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Piffer's Freewas: Preliminary Phase Report

#1
I attach a draft report of our results for the first phase of the Freewas.
It can either be downloaded directly from here or accessed through this link: https://drive.google.com/file/d/0B7hcznd...sp=sharing


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#2
(2014-Sep-16, 09:51:03)Duxide Wrote: I attach a draft report of our results for the first phase of the Freewas.
It can either be downloaded directly from here or accessed through this link: https://drive.google.com/file/d/0B7hcznd...sp=sharing


Could you check if your PC also picks out a disproportionate number of candidate IQ-alleles that didn't meet the significance threshold? For example, some of the Rietveld's (2014) other 69 educational alleles, some of which are bound to be false negatives.
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#3
(2014-Sep-17, 19:58:17)Chuck Wrote:
(2014-Sep-16, 09:51:03)Duxide Wrote: I attach a draft report of our results for the first phase of the Freewas.
It can either be downloaded directly from here or accessed through this link: https://drive.google.com/file/d/0B7hcznd...sp=sharing


Could you check if your PC also picks out a disproportionate number of candidate IQ-alleles that didn't meet the significance threshold? For example, some of the Rietveld's (2014) other 69 educational alleles, some of which are bound to be false negatives.


Yes, we're gonna run many checks and your suggestion will be included in the to-do list. I tried posting my paper on biorXiv but found out that their staff is pretty retarded. I submitted it and had it rejected 4 times in a row with the same explanation: your paper is inappropriate for this journal. Four times I asked why it is inappropriate and got no reply. Then I contacted the editor (a guy with poor grammar and who yet boasts about being "professional") and he said that using a pseudonym is inappropriate and he refused to reconsider his decision. Thus I decided to publish it on a smarter pre-print server such as Figshare and it was immediately published (pre-print servers should not undergo dumb editorial screening). Various citation formats are also available and a doi is provided (I really recommend Figshare over biorXiv).

The doi to reach my paper is this: http://dx.doi.org/10.6084/m9.figshare.1172301

Piffer, Davide; Gilfoyle, Bertram (2014): Detecting “polygenes” using signals of polygenic selection. Tools for increasing the power of GWAS.. figshare.
http://dx.doi.org/10.6084/m9.figshare.1172301
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#4
One thing: using 23andme is not straightforward. They use a different genome version. We should get a SNP-technology expert to consult with. Using Emily's linked to genomes (on that Harvard page) will be even harder. I could probably learn it, but that will take time. Should focus on perfecting the analyses for WV.
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#5
(2014-Sep-18, 20:51:03)Gilfoyle Wrote: One thing: using 23andme is not straightforward. They use a different genome version. We should get a SNP-technology expert to consult with. Using Emily's linked to genomes will be even harder. I could probably learn it, but that will take time. Should focus on perfecting the analyses for WV.


Yes I guess we should focus on perfecting the analysis for WV. We've got a long to-do list.
It'll take a while before we collect enough genomes from 23andMe to run a satisfying analysis.
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#6
Mention at isteve: http://www.unz.com/isteve/more-iq-genes/
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#7
Using Watson's genome seems dubious given the high error rate in it. There are reports saying that he appears genetically mixed race which is unlikely. Omri Tal wrote about it:

Quote:The study of Ahn et al. (2009) suggests that the pairwise distances among three individuals, a Korean (“SJK”), Craig Venter and James Watson, measured by multilocus ASD, are roughly similar despite the distinct geographical origin of SJK in relation to Venter and Watson (see also their Fig. 2E). These results are surprising in light of our model for n, which predicts that for worldwide distant populations (FST > 0.13) the probability for such an occurrence is virtually zero given as little as 200 independent and informative SNPs (Appendix F, Fig. F.1). In fact, with roughly 3.5 million SNPs sequenced in each individual genome,the pairwise distances Venter–Watson and Venter–SJK (or Watson–SJK) must show substantial discrepancy, since the ratio of average pairwise distances RAD is above 1.3 already at FST = 0.10 (see Fig. 5A). The paradoxical result is most likely an artifact of the high error rate and low coverage in Watson’s SNP calling (Yngvadottir et al., 2009).

Link: http://lesacreduprintemps19.files.wordpr...stance.pdf
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#8
(2014-Sep-25, 17:56:23)Dalliard Wrote: Using Watson's genome seems dubious given the high error rate in it. There are reports saying that he appears genetically mixed race which is unlikely. Omri Tal wrote about it:

Quote:The study of Ahn et al. (2009) suggests that the pairwise distances among three individuals, a Korean (“SJK”), Craig Venter and James Watson, measured by multilocus ASD, are roughly similar despite the distinct geographical origin of SJK in relation to Venter and Watson (see also their Fig. 2E). These results are surprising in light of our model for n, which predicts that for worldwide distant populations (FST > 0.13) the probability for such an occurrence is virtually zero given as little as 200 independent and informative SNPs (Appendix F, Fig. F.1). In fact, with roughly 3.5 million SNPs sequenced in each individual genome,the pairwise distances Venter–Watson and Venter–SJK (or Watson–SJK) must show substantial discrepancy, since the ratio of average pairwise distances RAD is above 1.3 already at FST = 0.10 (see Fig. 5A). The paradoxical result is most likely an artifact of the high error rate and low coverage in Watson’s SNP calling (Yngvadottir et al., 2009).

Link: http://lesacreduprintemps19.files.wordpr...stance.pdf


2009..outdated
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#9
So the Watson data have been updated since?
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#10
Yeah, it is curated by Ensembl: http://ftp.ftp.ensembl.org/pub/current_v...o_sapiens/

If it wasn't high quality it probably wouldn't be there.
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