Question: Nonfounder Ld Pruning
1
gravatar for Sudeep
8.9 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

I have a gwa data set with genotyping data only for nonfounders in the population Can any one suggest LD pruning methods for this data set? or can I assume that the samples in the data set are all founders and proceed with normal LD pruning? Thanks

linkage gwas • 3.5k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 8.9 years ago by Sudeep1.6k
1

let's face it, this is a tough question for most of us especially without too much detail. Can you help the few population geneticists (is that the correct term?) around by providing some detail about the type of data (genotyping platform), software you are using and the population? Further, have you ever seen a connection between (non)-founders and LD pruning been made in the literature, I couldn't find anything that would give a clue how these could be connected.

ADD REPLYlink written 8.9 years ago by Michael Dondrup46k

Do you have reason to think any of the nonfounders are siblings?

ADD REPLYlink written 8.9 years ago by David Quigley11k

@David some of the samples in the population are full siblings , some are half siblings and the rest are unrelated

ADD REPLYlink written 8.9 years ago by Sudeep1.6k

I guess you are using Plink and ask for an optimal set of parameters for its LD-pruning method?

ADD REPLYlink written 8.9 years ago by Michael Dondrup46k
1
gravatar for Jarretinha
8.7 years ago by
Jarretinha3.3k
São Paulo, Brazil
Jarretinha3.3k wrote:

Being founder or nonfounder isn't very important. The main question must be: for how long did the population mix (in generations)? As LD decays exponentially with time, most loci normally will be free of significant LD in less than a dozen generations unless selection/migration/demographic stochasticity/low recomb have a relevant role in your scenario. So, check the age of your population, if it's young proceed with LD pruning carefully (they're just like founders).

By the way, the founder effect is relevant only when effective population size is small. For most vertebrates (except some fishes, maybe) this is always the case. So, a priori, all vertebrates are founders (conservatively).

ADD COMMENTlink modified 8.7 years ago • written 8.7 years ago by Jarretinha3.3k
1
gravatar for Genotepes
8.6 years ago by
Genotepes950
Nantes (France)
Genotepes950 wrote:

Really depends on what you want to do with. If you want to do SNPs selection in LE for linkage, then take the same SNPs in 1000G and do the pruning there. You have more people and, moreover, if there is a "founder" effect in your pedigree which results in a long haplotype, you'd avoid breaking this very effect you are looking for by selecting only one SNP in this "block"

ADD COMMENTlink written 8.6 years ago by Genotepes950
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