What determine if a panel can be used for copy number analysis?
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6 months ago
whb ▴ 30

Just wondering what is (if any) the criteria for a targeted panel for copy number analysis? So targeted panel e.g. Agilent Glasgwow Cancer Core panel

https://www.agilent.com/cs/library/flyers/public/flyer-genomics-glasgow-panel-5994-1477en-agilent.pdf

Only some of the genes can be used for copy number variants. Is it the total size of the panel? or the size of the gene? or all the exons in the gene or certain % of the gene need to be targeted?

panel copy number targeted • 221 views
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I am a developer of CNV detection tools and I also don't understand what do they mean

It can be "it is not possible to detect short CNVs affecting this gene only", but normally somatic CNVs are quite long. The next page (page 3) shows that almost all the genes are suitable for CNA analysis - thus I assume it is not the case.

Maybe they performed some external validation and figured out this experimentally.

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