Calculating allele frequency

Question

[Maria333]

Hi,

A quick question; if I want to calculate the AF based on deletions and duplications, which one do I take into account for the calculation?

For example, I need to have the number of homozygous deletions or duplications to do the calculation but I could not find anywhere which copy number variant we need. Is it based on what CNVs take the majority on that specific gene or chromosome?

Thank you,
Maria

Answer 1

[Jorge Amigo]

You have to take into account that measuring AF is variant dependent, and not a regional or global measurement. for each variant you can calculate how frequent a particular allele is in your population. when dealing with SNPs you can calculate how frequent is each base, when dealing with indels you can calculate how frequent it is to see the reference or the indel, and with CNVs you can calculate how frequent it is to see each number of copies repeated.

[Maria333]

Thank you for your response Jorge. I have done exactly what you said. I have calculated how frequent each number of copies are. My question was whether I calculate the AF according to the copy numbers which represent the deletions or the copy numbers which represent the duplications.

[Jorge Amigo]

when dealing with copy number variation you know which is the motif and the number of times that it's repeated. the number of times the motif is repeated is what you would consider an allele.

say you have 6 copies on the reference, and on different samples you have 5, 5, 5, 5, 5, 6, 6, 7, 7, 7 copies. then the 5 copies would have a 0.5 AF, the 6 copies would have a 0.20 AF, and the 7 copies would have a 0.30 AF.