Minor allele frequency (MAF) is the frequency at which the ''second most common''
allele
An allele is a variant of the sequence of nucleotides at a particular location, or Locus (genetics), locus, on a DNA molecule.
Alleles can differ at a single position through Single-nucleotide polymorphism, single nucleotide polymorphisms (SNP), ...
occurs in a given population. They play a surprising role in
heritability
Heritability is a statistic used in the fields of Animal husbandry, breeding and genetics that estimates the degree of ''variation'' in a phenotypic trait in a population that is due to genetic variation between individuals in that population. T ...
since MAF variants which occur only once, known as "singletons", drive an enormous amount of selection.
Single nucleotide polymorphism
In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...
s (SNPs) with a minor allele frequency of 0.05 (5%) or greater were targeted by the
HapMap
The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap is used to find genetic variants affecting health, diseas ...
project.
MAF is widely used in
population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, s ...
studies because it provides information to differentiate between common and rare variants in the population.
As an example, a 2015 study sequenced the whole
genome
A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
s of
Sardinian individuals. The authors classified the variants found in the study in three classes according to their MAF. It was observed that rare variants (MAF < 0.05) appeared more frequently in coding regions than common variants (MAF > 0.05) in this population.
Interpreting MAF data
1. Introduce the reference of a SNP of interest, as an example:
rs429358, in a database (dbSNP or other).
2. Find MAF/MinorAlleleCount link. MAF/MinorAlleleCount: C=0.1506/754 (1000 Genomes, where number of genomes sampled = N = 2504);
National Center for Biotechnology Information: ''New SNP Attributes''
/ref> where C is the minor allele for that particular locus; 0.1506 is the frequency of the C allele (MAF), i.e. 15% within the 1000 Genomes database; and 754 is the number of times this SNP has been observed in the population of the study. To find the number, note that , where is to account for diploidy.
See also
* Allele frequency
Allele frequency, or gene frequency, is the relative frequency of an allele (variant of a gene) at a particular locus in a population, expressed as a fraction or percentage. Specifically, it is the fraction of all chromosomes in the population tha ...
References
Classical genetics
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