scholarly journals Support for the genetic hypothesis of the Black-white achievement gap using polygenic scores and tests for divergent selection

2020 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Educational Attainment ◽  
Cognitive Performance ◽  
Genetic Variants ◽  
Race Differences ◽  
Divergent Evolution ◽  
Math Ability ◽  
Gwas Snps ◽  
Polygenic Scores ◽  
Polygenic Selection ◽  
Genetic Hypothesis

Using the latest methods to detect divergent evolution and polygenic selection, I test the hypothesis that race differences (European-African) in IQ are due to genetic differences.The genetic variants identified by the largest GWAS of education showed clear signatures of differentiation between Africans and Europeans. Across different phenotypes (educational attainment, cognitive performance, math ability), GWAS SNPs had significantly higher average Fst than control SNPs. Contrary to a previous report, the same effect was found also for a GWAS based on a within-family design, that used differences in educational attainment between siblings to partial out shared environmental effects. Polygenic scores for all phenotypes and GWAS types (including within-family design) were higher for Europeans than for Africans.

scholarly journals Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data

Psych ◽  
2019 ◽  
Vol 1 (1) ◽  
pp. 55-75 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Monte Carlo ◽  
Educational Attainment ◽  
Spatial Autocorrelation ◽  
Association Studies ◽  
Random Noise ◽  
Genome Wide Association Studies ◽  
Socioeconomic Variables ◽  
1000 Genomes ◽  
Polygenic Scores ◽  
Polygenic Selection

Genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment (EA) were used to test a polygenic selection model. Weighted and unweighted polygenic scores (PGS) were calculated and compared across populations using data from the 1000 Genomes (n = 26), HGDP-CEPH (n = 52) and gnomAD (n = 8) datasets. The PGS from the largest EA GWAS was highly correlated to two previously published PGSs (r = 0.96–0.97, N = 26). These factors are both highly predictive of average population IQ (r = 0.9, N = 23) and Learning index (r = 0.8, N = 22) and are robust to tests of spatial autocorrelation. Monte Carlo simulations yielded highly significant p values. In the gnomAD samples, the correlation between PGS and IQ was almost perfect (r = 0.98, N = 8), and ANOVA showed significant population differences in allele frequencies with positive effect. Socioeconomic variables slightly improved the prediction accuracy of the model (from 78–80% to 85–89%), but the PGS explained twice as much of the variance in IQ compared to socioeconomic variables. In both 1000 Genomes and gnomAD, there was a weak trend for lower GWAS significance SNPs to be less predictive of population IQ. Additionally, a subset of SNPs were found in the HGDP-CEPH sample (N = 127). The analysis of this sample yielded a positive correlation with latitude and a low negative correlation with distance from East Africa. This study provides robust results after accounting for spatial autocorrelation with Fst distances and random noise via an empirical Monte Carlo simulation using null SNPs.

scholarly journals Evidence for Recent Polygenic Selection on Educational Attainment and Underlying Cognitive Abilities Inferred from GWAS Hits: A Monte Carlo Simulation Using Random SNPs

2017 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Monte Carlo ◽  
Educational Attainment ◽  
Spatial Autocorrelation ◽  
Predictive Power ◽  
Association Studies ◽  
Null Model ◽  
Genome Wide Association Studies ◽  
Polygenic Score ◽  
Polygenic Scores ◽  
Polygenic Selection

Background: The genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment were used to test a polygenic selection model. Methods: Average frequencies of alleles with positive effect (polygenic scores or PS) were compared across populations (N=26) using data from 1000 Genomes. A null model was created using frequencies of random SNPs. Results: Polygenic selection signal of educational attainment GWAS hits is high among a handful of SNPs within genomic regions replicated across GWAS publications. A polygenic score comprising 9 SNPs predicts population IQ (r=0.88), outperforming 99% of the polygenic scores obtained from sets of random SNPs (Monte Carlo p= 0.011). Its predictive power remains unaffected after controlling for spatial autocorrelation (Beta= 0.83). The largest polygenic score (161 SNPs) exhibits similar predictive power (Beta=0.8). Random polygenic scores are moderate predictors of population IQ (thanks to spatial autocorrelation), and their predictive power increases logarithmically with the number of SNPs, indicating an exponential reduction in noise. Conclusion: This study provides guidance for using GWAS hits together with random SNPs for testing polygenic selection using Monte Carlo simulations.

Evidence for recent polygenic selection on educational attainment and intelligence inferred from GWAS hits: a replication of previous findings using recent data.

2018 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Monte Carlo ◽  
Educational Attainment ◽  
Spatial Autocorrelation ◽  
Association Studies ◽  
Random Noise ◽  
Genome Wide Association Studies ◽  
Polygenic Scores ◽  
Highly Correlated ◽  
Using Data ◽  
Polygenic Selection

The genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment and the largest intelligence GWAS were used to test a polygenic selection model.Weighted and unweighted polygenic scores (PGS) were calculated and compared across populations (N=26) using data from the 1000 Genomes and HGDP-CEPH datasets. A set of 9 SNPs within genomic regions replicated across GWAS publications and a polygenic score calculated from the largest GWAS of educational attainment to date are highly correlated to a previously published factor (r= 0.96). These factors are both highly predictive of average population IQ (r=0.9), and are robust to tests of spatial autocorrelation. Monte Carlo simulations yielded highly significant p values. A subset of SNPs were found in the HGDP-CEPH sample (N= 127). The analysis of this sample yielded a positive correlation with latitude and a low negative correlation with distance from East Africa.This study provides robust results after accounting for spatial autocorrelation with Fst distances and random noise via an empirical Monte Carlo simulation using null SNPs and shows robust reproducibility of results from a previous study.

scholarly journals Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from GWAS Hits: A Replication of Previous Findings Using Recent Data

2017 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Monte Carlo ◽  
Educational Attainment ◽  
Spatial Autocorrelation ◽  
Association Studies ◽  
Selection Model ◽  
Genome Wide Association Studies ◽  
Polygenic Scores ◽  
Highly Correlated ◽  
Using Data ◽  
Polygenic Selection

Background: The genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment and the largest intelligence GWAS were used to test a polygenic selection model. Methods: Average frequencies of alleles with positive effect (polygenic scores or PS) were compared across populations (N=26) using data from 1000 Genomes. Factor analysis was used to extract a signal of polygenic selection. Results: A polygenic selection factor of educational attainment GWAS hits is high among a handful of SNPs within genomic regions replicated across GWAS publications and it is highly correlated to the genetic intelligence factor (r= 0.96). These factors are both highly predictive of average population IQ (r=0.9), and are robust to tests of spatial autocorrelation. Several Monte Carlo simulations yielded highly significant p values. Furthermore, the polygenic selection model shows high replicability, with the EA and intelligence factor scores being virtually identical to those from an older study (r=0.96-0.99). A larger sample of populations (N=53) produced similar results. Conclusion: This study shows robust results after accounting for spatial autocorrelation and Monte Carlo simulation using random SNPs and shows robust reproducibility of results from a previous study.

scholarly journals Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data

Psych ◽  
2019 ◽  
Vol 1 (1) ◽  
pp. 55-75 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Monte Carlo ◽  
Educational Attainment ◽  
Spatial Autocorrelation ◽  
Association Studies ◽  
Random Noise ◽  
Genome Wide Association Studies ◽  
Socioeconomic Variables ◽  
1000 Genomes ◽  
Polygenic Scores ◽  
Polygenic Selection

Genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment (EA) were used to test a polygenic selection model. Weighted and unweighted polygenic scores (PGS) were calculated and compared across populations using data from the 1000 Genomes (n = 26), HGDP-CEPH (n = 52) and gnomAD (n = 8) datasets. The PGS from the largest EA GWAS was highly correlated to two previously published PGSs (r = 0.96–0.97, N = 26). These factors are both highly predictive of average population IQ (r = 0.9, N = 23) and Learning index (r = 0.8, N = 22) and are robust to tests of spatial autocorrelation. Monte Carlo simulations yielded highly significant p values. In the gnomAD samples, the correlation between PGS and IQ was almost perfect (r = 0.98, N = 8), and ANOVA showed significant population differences in allele frequencies with positive effect. Socioeconomic variables slightly improved the prediction accuracy of the model (from 78–80% to 85–89%), but the PGS explained twice as much of the variance in IQ compared to socioeconomic variables. In both 1000 Genomes and gnomAD, there was a weak trend for lower GWAS significance SNPs to be less predictive of population IQ. Additionally, a subset of SNPs were found in the HGDP-CEPH sample (N = 127). The analysis of this sample yielded a positive correlation with latitude and a low negative correlation with distance from East Africa. This study provides robust results after accounting for spatial autocorrelation with Fst distances and random noise via an empirical Monte Carlo simulation using null SNPs.

scholarly journals Evidence for Recent Polygenic Selection on Educational Attainment Inferred from GWAS Hits

2016 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Educational Attainment ◽  
Cognitive Ability ◽  
Association Studies ◽  
Meta Analysis ◽  
Significant Snps ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Model Average ◽  
Polygenic Scores ◽  
Polygenic Selection

The genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment were used to test a polygenic selection model. Average frequencies of alleles with positive effect (polygenic scores or PS) were compared across populations (N=26) using data from 1000 Genomes. The PS of 161 GWAS significant SNPs in a recent meta-analysis was highly correlated to population IQ (r=0.863) and to the polygenic score of four alleles independently associated with general cognitive ability. High  correlations with PISA scores for a subsample were observed.SNP p value predicted correlation to population IQ and factors from the two previous GWAS (r= -.25). Factor analysis produced similar estimates of selection pressure for educational attainment across the three datasets. Polygenic and factor scores computed using the top 20 significant SNPs showed very high correlation to population IQ (r=0.88; 0.9). Similar findings were obtained using 52 populations from another database (ALFRED). The results together constitute a replication of preliminary findings and provide strong evidence for recent diversifying polygenic selection on educational attainment and underlying cognitive ability.

scholarly journals Can We Detect Polygenic Selection on Cognitive Ability Using GWAS Hits? Employing Random SNPs as a Null Model.

2017 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Educational Attainment ◽  
Spatial Autocorrelation ◽  
Predictive Power ◽  
Association Studies ◽  
Null Model ◽  
Genome Wide Association Studies ◽  
Polygenic Scores ◽  
Using Data ◽  
Genomic Regions ◽  
Polygenic Selection

Background: The genetic variants identified by three large genome-wide association studies (GWAS) of educational attainment were used to test a polygenic selection model.ethods: Average frequencies of alleles with positive effect (polygenic scores or PS) were compared across populations (N=26) using data from 1000 Genomes. A null model was created using frequencies of random SNPs.Results: Polygenic selection signal of educational attainment GWAS hits is high among a handful of SNPs within genomic regions replicated across GWAS publications. A polygenic score comprising 9 SNPs predicts population IQ (r=0.9), outperforming 99.9% of the polygenic scores obtained from sets of random SNPs. Its predictive power remains unaffected after controlling for spatial autocorrelation. Even random polygenic scores are moderate predictors of population IQ (thanks to spatial autocorrelation), and their predictive power increases logarithmically with the number of SNPs, indicating an exponential reduction in noise. Conclusion: This study provides guidance for using GWAS hits together with random SNPs for testing polygenic selection.

scholarly journals Polygenic Selection, Polygenic Scores, Spatial Autocorrelation and Correlated Allele Frequencies. Can We Model Polygenic Selection on Intellectual Abilities?

2017 ◽  
Author(s):  
Davide Piffer
Keyword(s):  
Educational Attainment ◽  
Spatial Autocorrelation ◽  
Predictive Power ◽  
Allele Frequencies ◽  
Polygenic Score ◽  
Polygenic Scores ◽  
Intellectual Abilities ◽  
Genomic Regions ◽  
Polygenic Selection ◽  
Selection Signal

The majority of polygenic selection signal of educational attainment GWAS hits is confined to a handful of SNPs within genomic regions replicated across GWAS publications. A polygenic score comprising 9 SNPs predicts population IQ (r=0.9), outperforming 99.9% of the polygenic scores obtained from sets of random SNPs. Its predictive power remains unaffected after controlling for spatial autocorrelation. Even random polygenic scores are moderate predictors of population IQ, and their predictive power increases logarithmically with the number of SNPs, indicating an exponential reduction in noise.Thus, the predictive power of polygenic scores has to be scaled in proportion to the number of SNPs composing them.

scholarly journals A Polygenic Score for Higher Educational Attainment is Associated with Larger Brains

2018 ◽  
Author(s):  
Maxwell L. Elliott ◽  
Daniel W Belsky ◽  
Kevin Anderson ◽  
David L. Corcoran ◽  
Tian Ge ◽  
...  
Keyword(s):  
Educational Attainment ◽  
Brain Imaging ◽  
Cognitive Performance ◽  
Test Performance ◽  
Brain Size ◽  
Cognitive Test ◽  
Size Difference ◽  
Uk Biobank ◽  
Polygenic Scores ◽  
Cognitive Test Performance

AbstractPeople who score higher on intelligence tests tend to have larger brains. Twin studies suggest the same genetic factors influence both brain size and intelligence. This has led to the hypothesis that genetics influence intelligence partly by contributing to development of larger brains. We tested this hypothesis with molecular genetic data using discoveries from a genome-wide association study (GWAS) of educational attainment, a correlate of intelligence. We analyzed genetic, brain imaging, and cognitive test data from the UK Biobank, the Dunedin Study, the Brain Genomics Superstruct Project (GSP), and the Duke Neurogenetics Study (DNS) (combined N=8,271). We measured genetics using polygenic scores based on published GWAS. We conducted meta-analysis to test associations among participants’ genetics, total brain volume (i.e., brain size), and cognitive test performance. Consistent with previous findings, participants with higher polygenic scores achieved higher scores on cognitive tests, as did participants with larger brains. Participants with higher polygenic scores also had larger brains. We found some evidence that brain size partly mediated associations between participants’ education polygenic scores and their cognitive test performance. Effect-sizes were larger in the population-based UK Biobank and Dunedin samples than in the GSP and DNS samples. Sensitivity analysis suggested this effect-size difference partly reflected restricted range of cognitive performance in the GSP and DNS samples. Recruitment and retention of population-representative samples should be a priority for neuroscience research. Findings suggest promise for studies integrating GWAS discoveries with brain imaging data to understand neurobiology linking genetics with individual differences in cognitive performance.

scholarly journals Genetic effects on educational attainment in Hungary

2020 ◽  
Author(s):  
Péter P. Ujma ◽  
Nóra Eszlári ◽  
András Millinghoffer ◽  
Bence Bruncsics ◽  
Péter Petschner ◽  
...  
Keyword(s):  
Educational Attainment ◽  
Genetic Variants ◽  
Educational Level ◽  
Statistical Power ◽  
Association Studies ◽  
Molecular Genetic ◽  
Genetic Effects ◽  
Genome Wide Association Studies ◽  
Genetic Studies ◽  
Polygenic Scores

AbstractEducational attainment is a substantially heritable trait, and it has recently been linked to specific genetic variants by genome-wide association studies (GWASs). However, the effects of such genetic variants are expected to vary across environments, including countries and historical eras. We used polygenic scores (PGSs) to assess molecular genetic effects on educational attainment in Hungary, a country in the Central Eastern European region where behavioral genetic studies are in general scarce and molecular genetic studies of educational attainment have not been previously published. We found that the PGS is significantly associated with highest educational level attained as well as the number of years in education in a sample of Hungarian volunteers (N=829). In an English (N=976) comparison sample with identical measurement protocols the same PGS had a stronger association with educational level, but not with years in education. In line with previous Estonian findings, we found higher PGS effect sizes in Hungarian, but not in English participants who attended higher education after the fall of Communism, although we lacked statistical power for this effect to reach significance. Our results provide evidence that polygenic scores for educational attainment are valid in diverse European populations.

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