Simulation Study With Cnp And Snp

622 words - 2 pages

I think that the simulation study was significantly improved, and the interpretation of the results would be more convinced now. It was shown that the additional information of CNP could increase the accuracy of predicting genotypic value, compared to using SNP information alone. The accuracy was heavily dependent on the level of the correlation of CNP genotype and CNP phenotype. However, the use of CNP information would be optimistic given that it was possible to accurately map CNP (mentioned in Discussion).
However, discussion about the effect of CNP on phenotypes was not particularly informative. The authors gave a further example of a CNP explaining 5% or 1% of phenotypic variance, and its expected accuracy (without actual simulation). However, the authors did not mention about the distribution of CNP effects in general (real situations). For example, what is density or frequency of the case that a CNP explains 1%, 5% or 10% of phenotypic variance? This may give an idea as to how useful the proposed approach is in the general case.
Although the pattern of LD structure roughly followed the expectation, the difference between measured and expected r^2 was substantial (Table 3). Especially, for the loci in the same position, the measured r^2 would be unusually low. The authors should provide a satisfactory explanation for this.
In the text, r^2 was used for both the accuracy of predicting genotypic values and the measure of LD between loci (confused).

I would recommend this paper for publication after the authors clearly address questions and comments above (and detailed comments below).
I think that the simulation study was significantly improved, and the interpretation of the results would be more convinced now. It was shown that the additional information of CNP could increase the accuracy of predicting genotypic value, compared to using SNP information alone. The accuracy was heavily dependent on...

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