Dan_USAAZ
Senior Member
- Messages
- 174
- Location
- Phoenix, AZ
I have a couple questions in regard to Genotype probabilities. The first relates to whether I am correctly identifying the MAF value and applying it appropriately to determine the genotype frequency. The second question relates to what frequency constitutes a “rare” genotype.
1) Based on the following algorithm provided by Valentijn in an older thread, have I correctly identified and applied the MAF value to determine the Genotype frequencies?
2) Often times, posts in this subforum asking about the potential for a problem SNP will get responses indicating that the SNP is too common to be pathogenic. It would need to be more rare in order to be a problem. My question is what MAF would meet this “rare” criteria? Would the above MAF be considered somewhat rare? Would the heterozygous frequency be considered rare enough to pursue further research into the mutation?
Thanks in advance for any input/corrections.
Dan
1) Based on the following algorithm provided by Valentijn in an older thread, have I correctly identified and applied the MAF value to determine the Genotype frequencies?
- Algorithm
Minor Homozygous = MAF x MAF
Heterozygous = (1-MAF) x MAF x 2
Major Homozygous = (1-MAF) x (1-MAF)
Heterozygous = (1-MAF) x MAF x 2
Major Homozygous = (1-MAF) x (1-MAF)
- MAF from dbSNP – (Is the MAF .0036 or .0036 divided by 18?)
- Calculation using MAF = .0036
Minor Homozygous = 0.0036 x 0.0036 = .000012 or 1 in 77,160 people
Heterozygous = (1 - 0.0036) x 0.0036 x 2 = .0072 or 1 in 140 people
Major Homozygous = (1 - 0.0036) x (1 - 0.0036) = .9928
Heterozygous = (1 - 0.0036) x 0.0036 x 2 = .0072 or 1 in 140 people
Major Homozygous = (1 - 0.0036) x (1 - 0.0036) = .9928
2) Often times, posts in this subforum asking about the potential for a problem SNP will get responses indicating that the SNP is too common to be pathogenic. It would need to be more rare in order to be a problem. My question is what MAF would meet this “rare” criteria? Would the above MAF be considered somewhat rare? Would the heterozygous frequency be considered rare enough to pursue further research into the mutation?
Thanks in advance for any input/corrections.
Dan