I am a clinician, and have no particular expertise in genomics. I'm confused by much of what I see on dbSNP. Any help would be greatly appreciated! Thank you in advance.
MAF/MinorAlleleCount:
What is the minor allele? What is the major allele? Is the major allele also known as the "wild type"?
"The MAF is actually the second most frequent allele value". True
What is the major allele?
The major allele is the most frequent allele for a SNP.
Is the major allele also known as the "wild type"?
Yes. However in some case when the MAF is near 0.5, the major allele can switch between population.
I'm not sure why reporting the second most frequent allele is helpful.
Example: SNP1. MAF = 5%. However, the MAF goes up to 25% in people with a specific disease (ex: Asthma). In conclusion, SNP1 is associated with Asthma because the minor allele is more present in an asthmatic population versus a control group.
I think we are reporting the minor allele because it's easier to see a difference when the numbers are small (ex: 20% to 30% versus 80% to 70%).
The MAF is actually the second most frequent allele value
Meaning that the wild type is the most frequent, correct? Can the MAF be used as an estimate of the allele frequency (i.e. Prevalence), with 1 - MAF as the allele frequency of the wild type?
Thanks Maxime. How does one interpret the MAF, and prevalence, when there are 3 alleles (e.g. rs307377). RefSNP Alleles: A/C/T (FWD). MAF/MinorAlleleCount: T=0.0481/241. In this example, how can I determine which is the wild type (i.e. Major allele)? It seems that "T" would be the second most frequent allele, but how can I determine which is the most frequent and the third most frequent based on this info? Thanks again!
You can't find the Major allele with only the MAF. You need to look at the "Population Diversity (in rs orientation)" section. For rs307377, the major allele is C. The third allele, A, was never call. Maybe it's an artefact.
Thanks Maxime! Is the major allele simply the other allele?
Yes
Meaning that the wild type is the most frequent, correct? Can the MAF be used as an estimate of the allele frequency (i.e. Prevalence), with 1 - MAF as the allele frequency of the wild type?
Yes
Thanks Maxime. How does one interpret the MAF, and prevalence, when there are 3 alleles (e.g. rs307377). RefSNP Alleles: A/C/T (FWD). MAF/MinorAlleleCount: T=0.0481/241. In this example, how can I determine which is the wild type (i.e. Major allele)? It seems that "T" would be the second most frequent allele, but how can I determine which is the most frequent and the third most frequent based on this info? Thanks again!
You can't find the Major allele with only the MAF. You need to look at the "Population Diversity (in rs orientation)" section. For rs307377, the major allele is C. The third allele, A, was never call. Maybe it's an artefact.