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IBC 2013, doi: 10.4051/ibce.2013.4.0002
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Factor Analysis of Population Allele Frequencies as a Simple, Novel Method of Detecting Signals of Recent Polygenic Selection: The Example of Educational Attainment and IQ.
Davide Piffer1,*
Via Molina 15, 54033- Carrara (MS) Italy
*Corresponding author
received: November 16, 2013 ; accepted: November 26, 2013 ; published : November 27, 2013
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Weak widespread (polygenic) selection is a mechanism that acts on multiple SNPs
simultaneously. The aim of this paper is to suggest a methodology to detect signals of
polygenic selection using educational attainment as an example. Educational attainment is a
polygenic phenotype, influenced by many genetic variants with small effects. Frequencies of
10 SNPs found to be associated with educational attainment in a recent genome-wide
association study were obtained from HapMap, 1000 Genomes and ALFRED. Factor analysis
showed that they are strongly statistically associated at the population level, and the resulting
factor score was highly related to average population IQ (r=0.90). Moreover, allele
frequencies were positively correlated with aggregate measures of educational attainment in
the population, average IQ, and with two intelligence increasing alleles that had been
identified in different studies. This paper provides a simple method for detecting signals of
polygenic selection on genes with overlapping phenotypes but located on different
chromosomes. The method is therefore different from traditional estimations of linkage
disequilibrium. This method can also be used as a tool in gene discovery, potentially
decreasing the number of SNPs that are included in a genome-wide association study,
reducing the multiple-testing problem and required sample sizes and consequently, financial

Keywords : polygenic, recent selection, educational attainment, intelligence, SNP, HapMap, 1000 genomes, race differences
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