A quick visualization method to help determine the sex of given samples in a GenomeStudio Methylation project

The following method assumes a working knowledge of the GenomeStudio Methylation Module, and the analysis of data from an Infinium Methylation Array, such as Methylation450K, MethylationEPIC, or MethylationEPIC v2, or a custom methylation array that contains a significant number of markers being assayed that are on the Y chromosome. It also assumes that there is a mixture of samples with regard to sex.

Step 1: filter the sample methylation profile for Y chromosome markers, then compare the intensities for the samples across the project.

• In the sample Methylation Profile table, click on the "Filter" button

• In the subsequent pop-up window, create a filter: "CHR = Y"

  • IMPORTANT NOTE - If your data was analyzed using the manifest "EPIC-8v2-0_A1.bpm", the chromosome designations are unlike all other MethylationEPIC manifests, in that they include a prefix "chr".

    In this case, the Value input for the chromosome must include this prefix, i.e. the filter must read "Chr = chrY", otherwise the filter will not recognize the chromosome designation correctly.

• Click on "OK". The displayed markers in the Sample Methylation Profile table will now consist only of Y-chromosome markers

Step 2 - inspect the Y-chromosome intensity values for the samples in the Sample Methylation Profile table.

• In the Sample Methylation Profile, click on the Box plot button

• In the subsequent pop-up window, select the "Intensity" sub column. Females will have near background intensities, while males will show elevated intensity boxes.

Alternative method

The following publication describes an alternate method utilizing the beta values from the X chromosome to determine sex from Infinium Methylation data:

Wang Y, Hannon E, Grant OA, Gorrie-Stone TJ, Kumari M, Mill J, Zhai X, McDonald-Maier KD, Schalkwyk LC. DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy. BMC Genomics. 2021 Jun 28;22(1):484. doi: 10.1186/s12864-021-07675-2. PMID: 34182928; PMCID: PMC8240370.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8240370/

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