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Questions about MR-JTI #7

Open novnex-cmd opened 3 years ago

novnex-cmd commented 3 years ago

Hi @egamazon @zdangm @gamazonlab

Thank you for sharing such a wonderful job. I would like to run MR-JTI analysis but I don't know how to explain the output file. The first line "expression ... " represents the effect of the expression on the trait. So does the second line “ldsc..." represents the heterogeneity estimates?

By the way, I wonder to know whether it is appropriate to include only SNPs with fdr<0.05 in GTEx for MR-JTI analysis. look forward for your help.

Many thanks.

Best regards,

Minglong Cai

zdangm commented 3 years ago

Hi Minglong, Thank you for using MR-JTI!

The first line "expression ... " represents the effect of the expression on the trait. Correct.

So does the second line “ldsc..." represents the heterogeneity estimates? The second line represents the effect of the LD-score which is considered as a covariate here. The following rows (one raw one SNP with potential pleiotropy effect) show the heterogeneity estimates. i.e., any SNP showing a significant 'extra effect' would result in heterogeneity.

whether it is appropriate to include only SNPs with fdr<0.05 in GTEx for MR-JTI analysis Sure. However, it needs at least 20 independent IVs (SNPs) to have a robust estimate. Very few genes could have > 20 independent IVs. So, we suggest using all the cis SNPs.

Please let me know if you have any questions. Best, Dan

novnex-cmd commented 3 years ago

Thank you for your help.

I have one more question. you recommend providing LD Score when using MR-JTI. Should we include all GTEx SNP or pruned SNP to calculate LD score? Look forward for your help.

Many thanks.

Minglong Cai

zdangm commented 3 years ago

Hi Minglong, All the SNPs should be included for LD score calculation. Please let me know if there is anything else I can help with. Dan

On Thu, Aug 19, 2021 at 8:29 AM novnex-cmd @.***> wrote:

Thank you for your help.

I have one more question. you recommend providing LD Score when using MR-JTI. Should we include all GTEx SNP or pruned SNP to calculate LD score? Look forward for your help.

Many thanks.

Minglong Cai

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