How To Find Assocation Between Snp'S And Growth And Milk Traits?

Question

[Hira]

i am doing work on growth hormone gene of goat. i have to find association between snp's and growth and milk traits. can someone tell which tests of stat will b applied to find this assocation between snp n growth and milk traits. n how they will be applies? i have values of weight, height etc of goats and i have the milk profile of the milk samples. i;ll be finding the snp's by sequencing the amplified pcr fragments.

Answer 1

[friveroll]

You are looking for the logistic regression model http://www.crcpress.com/product/isbn/9781420075755

As example in this paper http://www.nature.com/nature/journal/v483/n7389/full/nature10798.html, they sequenced the exons for gene receptor GPR120 in patients, then they check if the SNP mutation could affect the protein function, and finally they apply the logistic regression model to asses functional significance for that SNP mutation in the patients.

The programs they used to predict the affected protein function was:

• POLYPHEN http://genetics.bwh.harvard.edu/pph2/index.shtml
• SIFT http://sift.jcvi.org/
• SNAP http://www.rostlab.org/services/SNAP/
• PMUT http://mmb.pcb.ub.es/PMut/