MAF vs VAF

Question

[lauren.wahyudi]

Hi all.. Anyone can help explaining the difference between MAF (mutant allele) and VAF (variant allele) frequency? Thanks

[grant.hovhannisyan]

Could be Multiple Ambiguous Formats ...

[WouterDeCoster]

As far as I know the 'M' in MAF means minor and not mutant. I think VAF and MAF are the same.

[Sean Davis]

Note that even "minor allele frequency" is overloaded here. In a traditional sense, minor allele frequency refers to the frequency of an allele in a population of patients from a germline sampling. The variant allele frequency is typically used in a cancer setting to describe the proportion of reads with the variant allele within a single patient. The best option is to define what you mean very specifically; use in the literature is not a good guide, as is evidenced by the comments here.

[Len Trigg]

Yes, and I would favour the term Variant Allele Fraction (or Variant Allelic Fraction) rather than Variant Allele Frequency for this reason too!

[Kevin Blighe]

Looks like the MAF acronym is being repeatedly hijacked!

There is:

• MAF, minor allele frequeny
• MAF, mutation annotation format
• MAF, mutant allele fraction

Edit: As per Wouter's ultimate conclusion, you can consider mutant allele fraction and VAF as the same. Minor allele frequency is more used in GWAS studies.

[kloetzl]

Don't forget the Multiple Alignment Format.

[Ömer An]

Yet there is a gene called MAF

Answer 1

[AshleeThomson]

I know this post is really old, but I was wondering the same thing, and this recent paper gave a great explaination.

Variant Allele Frequency Analysis of Circulating Tumor DNA as a Promising Tool in Assessing the Effectiveness of Treatment in Non-Small Cell Lung Carcinoma Patients

... in the literature, VAF is often substituted by mutant allele frequency (MAF), which carries the same meaning. However, the term MAF may also be used as minor allele frequency and refers to the frequency of germline alleles in large cohorts analyzed by genome-wide association studies (GWASs) [52]. For this reason, a good practice is to use VAF as a metric of cancerous variants.