Question: CNV frequencies and MAF
2
gravatar for Leandro Lima
3.6 years ago by
Leandro Lima890
San Francisco, CA
Leandro Lima890 wrote:

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.

cnv xhmm maf • 2.0k views
ADD COMMENTlink modified 16 months ago by smarini10 • written 3.6 years ago by Leandro Lima890
2

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,

ADD REPLYlink written 3.6 years ago by Nandini550
2

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). 

ADD REPLYlink written 3.6 years ago by Jimbou680
0
gravatar for Leandro Lima
3.6 years ago by
Leandro Lima890
San Francisco, CA
Leandro Lima890 wrote:

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.

 

ADD COMMENTlink written 3.6 years ago by Leandro Lima890
0
gravatar for smarini1
16 months ago by
smarini10
smarini10 wrote:

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

ADD COMMENTlink written 16 months ago by smarini10

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

ADD REPLYlink written 16 months ago by Leandro Lima890
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