Corrections to GCTA proposed by Krishna Kumar et al 2015 ?

roberto
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Posts: 10

Corrections to GCTA proposed by Krishna Kumar et al 2015 ? Dec 30, 2015 10:56:31 GMT

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Post by roberto on Dec 30, 2015 10:56:31 GMT

Hello,

A paper in PNAS by Krishna Kumar et al (http://www.pnas.org/content/early/2015/12/17/1520109113.abstract) suggests that all estimations of h2 obtained with GCTA should be re-evaluated. They also have a proposition to 'denoise' GCTA's GRMs. Could you comment on this paper? (there is probably a detailed response in preparation?)

thank you very much in advance,

roberto

Jian Yang
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Posts: 362

Corrections to GCTA proposed by Krishna Kumar et al 2015 ? Jan 19, 2016 23:25:01 GMT

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Post by Jian Yang on Jan 19, 2016 23:25:01 GMT

The “denoising” approach will lead to underestimation of the variance explained by SNPs. For instance, it is shown in their Figure 6 that the heritability estimate is unbiased without adjustment (Figure 6A; an estimate of 0.62 is not significantly different from the true parameter 0.65 given SE = 0.22) and biased when the GRM is adjusted using the denoising approach (Figure 6B; an estimate of 0.17 is significantly different from 0.65 given SE = 0.22).

Please see gcta.freeforums.net/thread/257/commentary-krishna-kumar-pnas-2015 for a full commentary of the Krishna Kumar et al. paper.

roberto New Member Posts: 10	Corrections to GCTA proposed by Krishna Kumar et al 2015 ? Jan 20, 2016 16:03:39 GMT Quote Select Post Deselect Post Link to Post Member Give Gift Back to Top Post by roberto on Jan 20, 2016 16:03:39 GMT Thank you! reading the paper right now.

Corrections to GCTA proposed by Krishna Kumar et al 2015 ?

Post by roberto on Dec 30, 2015 10:56:31 GMT

Post by Jian Yang on Jan 19, 2016 23:25:01 GMT

Post by roberto on Jan 20, 2016 16:03:39 GMT