LOVD 2.0

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FS#46 - Variant checking to avoid duplicates

Attached to Project: LOVD 2.0
Opened by Raymond Dalgleish (rwmd) - Monday, 29 March 2010, 12:10 GMT+2
Last edited by Ivo F.A.C. Fokkema (ifokkema) - Thursday, 06 May 2010, 09:11 GMT+2
Task Type Bug Report
Category Backend / Core → Variant submission
Status Closed
Assigned To Ivo F.A.C. Fokkema (ifokkema)
Operating System All
Severity Medium
Priority Normal
Reported Version 2.0-25
Due in Version 2.0-26
Due Date 2010-05-03
Percent Complete 100%
Votes 0
Private No

Details

Whenever I want to add a patient gene variant, I always have to first check whether or not that variant already exists in the database. That usually is not a problem, but external submitters do not always check properly and it can lead to duplicates: the same variant is in the database twice and with different IDs. Would it be possible for LOVD to monitor the variant description and advise the submitter if that variant is already in the database?

Note from developers: This is about a bug in LOVD, where when adding a variant that is already in the database to an existing patient, LOVD does not check in the correct way if the variant already exists and may report that the variant already exists for the patient, while it does not.
This task depends upon

Closed by  Ivo F.A.C. Fokkema (ifokkema)
Thursday, 06 May 2010, 09:11 GMT+2
Reason for closing:  Fixed
Comment by Ivo F.A.C. Fokkema (ifokkema) - Monday, 29 March 2010, 18:07 GMT+2
Hi Raymond,

Thank you for your suggestion. I assume here that the ID you mention is the internal (completely numeric) variant ID? Because LOVD already checks the variant name to generate/check the variant's DBID field. The numeric internal variant ID is only different if at least one variant field is different from the "original".

We believe that new submissions to the database, even if the variant is already in the database, is welcome. It can provide information on the worldwide frequency of the variants and more detailed information on possible phenotypes associated with the variant, even though I agree that it can clutter the view if a very frequent mutation is being submitted all the time.

If I understand correctly, you prefer not to have any duplicates in the database? Maybe I could add a setting in LOVD that allows this kind of control.

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