Question: Is Imputation Compulsory For Association Study?
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gravatar for kumar.vinod81
6.9 years ago by
kumar.vinod81280
New Delhi
kumar.vinod81280 wrote:

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 • 1.4k views
ADD COMMENTlink modified 6.9 years ago by Larry_Parnell16k • written 6.9 years ago by kumar.vinod81280

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

ADD REPLYlink written 6.9 years ago by Giovanni M Dall'Olio26k

Out of total 1,150,000, my data has near 100,000 missing SNP sites. What should I do

ADD REPLYlink modified 6.9 years ago by Giovanni M Dall'Olio26k • written 6.9 years ago by kumar.vinod81280
2
gravatar for Larry_Parnell
6.9 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

ADD COMMENTlink written 6.9 years ago by Larry_Parnell16k

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

ADD REPLYlink written 6.9 years ago by kumar.vinod81280
1

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.

ADD REPLYlink written 6.9 years ago by Larry_Parnell16k
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