From listmaster animalgenome.org Tlistmaster Feb 21 11:08:29 2019
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From: "Rothschild, Max F [AN S]" <mfrothsciastate.edu>
Subject: Re: software for exact p-values for association
analysis on single step gblup
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Date: Thu, 21 Feb 2019 11:08:29 -0600
Dear colleagues
I admit I maybe out of my depth but it is hard for me to understand how the
tests can be exact.
Please explain.
Best
Max
________________________________
.From: Steibel, Juan <steibeljmsu.edu>
.Sent: Wednesday, February 20, 2019 8:14:10 PM
.To: Members of AnGenMap <angenmapanimalgenome.org>
.Subject: Re: software for exact p-values for association analysis on single
step gblup
Dear Yuri
It is in fact a fixed SNP effect test derived from an animal centric GBLUP.
I recommend you take a look on the following paper (especially the appendix):
https://onlinelibrary.wiley.com/...oi/10.1111/age.12378
https://www.ncbi.nlm.nih.gov/pubmed/26607299
Meta-analysis of genome-wide association from genomic prediction models. -
PubMed - NCBI https://www.ncbi.nlm.nih.gov/pubmed/26607299
Anim Genet. 2016 Feb;47(1):36-48. doi: 10.1111/age.12378. Epub 2015 Nov 26.
Meta-Analysis; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't,
Non-P.H.S. www.ncbi.nlm.nih.gov<http://www.ncbi.nlm.nih.gov>;
Where we show analytically the equivalence between a "snp-test" in a GBLUP
model and the EMMAX approach used for GWA (which is the answer to your
question, I guess).
Also, here are some simulation results showing the properties of the test when
we first proposed it: https://www.ncbi.nlm.nih.gov/pubmed/25038782
Rapid screening for phenotype-genotype associations by linear transformations
of genomic evaluations. - PubMed - NCBI
BMC Bioinformatics. 2014 Jul 19;15:246. doi: 10.1186/1471-2105-15-246. Research
Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
www.ncbi.nlm.nih.gov<http://www.ncbi.nlm.nih.gov>;
These two paper (and others) are cited in Andres' manuscript as the basis for
their implementation in BLUPF90.
Cheers
JP
________________________________
.From: Yuri Tani Utsunomiya <ytutsunomiyagmail.com>
.Sent: Wednesday, February 20, 2019 9:43 AM
.To: Members of AnGenMap <angenmapanimalgenome.org>
.Subject: Re: software for exact p-values for association analysis on single
step gblup
Dear Andres,
I am a little bit confused with the proposed test.
As far as my limited knowledge goes, classic t-distributed statistics are
ratios between estimates of parameters of interest and their respective
standard errors. In the manuscript, the denominator of the ratio seems to
be the square root of the variance due to the tested marker instead (i.e.,
marker standard deviation), which is not the same as the standard error of
the estimate. The latest information I had was that the standard errors of
marker effects in GBLUP and ssGBLUP do not have a simple or even known
expression for fast computation, and therefore they should be approximated
with resampling procedures such as bootstraping, subsampling or
jackknifing. Please do not take this observation as a critic, but rather as
a question that - I believe - many of us users of blupf90 have. Last but
not least, I apologize if my read of the proposal is incorrect.
Cheers,
Yuri Utsunomiya
On Wed, Feb 20, 2019 at 10:36 AM Andres Legarra-Albizu <andres.legarrainra.fr> wrote:
> Dear all,
>
> thanks to collaborative work and extensive programming, I, on behalf of all
> the blupf90 team, am happy to announce that the blupf90 suite now computes
> exact p-values for gwas analysis - same as “one at a time” classical
> gwas by regression. The authoritative reference is this biorxiv deposit:
>
> MS ID#: BIORXIV/2019/555243
>
> MS TITLE: Exact p-values for large-scale single step genome-wide
> association, with an application for birth weight in American Angus
>
> These requires the use of OPTION snp_p_value in programs blupf90 (or
> blupf90test) and postGSf90. More details in the corresponding sections in
> the wiki:
>
> http://nce.ads.uga.edu/...application_programs
>
> regards, Andres
>
> --
> Andres Legarra
> +33 561285182
> INRA, UMR1388 GenPhySE
> CS 52627
> 31326 Castanet Tolosan, France
--
*Yuri T. Utsunomiya*
DVM/MSc/PhD
Sao Paulo State University (UNESP - Brazil)
School of Veterinary Medicine - Department of Support, Production and
Animal Health (Araçatuba/SP)
International Atomic Energy Agency (IAEA) Collaborating Centre on Animal
Genomics and Bioinformatics
Laboratory of Animal Biochemistry and Molecular Biology
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