These results have implications for a common analytical approach applied to large-scale SNP data. GWAS analysis often begins by discarding all genotypes for SNPs of low MAF, typically for those with MAF<10% [3,4]. This practice results in a huge loss of data. For example, 35.5% of SNPs on the Affymetrix chips have MAFs below 10%. In addition, discarding low MAF SNPs may hamper our ability to detect rare disease-causing polymorphisms [5].
