common factor gwas

[Maryam Marzban]

Dear GenomicSEM Support Team,

I have used the Genomic SEM model and would like to confirm whether my specification correctly produces the common factor GWAS for my components. The model I used is:

model <- '
F1 =~ 1*metdMHDLCE + metdMHDLC + metdMHDLFC + metdMHDLL + metdMHDLPL + metdMHDLP
metdMHDLP ~~ 0.001*metdMHDLP
F2 =~ 1*Belen_Sumstat
HF =~ 1*F1 + F2
HF ~ SNP
'

Could you please confirm whether this model correctly estimates the SNP effects for both components?
My goal is to perform a common factor GWAS where F1 represents the metabolite traits and F2 represents Alzheimer’s disease, and to determine whether HF correctly captures the shared genetic factor between these two components.

I would greatly appreciate your clarification.

Best regards,
Maryam

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Maryam Marzban

MSc , PhD of epidemiology 

Assistant professor of Epidemiology

Bushehr University of Medical Science

Department of Epidemiology and Biostatistics

[Elliot Tucker-Drob]

People have asked about factors with two indicators several times before. If you search through the archive you should be able to find our find our previous words of caution about having only two indicators.

You could consider whether GWAS by subtraction is relevant to your research question. 

Also in your model, f2 has only one indicator so you can just use that indicator directly rather than making a f2 factor. 

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