Re: [SO-devel] SOFA terms for CNVs/CNPs?

[Karen E. <kei...@ge...>]

Hi Marcela
Sorry for the delay in getting back to you.
I was travelling for the past week or so.

CNP/ CNV
In SO we have separated the kind of variation, form the effect that  
it has.
So there is a classification of the consequences of mutation which  
can be used to further describe the actual site of the variation that  
you would annotate in sequence.
For example, 'mutation_affecting_gene_structure' and  
'mutation_causes_exon_loss'

Would it make sense to you to annotate the region as  
"sequence_variant'  and further clarify this with an attribute such  
as 'mutation_affecting_copy_number'?

There is no term in SO or SOFA for inversion breakpoint.
We can add it.

--Karen


On Apr 4, 2007, at 1:34 PM, Marcela K. Tello-Ruiz wrote:

> Hi Richard,
>
> Very sorry, just realized my first message wasn't very clear...
>
> In addition to a SOFA term for CNV/CNP, I was also asking if there  
> is an
> appropriate term for "inversion breakpoint" (as described in Feuk  
> et al.
> 2005 or Tuzun et al. 2005).  I would not urge you to add one, just
> thought about it while going over some large chromosomal  
> rearrangements.
>
> Btw, thanks for your input, agree with you that
> chromosomal_structural_element would not be correct.
>
> Marcela
>
>
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