Minor allele frequency
Minor allele frequency (MAF) is the frequency at which the second most common allele 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.{{Cite journal|last1=Hernandez|first1=Ryan D.|last2=Uricchio|first2=Lawrence H.|last3=Hartman|first3=Kevin|last4=Ye|first4=Chun|last5=Dahl|first5=Andrew|last6=Zaitlen|first6=Noah|date=September 2019|title=Ultrarare variants drive substantial cis heritability of human gene expression|journal=Nature Genetics|volume=51|issue=9|pages=1349–1355|doi=10.1038/s41588-019-0487-7|pmid=31477931|pmc=6730564|issn=1546-1718}}
Single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.05 (5%) or greater were targeted by the HapMap project.{{cite journal|last=The International HapMap Consortium|title=A haplotype map of the human genome|journal=Nature|year=2005|pages=1299–1320|doi=10.1038/nature04226|pmid=16255080|volume=437|issue=7063|pmc=1880871|bibcode=2005Natur.437.1299T}}
MAF is widely used in population genetics studies because it provides information to differentiate between common and rare variants in the population.
As an example, a 2015 study sequenced the whole genomes of {{formatnum:2120}} 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.{{cite journal|author=Sidore, C., y colaboradores |title=Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers |year=2015 |journal=Nature Genetics |volume=47 |issue=11 |pages=1272–1281 |doi=10.1038/ng.3368 |pmid=26366554 |pmc=4627508}}
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);[https://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html National Center for Biotechnology Information: New SNP Attributes] 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.