Question: Use of ISCN in public knowledgebases
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gravatar for bdolin
9 weeks ago by
bdolin50
bdolin50 wrote:

Greetings,

I'm struggling with finding an example of ISCN notation for [1] Trisomy 21 as detected by FISH; [2] Trisomy 21 as detected by microarray, and wondering if anyone can help? Also curious to know if there is publically accessible ISCN validator?

It seems as though ISCN could be very useful - for instance, as an index into dbVAR. But I can't seem to find any ISCN representations on dbVAR. Does anyone have any insight into the greater use of ISCN for helping to query public knowledge stores, particularly for complex / structural variants?

Thanks!

sequence • 115 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by bdolin50

For microarrays: (copy/pasted from here)

arr(X)×2,(Y)×1 : Microarray analysis shows a single copy gain of the X chromosome in a male.

In the same paper, authors summarize chapters related to ISH.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by cpad01121.7k
0
gravatar for bdolin
9 weeks ago by
bdolin50
bdolin50 wrote:

I received a response back from the dbVar folks, regarding the 2 questions I posed to them: [1] Is there a way to search dbVar by ISCN? [2] Is there a way to see the ISCN strings that have been submitted?

Here is their response: "... Examining the indexing field under "Advanced" and checking relevant document here: https://www.ncbi.nlm.nih.gov/dbvar/content/help/#entrezsearch I don't see a way to do this. The data here may be of some use - to help approximate the band into base equivalents, then used for search. ftp://ftp.ncbi.nlm.nih.gov/pub/gdp/ ..."

ADD COMMENTlink written 9 weeks ago by bdolin50
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