Question: Why different reference panels change the signal for a SNP?
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gravatar for anamaria
5 weeks ago by
anamaria110
anamaria110 wrote:

Hello,

can someone please explain to me why here for fig 2 https://www-nature-com.proxy.cc.uic.edu/articles/ng.3643/figures/2

signal for this SNP changes between different versions of reference panels. In particular in between HapMap 2 and HRC?

Here is a description of those two panels:https://imputationserver.readthedocs.io/en/latest/reference-panels/

ADD COMMENTlink modified 4 weeks ago by curious450 • written 5 weeks ago by anamaria110
1
gravatar for curious
4 weeks ago by
curious450
curious450 wrote:

I can't see your paper, its behind a paywall but is it just showing better signal in association from imputing with HRC?

Take a look at that second link what are the big differences between hapmap and HRC?

Also take a look at the benefits section of the HRC website, might give you some clues:

http://www.haplotype-reference-consortium.org/

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by curious450

Thanks for the link. Yes I understood that the power to detect the low frequency SNPs increases...HRC panel has much more SNPs and is done on immensely more subjects. I also did a plot to compare my imputed data with HRC ("new") with imputed data for HapMap2 ("old") and indeed that is the case. Also only around 850000 SNPs are overlapping between imputation with those two reference panels. So new significant variants can be found with HRC. But I am wondering if GWAS for data imputed with HapMap 2 showed a signal for a particular SNP is it possible that with imputation with HRC that signal is lost (the p value for that SNP is much higher)

Bdw the paper name is: "A reference panel of 64,976 haplotypes for genotype imputation" and I refer to Fig2.

enter image description here

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by anamaria110
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