usage of PLINK in the family study

Question

[teesnadi]

Hello,

Could anybody tell me whether PLINK can be used to test association for Family based study or not? Not families but when this is the case for single multigeneration family with multiple affected persons of some genetic disorder.

thanks

Teesta

Answer 1

[Fabio Marroni]

Sure, there's a full module for Family based analysis! It can perform Transmission Disequilibrium Test (TDT), or association analysis for disease traits (DFAM) or quantitative traits (QFAM).Give a look to the docs here.

[teesnadi]

Thank you so much Fabio. you are absolutely right. but as per I know TDT is for nuclear families and DFAM is also for multiple families not single multigeneration family. I am dealing with precisely one single multigeneration family and thats why got confused with several application PLINK, whether --assoc application should be apply or not? whether --fisher can be applied for this case or not? and most precisely I want to ask about the imputation application of PLINK.

Can we impute the seq data or array data for the same? actually, I have whole genome snp array data as well as whole exome sequencing data for large multigeneration family and was trying to do the imputation since long time, but never able to do it successfully. then I extend my search and find that there is population data usually use in the imputation application of PLINK, thus again I got confused about the application of PLINK for single family.

[Fabio Marroni]

You are right, the support of PLINK for family data is basic. Ithink you should turn to tools thought to be based on family data, such as Merlin and Mendel. If the family is not huge, then Merlin can handle it and perform several association analysis.

I think you cannot perform standard imputation with family-based data, but again I think Merlin and Mendel can reconstruct genotype and haplotype based on transmission.

[teesnadi]

thanks Fabio