NEFF Calculations and Relatedness Clarifications

[Tomas Gomes]

Hi there,

As I'm calculating Sum of Neffs for different GWAS summary statistics, I'm encountering a couple of GWAS with trios or related individuals. The Walters et. al 2018 Alcohol Dependence GWAS, for example, provides sumstat download options for both a larger sample population including related individuals and a smaller one excluding related individuals (https://figshare.com/articles/dataset/sud2018-alc/14672187). Others do not give much choice.

Logically, I'm assuming this impacts Neff calculations since individuals are no longer fully independent, although I'm unclear on the extent. Is there a way to account for relatedness in the calculations? Should these sumstats be avoided completely, are there workarounds, or is it acceptable?

Thanks for your patience,

Tomas

[Elliot Tucker-Drob]

Neff_hat, ie inferred from betas and SEs is the way to go in that sort of situation. We provide examples on the wiki. 

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