[Solved] mostly.
Were the 3 educational attainment alleles from Rietveld 2013 supposed to be replicated in the latest 2014 PNAS paper with the 69 genes and the 3 that survived? They went looking for educational attainment alleles in the first part of the paper and none of the Rietveld genes were even statistically significant. The study had a population well related to the original discovery sample in Rietveld and it had the best sample size too. Correction it was the same sample with very minor changes.

Isn't that a problem?

They replicate 4 times in small samples to behavior and education(g) even in different ethnic groups but didn't in the bigger more powered study to education and cognition in the same ethnic group and SAME sample they were originally found in.

Shouldn't they have at least been statistically significant out of the 69?

Can opponents use this against Piffers 3 alleles?

Link to the 2014 paper.
http://www.pnas.org/content/111/38/13790.abstract

You should do an effort to make your sentences clear (notably the 2nd paragraph). It's a real pain for me to read you. And that's not the first time, coming from you. Also, the name of the guy is Rietveld.

Oh, and you should list the studies you're referring to.

Were they supposed to be replicated in the latest PNAS paper with the 69 genes and the 3 that survived? They went looking for educational attainment alleles in the first part of the paper and none of the Ritvield genes were even statistically significant. The study had a population well related to the original discovery sample in Ritvield and it had the best sample size too. Correction it was the same sample with very minor changes.

I don't understand the confusion. Rietveld (2013) and Rietveld (2014) used practically the same samples. Quoting the latter:

“The first stage of our two-stage procedure consisted of conducting a GWAS meta-analysis on years of schooling in a pooled Education Sample (n = 106,736) using the same analysis plan as in the work by Rietveld et al. (11) and the same cohorts, except for omitting the individuals who we include in the second stage. To obtain our set of education-associated SNPs, we selected all SNPs with P value < 10−5 from the first-stage meta-analysis results and then pruned for linkage disequilibrium."

Using the same sample, Rietveld (2014) naturally "replicated" Rietveld (2013) with regards to educational alleles. e.g., table s4. The major educational alleles from Rietveld (2013) just didn't show up as major cognitive allele in Rietveld (2014).

Were they supposed to be replicated in the latest PNAS paper with the 69 genes and the 3 that survived? They went looking for educational attainment alleles in the first part of the paper and none of the Ritvield genes were even statistically significant. The study had a population well related to the original discovery sample in Ritvield and it had the best sample size too. Correction it was the same sample with very minor changes.

I don't understand the confusion. Rietveld (2013) and Rietveld (2014) used practically the same samples. Quoting the latter:

“The first stage of our two-stage procedure consisted of conducting a GWAS meta-analysis on years of schooling in a pooled Education Sample (n = 106,736) using the same analysis plan as in the work by Rietveld et al. (11) and the same cohorts, except for omitting the individuals who we include in the second stage. To obtain our set of education-associated SNPs, we selected all SNPs with P value < 10−5 from the first-stage meta-analysis results and then pruned for linkage disequilibrium."

Using the same sample, Rietveld (2014) naturally "replicated" Rietveld (2013) with regards to educational alleles. e.g., table s4. The major educational alleles from Rietveld (2013) just didn't show up as major cognitive allele in Rietveld (2014).

Ok your link shows up empty for me but I have seen the tables and am looking at them now. I only see the 3 from Rietveld 2013 in the winners curse table. Not in the 69, so does that mean they were actually in addition to the 69 and they were just left out? I don't see them in table S4 unless I have gone blind, or is the winners curse in table S5 actually in addition to the 69? This is what is confusing me.

Tables are here: http://www.pnas.org/content/suppl/2014/09/06/1404623111.DCSupplemental/pnas.1404623111.sapp.pdf

The first Rietveld(2013) alleles were previously associated with health outcomes. Seems like they could not be cognitive alleles but rather health in parts other than the brain which in turn effects education. Health can effect personality too like in the Chinese replication. Also that study seems to be a rather strange one, did they check for education or was it only those two odd memory and word tests? Surely they had the educational score of the +-300 students?

Chinese replication: http://openpsych.net/forum/attachment.php?aid=505

@ Meng Hu I will add the links and try make it clearer.

Were the 3 educational attainment alleles from Rietveld 2013 supposed to be replicated in the latest 2014 PNAS paper with the 69 genes and the 3 that survived? They went looking for educational attainment alleles in the first part of the paper and none of the Rietveld genes were even statistically significant. The study had a population well related to the original discovery sample in Rietveld and it had the best sample size too. Correction it was the same sample with very minor changes.

Isn't that a problem?

They replicate 4 times in small samples to behavior and education(g) even in different ethnic groups but didn't in the bigger more powered study to education and cognition in the same ethnic group and SAME sample they were originally found in.

Shouldn't they have at least been statistically significant out of the 69?

Can opponents use this against Piffers 3 alleles?

Link to the 2014 paper.
http://www.pnas.org/content/111/38/13790.abstract

This study by Ward et al. replicated their effects on scholastic performance in an independent sample of English students:
Genetic Variation Associated with Differential Educational Attainment in Adults Has Anticipated Associations with School Performance in Children
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0100248

Another study done on a Chinese sample replicated their effects on maths and language ability (see attached file).

Ok your link shows up empty for me but I have seen the tables and am looking at them now. I only see the 3 from Rietveld 2013 in the winners curse table. Not in the 69, so does that mean they were actually in addition to the 69 and they were just left out? I don't see them in table S4 unless I have gone blind, or is the winners curse in table S5 actually in addition to the 69? This is what is confusing me,

Yes, the alleles are shown in table s5/6. Effects with winner’s curse corrections are given. Read the section starting with: "The “winner’s curse” refers to the fact that the estimated effect size for a SNP (and therefore the R2 associated with the SNP) newly discovered to be statistically significant tends to be much higher than the unbiased effect size estimated subsequently in replication samples....We now apply these winner’s-curse-correction methods to actual data. We begin with the findings of (1) for educational attainment, where we can compare the unbiased replication stage estimates to the results from applying the winner’s-curse-correction methods to the inflated discovery-stage estimates."

Yes, one could argue that the 3 educational alleles aren't neurological g alleles, but rather some other (generally) correlated trait ones. Oh.

Ok your link shows up empty for me but I have seen the tables and am looking at them now. I only see the 3 from Rietveld 2013 in the winners curse table. Not in the 69, so does that mean they were actually in addition to the 69 and they were just left out? I don't see them in table S4 unless I have gone blind, or is the winners curse in table S5 actually in addition to the 69? This is what is confusing me,

Yes, the alleles are shown in table s5/6. Effects with winner’s curse corrections are given. Read the section starting with: "The “winner’s curse” refers to the fact that the estimated effect size for a SNP (and therefore the R2 associated with the SNP) newly discovered to be statistically significant tends to be much higher than the unbiased effect size estimated subsequently in replication samples....We now apply these winner’s-curse-correction methods to actual data. We begin with the findings of (1) for educational attainment, where we can compare the unbiased replication stage estimates to the results from applying the winner’s-curse-correction methods to the inflated discovery-stage estimates."

Yes, one could argue that the 3 educational alleles aren't neurological g alleles, but rather some other (generally) correlated trait ones. Oh.

Ok thanks thats what I wanted to know. So problem solved.

When SNPs are confirmed, it need not be the genes in that SNP that is causally relevant, but some nearby gene. Genes tend to travel together in smaller groups due to the way recombination works. Doing GWAS on full-genome scans will solve this problem, but it will drastically increase the sample size needed for genome-wide significance.

Or they do nothing.

Yes, one could argue that the 3 educational alleles aren't neurological g alleles, but rather some other (generally) correlated trait ones. Oh.

Possible but unlikely.
This study by Ward et al. replicated their effects on scholastic performance in an independent sample of English students:
Genetic Variation Associated with Differential Educational Attainment in Adults Has Anticipated Associations with School Performance in Children
http://www.plosone.org/article/info%3Ado...ne.0100248

Another study done on a Chinese sample replicated their effects on maths and language ability (see attached file).

Yes, one could argue that the 3 educational alleles aren't neurological g alleles, but rather some other (generally) correlated trait ones. Oh.

Possible but unlikely.
This study by Ward et al. replicated their effects on scholastic performance in an independent sample of English students:
Genetic Variation Associated with Differential Educational Attainment in Adults Has Anticipated Associations with School Performance in Children
http://www.plosone.org/article/info%3Ado...ne.0100248

Another study done on a Chinese sample replicated their effects on maths and language ability (see attached file).

1st thing to note is that, some of the 3(maybe all 3, not sure) were previously associated with health outcomes, cardiovascular and something else cant remember.

The Chinese study used memory and word tests. It wasn't on education really. They should have easily been able to use an IQ test or even check their educational attainment but they didn't. Couldn't have been that hard. Also note the sample is +-300, its very small. Also it replicated associations only for two of them correct? I see only two.

Basically these three alleles were replicated in mostly very similar samples to education and one very small sample of Chinese to some strange memory tests. Then it did not replicate in the same discovery sample to cognition. Seems dodgy to me.

Do you know how far the SNPs are to the genes they were associated with?

Chinese study link again so you don't have to scroll up.
http://openpsych.net/forum/attachment.php?aid=505