Minor allele frequency (MAF) is the frequency at which the ''second most common''
allele
An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution.
::"The chro ...
occurs in a given population. They play a surprising role in
heritability since MAF variants which occur only once, known as "singletons", drive an enormous amount of selection.
Single nucleotide polymorphisms (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, disease a ...
project.
MAF is widely used in
population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, ...
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
In the fields of molecular biology and genetics, 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 g ...
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
Locus (plural loci) is Latin for "place". It may refer to:
Entertainment
* Locus (comics), a Marvel Comics mutant villainess, a member of the Mutant Liberation Front
* ''Locus'' (magazine), science fiction and fantasy magazine
** ''Locus Award' ...
; 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.
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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