Question: Minor allele frequency - homoplasmy and heteroplasmy
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gravatar for baxy
2.9 years ago by
baxy150
baxy150 wrote:

Hi,

Could anyone help clarify these concepts?

  1. MAF refers to minor allele frequency, right? so given 10 ppl if there are 3 alleles, with frequencies of 0.50 (G), 0.4 (A), and 0.1(C) MAF is 0.4, right? which means 4 ppl have A?

  2. In case of mtDNA the above case would refer to what exactly? So again I have 10 ppl and MAF is 0.4 what does this mean? Or in case of mtDNA this only refers to one individual and then we talk about homo- and heteroplasmy?

  3. Given the ref sequence has A and my samples have all G's, then we are talking about homoplazmy, right?

  4. What happens in case of heteroplasmy? Let say I have a ref sequence with A and my 100 mapped reads have 60 G's and 40 A's, what is MAF here ? Is this homo- or heteroplasmy?

I am quite confused about these concepts so I would appreciate if someone would be so kind to clarify a bit.

Thank you

snp next-gen • 1.0k views
ADD COMMENTlink written 2.9 years ago by baxy150

I don't think "minor allele frequency" makes sense in the context of more than 2 alleles; it's not specific enough. Fortunately, that's rare. Wikipedia defines it as the frequency of the second-most common allele in a population, but it would be very misleading to talk about in the context of more than two alleles. Also, it's commonly used to describe a population of organisms, but you could use it in other scenarios too. Mitochondria within a single person are a population too, after all. In your question 4 I would say that's heteroplasmy with a MAF of 0.4 since the minor allele is A even though it's the ref.

ADD REPLYlink written 2.9 years ago by Brian Bushnell17k
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