Question: Genetic rsisk score, polygenic risk score
gravatar for J.F.Jiang
3.1 years ago by
J.F.Jiang750 wrote:

Hi all, I am dealing with couple of SNPs to predict the risk. As suggested by several references, wGRS or PRS will be the good choice. However, most refs used quantile 1 as average risk (20% proportion), quantiles 2-4 as intermediate risk, and quantile 5 as high risk. I am confusing that if the incidence of the disease is less than 1%, how can we say 20% individuals will be at high risk? Is there any other better soltion?

An other question is that some alleles were reported as risk alleles with <1 OR, which means the allele is "protective", should we inverse the OR and change the other allele as risk to calculate the GRS? If not, I think the category of outcomes should contain low risk, which means the outcomes should be grouped into low risk, below average risk, average risk, above average risk, and high risk?

Could any one give me some suggestions?

prs grs • 2.0k views
ADD COMMENTlink modified 18 months ago by bikash.k0 • written 3.1 years ago by J.F.Jiang750
gravatar for bikash.k
18 months ago by
bikash.k0 wrote:
  1. Though incidence of the disease is less than 1%, out of 100 people with risk allele 20 individual will manifest the disease.
  2. Most of the time, assigning association of SNP (risk or protective) is based on OR (<1 protective, >1 risk), however based on type of algorithm used to derive OR, the inference may vary. Therefore despite of OR<1, allele might be risk. Hence, always look up to distribution (frequency) of allele among Case and Control.
ADD COMMENTlink written 18 months ago by bikash.k0
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