Is a minor allele fixed of one particular snp, or it can be shifted to major? If so, which criterion should we use? Thank you!
I think for very common SNPs with a MAF close to 0.5, it is not uncommon that the minor allele will 'flip', even in populations of similar ancestry. To my understanding there is no convention as to which allele is minor and which is major, it is dataset specific. However the designation of 'alternative' and 'reference' alleles is more robust to these types of ambiguities.
SNVs can have multiple alleles, and each allele can be found in different frequencies among various population groups. Biallelic SNVs are relatively more common, and the allele found less frequently is the minor allele. Given that alleles can be found in varying frequencies in different population groups, it is very much possible that the minor allele among Caucasians might be the major allele among Africans.
If you are asking about a minor allele pervading to become the major allele, that would be owing to positive Darwinian selection, IMO.
I have seen instances of the former - I do not have examples of the latter.
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
If considering the minor allele as dataset specific, is it problematic that the alleles shift across different datasets even in populations? As far as I know "reference" allele is also not always the minor. Thanks.
If you have you data coded as 1 (major) and 2 (minor), then problems may occur where comparing between studies or when merging datasets as there is no way to be sure that the minor allele is the same in both datasets. Most of the time this will not be an issue when comparing datasets of similar ancestry, unless the allele is very common. Using ACTG rather than 'major' or 'minor' is the only way to be sure you are comparing the same allele.