Table 1 Comparison of previous large-scale GWASs of EA

From: Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals

 

Additive GWAS, autosomes

Additive GWAS, X chromosome

Dominance GWAS, autosomes

  

SNPs

PGI R2

 

SNPs

PGI R2 (C + T, P < 1)

 

SNPs

 

N

No. of SNPs

No. of loci

Mean χ2

LDpred, HapMap3 SNPs

C + T, P < 5 × 10−8

N

No. of SNPs

No. of loci

Mean χ2

Male

Female

Pooled

N

No. of SNPs

No. of loci

Mean χ2

EA1

126,559

2,310,444

4

1.24

2.64%

0.03%

-

-

-

-

-

-

-

-

-

-

-

EA2-D

293,723

9,256,490

74

1.46

5.81%

0.46%

-

-

-

-

-

-

-

-

-

-

-

EA2-C

405,072

9,918,450

162

1.63

6.91%

0.93%

-

-

-

-

-

-

-

-

-

-

-

EA3

1,131,881

10,016,266

1,271

2.91

10.09%

4.03%

694,894

205,865

10

2.60

0.04%

0.00%

0.01%

-

-

-

-

EA4

3,037,499

10,675,380

3,952

4.90

13.28%

7.18%

2,713,033

211,581

57

5.24

0.29%

0.10%

0.19%

2,574,253

5,870,596

0

1.00

  1. Summary overview of GWASs meta-analyses of educational attainment. No. of SNPs is the number of markers included in the final GWAS meta-analysis of number of years of schooling completed; no. of Loci is the number of approximately independent SNPs that reached genome-wide significance; and mean χ2 is the average test statistic for SNPs with MAF > 1% and N > 0.9 × Nmax, where Nmax is the maximum sample size across all SNPs. To maximize comparability across studies, PGIs are generated using SNPs available in all GWAS (all five GWASs for autosomal PGI and EA3-EA4 for the X chromosome PGI) and uniform procedures described in the Supplementary Note. C + T stands for clumping and thresholding. The autosomal PGI R2 values are sample-size weighted averages of the incremental R2 values from the Health and Retirement Study and the National Longitudinal Study of Adolescent to Adult Health. The X chromosome PGI R2 values are the incremental R2 values from the Health and Retirement Study. The incremental R2 is the increase in R2 after adding the PGI to a regression of EA on controls (a full set of dummy variables for year of birth, an indicator variable for sex, a full set of interactions between sex and year of birth and the first ten principal components of the genomic relatedness matrix). EA1, Rietveld et al.61 combined meta-analysis of discovery and replication cohorts; EA2-D, Okbay et al.62 meta-analysis of discovery cohorts; EA2-C, Okbay et al.62 meta-analysis of discovery and replication cohorts; EA3, Lee et al.2 meta-analysis of discovery cohorts; EA4, current study.
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