Since raw genotype data may not always be available for analysis, MAGMA also provides more traditional SNP-wise gene analysis models of the type implemented in PLINK and VEGAS. These SNP-wise models first analyse the individual SNPs in a gene and combine the resulting SNP p-values into a gene test-statistic, and can thus be used even when only the SNP p-values are available. Although evaluation of the gene test-statistic does require an estimate of the LD between SNPs in the gene, estimates based on reference data with similar ancestry as the data the SNP p-values were computed from has been shown to yield accurate results [17,19].
