Question: Do you always need to clump polygenic risk scores?
0
gravatar for rkl
6 weeks ago by
rkl0
rkl0 wrote:

Hi,

I have always clumped my polygenic risk score but I recently I came across a paper that did not perform clumping on polygenic risk scores created at quite liberal thresholds. Does this not worsen the predictive accuracy and bias the effect estimates by over representing regions in high LD?

snp • 105 views
ADD COMMENTlink modified 6 weeks ago by Sam2.6k • written 6 weeks ago by rkl0
1
gravatar for Sam
6 weeks ago by
Sam2.6k
New York
Sam2.6k wrote:

Depends on the algorithm used. If you follow the traditional p-value thresholding approach, then clumping is necessary to avoid bias by LD as suggested by you. However, if they are using more sophisticated models that already accounts for LD e.g. LDpred, lassosum, PRS-CS etc, then they don't need to perform clumping as these methods already accounted for the whole LD structures.

ADD COMMENTlink written 6 weeks ago by Sam2.6k
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