This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Use of ISCN in public knowledgebases

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
• 2,119 views • link
updated by Jng • Jng • written by bdolin bdolin

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.

• 0 views • link
written by cpad0112 cpad0112

2 answers

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/ ..."

• 0 views • link
written by bdolin bdolin

Did you ever find an ISCN validator? The Cydas tool used to be running based on 2005 but could not confirm FISH. ISCN just now released 2020 rules. Be happy to chat further. Given access to HGVS SNV tools like Mutalyzer and VariantValidator, such a tool would be greatly beneficial.

• 0 views • link
written by Jng • Jng

Log in to answer this question.

More posts like this