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Is Imputation Compulsory For Association Study?

is imputation compulsory for association studies?

My results are completely different in before and after imputation. Which data I should believe for my further work. Should I believe, the imputed data or the data without imputation are more stronger? What is more trustful? I am working in plant so imputation was performed without any reference panel using fastPHASE.
Thanks

imputation association
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updated by Larry_Parnell Larry_Parnell • written by kumar.vinod81 kumar.vinod81

How many missing genotypes do you have? How many markers does the imputation add?

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Out of total 1150000, my data has near 100000 missing SNP sites. What should I do

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written by kumar.vinod81 kumar.vinod81

1 answer

Of course, the most trustful genotype data are those measured directly. If you have such different association results with genotyped and imputed data, it sounds to me that there was a problem with the imputation or the assignment of imputed genotypes to each subject. Imputation of genotypes can help to fine map the association, but with your results I would consider another mechanism to perform that fine mapping.

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written by Larry_Parnell Larry_Parnell

Thanks, but what are the other mechanism used in such situation ?

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written by kumar.vinod81 kumar.vinod81

Plants are easy to make as RILs and so crossing strains may be beneficial. One could sequence across regions to which the trait was mapped. Or use synteny with a another plant - I did this with Arabidopsis to find targets in soybean.

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written by Larry_Parnell Larry_Parnell

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