CNV frequencies and MAF

Question

[Leandro Lima]

Hello everybody.

I have a question regarding the MAF in CNVs. What do people mean when they say CNV with MAF ≤1%?

I know it's important to check if the CNV is common or not (we can use DGV to do it). But I'm not sure about what the MAF means (in CNVs). Is it a mean (or min) MAF in the region? Or this is just a wrong way to say that 1% is the frequency of the CNV?

Thank you in advance

[NB]

I don't work on CNVs but I would just think its the minor allele frequency, similar to MAFs in SNPs which can be checked on dbSNP, so CNV with MAF ≤1% would indicate rare CNVs,

[Jimbou]

Yes, it's the minor allele frequency. Nevertheless, there is no information about the type of CNV (e.g. deletion or duplication) and often, mostly in DGV, it's a genotype frequency (3 of 100 samples carry a CNV) not the allele frequency (3 of 200 alleles).

Answer 1

[Leandro Lima]

Hi Badnan and Jimbou.

Thank you for the replies. I think I was just confused about the nomenclature. I'm used to say that a single position is an allele, but the definition of allele can be applied to loci with any length (e.g. CNV regions).

And thank you Jimbou for the explanation about the frequencies.

[smarini1]

Hello Leandro,

I'll be very grateful if could explain me how you compute the frequency from DGV. I've downloaded the database, but the frequency column is empty.

Thank you a lot

[Leandro Lima]

Hi @smarini1

Sorry, but for now it's only possible to check for occurrence in a certain number of samples (and DGV gives this information), not the frequency.

Leandro