The figure below is from Reitveld et al.’s (2013) study entitled “GWAS of 126,55
ID: 149727 • Letter: T
Question
The figure below is from Reitveld et al.’s (2013) study entitled “GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment”. What is the probability that alleles at locus rs9320913 are associated with educational attainment purely by chance (either as a raw decimal or a percent) [note: y-axis = LoD]?
Reitveld et al. (2013) [which, by the way, had 203 authors!!!], found that the combined effects of the three loci with highest LoD scores (of which rs9320913 is one) explained ~2% of the variance in educational attainment and cognitive function. If the LoD score is so strong, explain why these genes, although strongly associated with the traits of interest, have so little impact on phenotype
rs9320913 rs9320913 100 10 0.8 06 80 04 0 2 T60 40 - 20 KLHL32 MIR21 13 --C6orf168 C6orf167 FBxL4 98.5 Position on chr6 (Mb) 97.5 98 99.5Explanation / Answer
Q: What is the probability that alleles at locus rs9320913 are associated with educational attainment purely by chance (either as a raw decimal or a percent) [note: y-axis = LoD]?
Ans: Looking at ‘r2’ value (ex: red dots 0.8) and p-value of –log 8-10 (-0.90 to -1) the probability that alleles at locus rs9320913 is 1/80 = 0.0125 chance, by looking at this value we can predict that the education attainment is purely by chance.
Q: If the LoD score is so strong, explain why these genes, although strongly associated with the traits of interest, have so little impact on phenotype
Ans: even though cognitive and educational attainment having 0.8 ‘r2’ high value and low p-value (-0.90 to -1) which signifies strongly associated with the traits of interest but they cannot define phenotype, because we cannot predict genotype by simply looking at phenotype or in other words it’s impossible to to predict cognitive or educational attainment locus genes based on the phenotype.
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