Ploidy Analysis in R
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4.4 years ago
gargar • 0

Hi,

I don't know how to analyze the number of ploidy of aberrant genomes (q2n, q3n, q4n, etc) in Illumina 450K Infinium methylation data using R (I don't even know if it is possible).

Do you know how can I do it?

Thankyou,

R SNP Methylation 450K ploidy • 1.6k views
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4.4 years ago

This is certainly not a common task, hence, no comments or answers. However, a good starting point for you would be to build upon existing packages that can determine copy number from the 450K methylation array:

Once you identify global profiles of copy number, you can apply some extra customised steps to estimate ploidy. I did this previously (unpublished) but based on NGS depth of coverage profiles. It was surprisingly precise.

Edit: In fact, there appears to be a possible logical next step: If you derive global copy number segment profiles using one of the above-mentioned programs, then you could feed these into ABSOLUTE in order to detect ploidy.

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Hi Kevin,

I have global copy number segment profiles using conumee. From this, I would like to test whether the chromosome 1q is gained or lost. Could please suggest how to do this?

Many thanks.

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Yes, if you have segment data, you can feed this into ABSOLUTE: http://archive.broadinstitute.org/cancer/cga/absolute_run

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Hi Kevin, do you know of any literature regarding this workflow? Also, right now, only platforms ‘SNP_250K_STY’, 'SNP_6.0' and 'Illumina_WES' seem to be supported by ABSOLUTE. Which one would you choose for processing conumee data?

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The conumee tutorial seems to be based on Illumina 450k data: http://bioconductor.org/packages/release/bioc/vignettes/conumee/inst/doc/conumee.html#perform-cnv-analysis

Can you adapt that to your own data?

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Hey, thanks for your reply! I'm analyzing EPIC methylation data. The conumee data processing I've already done (so I have global segmented CN profiles), and now I'm curious if it would be possible to call absolute copy numbers (i.e. ploidy) on the conumee output. For that, I was thinking of using ABSOLUTE. But it seems that you have to choose a platform (‘SNP_250K_STY’, 'SNP_6.0' or 'Illumina_WES') in order to run the algorithm, so I'm not sure which to choose, since MethylationEPIC/conumee is not supported.

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