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3.5 years ago
Seeker
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Hello!
Which is correct when considering minor allele freq (MAF) for a given gene?
1) Add all MAFs together and square result. Multiply times population to get total number of homozygous recessive individuals in a population; or 2) Square each MAF and multiply by population to get homozygous individuals. Add all homozygous individuals to get total number of homozygous recessive individuals?
Please let me know if I need to clarify anything.
Thanks so much!
Michelle
As you indicated MAF is going for a variant not a gene. Also being recessive or dominant is character for a traint not for an individual. Would you please share more details about your research question and hypothesis. What you have and what you want to know? Maybe more details help to clarify the question.
Hi Hamid! Thank you for your reply.
Sorry for the confusion. This is the goal:
To predict the estimated population prevalence of homozygotic individuals with pathogenic alleles in a specific gene.
Today, I read a couple of articles that identified a number of pathogenic alleles aligned to a specific gene in gnomAD. Two different articles calculated the estimated homozygotic population in different ways. I will try and describe both mechanisms below:
Method 1) In the first article, the author identified 25 pathogenic alleles associated with a specific gene. Next, they squared each individual allele frequency to reach q(squared). Third, they multiplied q(squared) by the global population. Lastly, the author summed the number of calculated homozygotic individuals to reach the total estimated prevalence of homozygotic individuals with these pathogenic alleles.
Method 2) In the second article, the author identified the pathogenic alleles and then totaled the allele frequencies defined as q. Next, they squared the summed allele frequency to reach q(squared). Third, the author multiplied q(squared) by the global population to calculate the estimated number of homozygotes in the global population.
There are far more estimated homozygotic individuals in the global population using Method 2 over Method 1. I'm hoping you can give me insight as to which method is correct.
Thank you!
Michelle