Re: Probes on UCSC

[Cansu Yanginlar-Jacobs]

Dear Maximilian,

I hope you had a pleasant flight back home.

It was great to hear about the projects you are currently working on at the ISV meeting, especially the upcoming CNV track based on NGS and array-based data, if I understood correctly. As we briefly discussed, we are currently developing a BED file for all our MLPA and digitalMLPA probes, and it may be useful to include this information in the CNV track, particularly if users would like to confirm their findings with an orthogonal method.

I have included my colleague @Bas Lamers in cc who is leading this project. Would it be possible to share with him what would be the requirements from your side to include our probes in the CNV track and share any tips you may have for the BED file in general. Bas will also know our timelines etc the best if you need this information for your planning.

Looking forward to hearing from you.

Regards,

Cansu

Cansu Yanginlar Jacobs

Technical Support Specialist

MRC Holland

 

Phone: +31 88 8657203 Technical Support: in...@mrcholland.com Orders: or...@mrcholland.com Distribution: distri...@mrcholland.com Website: www.mrcholland.com

 

 

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From: Maximilian Haeussler <mhae...@ucsc.edu>
Sent: Friday, May 22, 2026 11:45 AM
To: Cansu Yanginlar-Jacobs <c.yan...@mrcholland.com>
Subject: Re: Probes on UCSC

 

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On Fri, May 22, 2026 at 11:41 Maximilian Haeussler <mhae...@ucsc.edu> wrote:

Let’s follow up !

[Cansu Yanginlar-Jacobs]

Dear Maximilian,

I hope you had a pleasant flight back home.

It was great to hear about the projects you are currently working on at the ISV meeting, especially the upcoming CNV track based on NGS and array-based data, if I understood correctly. As we briefly discussed, we are currently developing a BED file for all our MLPA and digitalMLPA probes, and it may be useful to include this information in the CNV track, particularly if users would like to confirm their findings with an orthogonal method.

I have included my colleague @Bas Lamers in CC who is leading this project. Would it be possible to share with him the requirements from your side for including our probes in the CNV track, as well as any general recommendations for the BED file? Bas can also provide more details on timelines if needed for your planning.

I look forward to hearing from you.

[Maximilian Haeussler]

Hi Cansu,

Thank you for reaching out about including MRC Holland's MLPA and digitalMLPA probes. This sounds like a valuable contribution that could benefit our users.

For data contributions, we generally require:
- BED format files with column definitions, ideally as a bigBed file, but a BED file also works.
- An HTML fragment describing the probe methodology and validation
- Some information about data licensing and attribution requirements, if any, and the reference assembly used

We could add your probes to our "Array Probesets" track: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=genotypeArrays

Looking forward to collaborating on this project.

Best regards,

Max

[Maximilian Haeussler]

• An HTML fragment describing the probe methodology and validation

• Is this the section that is shown under ‘Array Probesets (genotypeArrays) Track Description’ when you click on one of the probes? If so, we could use the format of the other probesets as an example. Alternatively, if you have any more information on the requirements for this section, we would be happy to hear.

Yes 

 

• Some information about data licensing and attribution requirements

• Do you have a specific format for this or can we find an example somewhere, to ensure that we provide suitable data?

No, just let us know that we can share the data freely. 

 

• Until now, we have been using the Description field in the BED file for entering HTML with information on the specific probe out of the probe set and links to our website. I have attached an example of our HTML for reference. Is it possible to include such HTML in the (big)BED files that you publish via the ‘Array Probesets’ track?

No, the generic text from your bigBed description goes into the documentation page. The probe-specific ID should become it's own extra field (or the BED name). And you can send us an HTML fragment with a $<fieldName> placeholder in it for the mouseover. 

  

• And lastly, how are updates to the ‘Array Probesets’ track typically managed? For example, would it be possible to periodically update the track when new products or probesets become available?

Yes, just send us a new file.

[Bas Lamers]

Dear Max,

 

It’s great to hear that it is possible to add our MLPA and digitalMLPA probe locations to the Array Probesets track. We think that this could be helpful for our users, so we are very excited about this collaboration.

 

As Cansu mentioned we have been working on a BED file for sharing probe locations through the UCSC browser through either the Track Hub or a Session. Currently we are still working on the details of these BED files, and expect to be ready by the summer.

 

In the meantime I do already have some questions regarding the following requirements:

 

• An HTML fragment describing the probe methodology and validation

• Is this the section that is shown under ‘Array Probesets (genotypeArrays) Track Description’ when you click on one of the probes? If so, we could use the format of the other probesets as an example. Alternatively, if you have any more information on the requirements for this section, we would be happy to hear.

 

• Some information about data licensing and attribution requirements

• Do you have a specific format for this or can we find an example somewhere, to ensure that we provide suitable data?

 

• Until now, we have been using the Description field in the BED file for entering HTML with information on the specific probe out of the probe set and links to our website. I have attached an example of our HTML for reference. Is it possible to include such HTML in the (big)BED files that you publish via the ‘Array Probesets’ track?

 

• And lastly, how are updates to the ‘Array Probesets’ track typically managed? For example, would it be possible to periodically update the track when new products or probesets become available?

 

Looking forward to hearing from you and collaborating on this.

 

Best regards, 

 

Bas Lamers

Software development

MRC Holland

Amsterdam, the Netherlands

 

Phone: +31 88 8657200

Technical Support: in...@mrcholland.com Orders: or...@mrcholland.com

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