Standardized FASN DNA Methylation Analysis

Methylation pipelines were conducted according to our previously published study (21 (link)). Briefly, for JHU and NCI (GSE183019) cohorts, raw Infinium EPIC array methylation data were processed and normalized via SWAN (Subset quantile Within-Array Normalization) method using minfi in R. Individual beta values for CpGs were then obtained for all 850,000 methylation sites. DNA methylation beta values are continuous variables between 0 and 1, representing the proportion of methylation for a given CpG site, calculated as the ratio of the intensity of the methylated bead type to the combined methylated and unmethylated bead intensity for the specific probe. Overall annotation for CpGs was used to select all 56 probes located up to 1,500 bp upstream or within the FASN gene body. Mean beta value for FASN was obtained by calculating the average beta for all 56 probes per sample. For TCGA and NCI cohorts, mean FASN beta values were obtained by calculating the average beta across 55 and 56 probes, respectively, as TCGA methylation data was obtained from Illumina 450k methylation arrays containing only 55 probes.

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Dairo O., DePaula Oliveira L., Schaffer E., Vidotto T., Mendes A.A., Lu J., Huynh S.V., Hicks J., Sowalsky A.G., De Marzo A.M., Joshu C.E., Hanratty B., Sfanos K.S., Isaacs W.B., Haffner M.C, & Lotan T.L. (2024). FASN Gene Methylation is Associated with Fatty Acid Synthase Expression and Clinical-genomic Features of Prostate Cancer. Cancer Research Communications, 4(1), 152-163.

Publication 2024

450k methylation arrays

Corresponding Organization :

Other organizations : Johns Hopkins University, Fred Hutch Cancer Center, Johns Hopkins Medicine

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

DNA methylation beta values for CpG sites within the FASN gene body

control variables

None explicitly mentioned

controls

No positive or negative controls were specified by the authors.

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