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Best implementation of negative binomial association test for GWAS data?

I am being asked to implement a negative binomial association test on Immunochip data.

I ran the logistic model on a dichotimization of the response variable, but we did not find any associations at genome-wide levels of significance, so I am now being ask to consider the response variable as a continuous variable and test again using the negative binomial.

Does anyone know which are the best implementations of such a test for genetic data? Currently the files are in Plink format, although I can convert them if necessary.

Thank you.

statistics negative binomial gwas association
• 4,098 views • link
updated by Ram Ram • written by LauferVA LauferVA

2 answers

Negative binomial is for modeling count data. What are your counts?

If you dichotomized the response variable as you say, then logistic regression makes sense. If you want to re-try on the continuous response variable, then just run a linear model.

Is your model like:

response ~ genotype + age + ...

?

• 0 views • link
updated by Ram Ram • written by brentp brentp

Yes, it is:

radiographic severity ~ genotype + age + sex + PC1 + ...

So I gather from your answer that you would just go with a standard R package, in other words, there is not a significantly better test that's adapted to genetic data?

Thank you

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updated by Ram Ram • written by LauferVA LauferVA

Not sure if you still want this, but I have R code to perform a neg binomial GWAS. Our data had lots of zero counts, but we felt that going to the full zero inflated models was a step too far.

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updated by Ram Ram • written by jstats • jstats

Hi Jstats,

Just seeing this. May I ask you why you thought it was going too far?

Also, I would take the R code for the association testing although I already wrote my own .. but it would be good for comparison.

However, if you can, what I would be more interested in is your procedure in model selection and decision making process in using negative binomial regression instead of ZINB. I don't have access to any code written in R that walks me through that part of it ...

Thanks very much.

• 0 views • link
updated by Ram Ram • written by LauferVA LauferVA

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