850k array methylation annotation

[Tony Sorial]

Hi team,

I am wondering if there is any estimated date when 850k EPIC array methylation CpG annotation will be available in Hg19/38?

Is it possible to request such data/manually add the tracks?

Best wishes,

Tony

Tony Sorial (MBChB, PGCert, MRes, MRCSEng)    Wellcome Trust 4Ward North/RCS Shears Research Fellow PhD Candidate - Newcastle University Frances and Augustus Newman Fulbright Scholar (2021-22) - Washington University in St Louis (MO) Fulbright Scholars www.ncl.ac.uk/medical-sciences/people/profile/tonysorial.html e:  tony....@ncl.ac.uk

[Matthew Speir]

Hello, Tony.

We've made note of your request to add methylation array tracks to the UCSC Genome Browser. Requests like yours help us prioritize what data to import.

Just to be sure, is this the array you're referring to: https://support.illumina.com/array/array_kits/infinium-methylationepic-beadchip-kit/downloads.html? If not, can you point us to the page for the array you're looking at so we can be sure we're looking at the right files?

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UC Santa Cruz Genomics Institute

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[Tony Sorial]

Dear Matthew

Exactly that data please

We use it to localise the array CpG sites and design assays to look at them in more detail

And also to see the relation of the cpg sites to genes

Any idea how long it will take to get the data added to the genome browser?

Best wishes,

Tony

Tony Sorial (MBChB, PGCert, MRes, MRCSEng)    Wellcome Trust 4Ward North/RCS Shears Research Fellow

PhD Candidate - Newcastle University

UK-US Fulbright Commission Scholar (2020-21) - Washington University in St Louis (MO) Fulbright Scholars

www.ncl.ac.uk/medical-sciences/people/profile/tonysorial.html e:  tony....@ncl.ac.uk

On Apr 21, 2022, at 11:02, Matthew Speir <msp...@ucsc.edu> wrote:



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[Gerardo Perez]

Hello, Tony.

Thank you for confirming the array.

Unfortunately, we cannot provide a precise timeline for when the 850k methylation array track would be released; however, the data is available as a custom track on h19:

http://genome.ucsc.edu/s/rhead/450k.EPIC.beadchip

The custom track has not been reviewed by our Quality Assurance team, so we ask to exercise caution. It would be great to get feedback if the custom track is helpful.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Tony Sorial]

Hi Gerardo,

That’s great thanks

I wasn’t look for an exact figure just something ballpark to aim for

I believe when the data is exported from the array it provides genomic locations for every CpG

If I was able to share that data with you would that help the process?

I will try the other file in the interim - we can double check it using the chromosomal location from the array export 

Best wishes,

Tony

Tony Sorial (MBChB, PGCert, MRes, MRCSEng)    Wellcome Trust 4Ward North/RCS Shears Research Fellow PhD Candidate - Newcastle University UK-US Fulbright Commission Scholar (2020-21) - Washington University in St Louis (MO) Fulbright Scholars www.ncl.ac.uk/medical-sciences/people/profile/tonysorial.html e:  tony....@ncl.ac.uk

On Apr 25, 2022, at 19:25, Gerardo Perez <gpe...@ucsc.edu> wrote:



[Gerardo Perez]

Hello, Tony.

Thank you for your inquiry.

We have updated the Illumina 450K/850K tracks and you should now be able to search for cg16791304 on the hg19 Genome Browser.

Thank you again for bringing this to our attention.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

On Wed, Sep 7, 2022 at 7:36 AM Tony Sorial <Tony....@newcastle.ac.uk> wrote:

Warning/Error(s):

• Sorry, couldn't locate cg16791304 in Human Feb. 2009 (GRCh37/hg19)

Please see error message, I can see the track but can’t actually find the CpG

Any advice?

Thanks in advance

On 7 Sep 2022, at 09:28, Maximilian Haeussler <mhae...@ucsc.edu> wrote:

Hi Tony, please make sure that you are on the hg19 assembly. The EPIC array was only released on the hg19 (aka "Grch37") version of the human genome.

Are you sure that you can't find it?

Here is a direct link:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chr21&g=genotypeArrays

On Wed, Sep 7, 2022 at 4:21 PM Tony Sorial <Tony....@newcastle.ac.uk> wrote:

Hi Max,

I need to check if this is the correct array, is this the illumina EPIC CpG array

It still doesn’t seem to be working for me, are your team able to remotely add the track to my account?

BW

Tony

On 1 Sep 2022, at 05:16, Maximilian Haeussler <mhae...@ucsc.edu> wrote:

Hi Tony, 

I think the track was released a few days ago, under "Variants" and "Microarray Probesets". See http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1439656067_7IAgLFP4NdFnaMAIiaBTGEXH9wME&db=hg19&c=chrX&g=genotypeArrays

Does this solve your problem? What do you think of the track name - would you search under "microarray probesets" when looking for the 850k CytoSnp array?

best

Max

On Wed, Aug 31, 2022 at 11:35 PM Tony Sorial <Tony....@newcastle.ac.uk> wrote:

cg16791304

Hi team,

I am now struggling to find CpG’s on UCSC again, did we get any update on a timeline for the 850k (epic) array annotation

BW

Tony

I don't understand this. What do you mean with "exported from the array" - can one "export" from an array?

We usually show the probes, not the CpGs. Do you want to see the targeted CpGs?

What I mean is, when we get the data from a sample, we get a probe ID (for example cg14598846) and we also get a genomic location for the CpG, I think what you have already from the manufacturer means you don’t need anything from me!

 

If I was able to share that data with you would that help the process?

I don't understand either, sorry. We found the array probe file on the manufacturer's download server.  

see above

I will try the other file in the interim - we can double check it using the chromosomal location from the array export 

Either 19 or 38 is fine, whichever is quickest 

Do you need it for hg19 or hg38? The manufacturer only provides hg38 annotations at the moment.

 

Hope that clarifies, thanks again for your help

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