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Table 1 Definition of the evaluated scenarios and of the chosen parameters

From: Opportunities and limits of combining microbiome and genome data for complex trait prediction

Scenario

Abbreviation

\({\varvec{N}}_{{{\varvec{QTN}}}}\)

\({\varvec{N}}_{{{\varvec{OTU}}}}\)

\({\varvec{N}}_{{{\varvec{OTU}}\left( {\varvec{g}} \right)}}\)

\(h^{2}\)

\(b^{2}\)

Null

0

–

–

–

0

0

Genome

G

100

0

0

\(r^{2}\)

0

 

G500

500

0

0

\(r^{2}\)

0

Microbiome

M

0

25

0

0

\(r^{2}\)

Indirect

I

0

25

25

0

\(r^{2}\)

Joint

J

100

25

0

\(r^{2}\)/2

\(r^{2}\)/2

 

J500

500

25

0

\(r^{2}\)/2

\(r^{2}\)/2

Recursive

R

100

25

25

\(r^{2}\)/2

\(r^{2}\)/2

 

R500

500

25

25

\(r^{2}\)/2

\(r^{2}\)/2

  1. \(N_{QTN}\): number of SNPs with a direct causal effect on the phenotype y; \(N_{OTU}\): number of OTU with a direct effect on y; \(N_{OTU\left( g \right)}\): number of OTU with a direct effect on y that are genetically determined, i.e., they are a subset of \(N_{OTU}\); \(h^{2}\) is heritability, \(b^{2}\) is microbiability, and \(r^{2} = h^{2} + b^{2}\). For \(r^{2}\), values of 0.50 and 0.25 were considered. Causative OTU and SNPs were randomly sampled