UCSC and problem with ClinVar / LOVD variants

[Konstantinos Varvagiannis]

Dear Colleague,

I am writing concerning a problem concerning the UCSC representation of ClinVar and LOVD variants.

I might be doing something wrong but as I am searching for a variant that figures both in ClinVar (here) and the LOVD database (here), I cannot manage to see it in the UCSC browser (link for the graphic here). This happens even though both ClinVar and LOVD fields are set to dense. For your convenience I also send you the graph in pdf format.

Could you please help me with this matter?

Thank you in advance for your time and your consideration.

Sincerely,

Konstantinos Varvagiannis

University of Geneva

Konstantinos VARVAGIANNIS

Médecin Interne

Département de Génétique Médicale

Hôpitaux Universitaires de Genève

Tél. +41 (0) 22 37 95 722 / +41 (0) 79 55 33 511

[Matthew Speir]

Hi Konstantinos,

Thank you for your questions about our LOVD and ClinVar variant tracks. The reason this variant is not found in the ClinVar track is because we have not updated the data in our ClinVar track since March 2013, and the variant you point out was added to the ClinVar database in February 2014. We do plan on updating this ClinVar track in the future, but I'm not sure exactly when that will happen. The reason it doesn't show in the LOVD track is a little more complex. We update the LOVD track on a weekly basis with the latest data from LOVD. However, these updates only include data from those LOVD instances that synchronize with the main site in the Netherlands, http://www.lovd.nl/3.0/home. You will have to contact the people at LOVD for more information about why the particular LOVD instance you pointed out, http://www.genomed.org/lovd2/home.php, seems to be missing.

I hope this 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.

Matthew Speir
UCSC Genome Bioinformatics Group

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