K Infinium Methylation BeadChips (Illumina) and GenomeStudio software

dependent variables

Genome-wide single nucleotide polymorphism (SNP) genotyping
DNA methylation levels summarized as β-values ranging from 0 (unmethylated) to 1 (fully methylated)

control variables

Human CytoSNP-12 Infinium HD BeadChips and GenomeStudio software (Illumina) used for data filtering and analysis
Confirmatory bisulfite DNA sequencing conducted as described

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