Contact our Customer Care Team:
Freecall 1300 247 301
Phone +61 3 9321 3700
CustomerCare@agrf.org.au
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Select array sets, then click a genome version to load.

GDA family

GSA family

Various arrays

Contact our Customer Care Team:
Freecall 1300 247 301
Phone +61 3 9321 3700
CustomerCare@agrf.org.au
www.agrf.org.au

The EPIC array numbers on the UsetR diagram correspond to nearby SNPs, not the actual methylation probes (cpg sites) on the EPIC array. Those SNPs are located within a distance of about 1kb around the methylation probes. The number of methylation probes for the EPIC array within the queried gene(s) presented in the bar chart figures on the left side.

Table with all matched SNPs detected in all selected genes.
UpSetR diagram
The EPIC array number on the UpsetR diagram and the heatmap correspond to nearby SNPs, not the actual methylation probes (cpg sites) on the EPIC array. Those nearby SNPs are located within a distance of about 1kb around the nearest methylation probes.

Table with results for matched SNPs found in selected manifests.

MethylationEPIC v2 and selected genotyping content search application

This R-Shiny application provides a user-friendly interface for searching, comparing, and analysing the content of Illumina's mainstream genotyping and methylation chips. This application searches for Gene and SNP IDs. It consists of three main tabs: 'Genes', 'SNPs', and 'Info'.

Genes Tab: Users can input RefSeq gene IDs to generate bar plots showing the number of associated markers: SNPs for genotyping arrays and CpG sites for the EPIC methylation v2.0 chip. The search looks for letter patterns; case-sensitive multiple matches may occur, especially for genes with numerical suffixes. Detailed information about markers with matched gene symbols is displayed in a table. The UpSet plot shows the total number of matched SNPs for the EPIC array. The methylation array does not use probes for SNPs; they are not physically present on the EPIC chip. The SNPs shown are RS-IDs collected within a ~1Kb window around CpG probes on the array, matched by gene symbol. Therefore you may observe more hits in the UpSet plot than shown on the EPIC bar in the bar chart. This approach estimates nearby SNP overlap with genotyping chips for the queried genes.

SNPs Tab: Users can input SNP rs-ids manually or upload a file. The application searches for exact matches across selected genotyping chip content and SNPs located near EPIC CpG probes. A heatmap summarises SNP counts by gene (rows) and chip (columns). The UpSet plot on this tab uses only exact rs-id matches. Searching the ~13M EPIC-associated SNP space may be slow.

Info Tab: Summarises array content metrics (gene coverage and site counts) and provides methodological notes.

Overall, the application simplifies comparisons of microarray content by providing visualisations and statistics for selected genes and SNPs of interest.

Array Content Summary

Note: Chromosome coordinates are referenced to hg19. Array annotation files were downloaded from Illumina and harmonized: rs-ids were used as a key to aggregate gene / transcript labels across genotyping chips.

The EPIC annotation chromosome coordinates were lifted from hg38 to hg19 (rtracklayer + GenomicRanges using the UCSC chain file: hg38ToHg19.over.chain.gz).

Source code & documentation: GitHub Repository

Disclaimer:

This application is in development and provided for general informational purposes only. The Australian Genome Research Facility (AGRF) and the developer assume no responsibility for decisions made using the results. Users should independently verify any critical findings. Use at your own risk.

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