From listmaster animalgenome.org Tlistmaster Feb 21 11:10:36 2019
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From: Yuri Tani Utsunomiya <ytutsunomiyagmail.com>
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 11:10:36 -0600
Thanks Juan!
Much clearer now with Appendix S1 from
https://www.ncbi.nlm.nih.gov/...articles/PMC4738412/
The description in MS ID#: BIORXIV/2019/555243 was a little bit confusing
to me (and also to Daniel as I see).
Do you know if equivalence of t-values between GBLUP and EMMAX break after
iterating on marker weights?
Cheers
On Wed, Feb 20, 2019 at 11:14 PM Steibel, Juan <steibeljmsu.edu> wrote:
> 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. 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.
> 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/...n_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
--
*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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