Table 2 Comparison of chi-square values from the PLINK TDT and MI-GWAS LRT for inherited genetic effects for a randomly selected set of SNPs on chromosome one and most significant autosomal SNPs.
SNP | PLINK TDT chi-square value | MI-GWAS log-linear modeling chi-square value | Percent Differencea |
|---|---|---|---|
Chromosome 1 SNPs | Â | Â | Â |
SNP 1 | 0.02 | 0.02 | 0.00 |
SNP 2 | 2.22 | 2.22 | 0.00 |
SNP 3 | 0.91 | 0.91 | 0.00 |
SNP 4 | 0.09 | 0.09 | 0.00 |
SNP 5 | 0.24 | 0.24 | 0.00 |
SNP 6 | 1.58 | 1.58 | 0.00 |
SNP 7 | 2.97 | 2.98 | 0.00 |
SNP 8 | 1.22 | 1.22 | 0.00 |
Most significant autosomal SNPs | Â | Â | Â |
SNP 9 | 22.34 | 24.06 | 0.08 |
SNP 10 | 22.29 | 22.57 | 0.01 |
SNP 11 | 21.48 | 21.64 | 0.01 |
SNP 12 | 20.78 | 21.02 | 0.01 |
SNP 13 | 19.56 | 19.77 | 0.01 |