PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size

Table 1 Comparison of PedGenie to the standard distribution using simulated data for independent individuals and nuclear families

			----Odds Ratio----		--- Difference in Means---
	Chi Square²	Chi Square Trend²	HET vs WT²	HOM vs WT²	HET vs WT²	HOM vs WT²	ANOVA²	Trio TDT²	Sib TDT³	Comb TDT³	QTDT⁴
Statistic	0.292	0.288	0.968	0.949	0.149	0.130	0.017	2.463	1.667	1.563	1.77
p-value standard distribution	0.864	0.592	0.632	0.754	0.882	0.896	0.983	0.117	0.096	0.118	0.077
95% CI standard distribution	-	-	0.846–1.107	0.682–1.320	-	-	-	-	-	-	-
Mean empirical p-value (SD)	0.865 (0.008)	0.591 (0.012)	0.633 (0.021)	0.749 (0.021)	0.882 (0.007)	0.896 (0.007)	0.983 (0.003)	0.117 (0.008)	0.087 (0.006)	0.118 (0.007)	0.078 (0.006)
P value: interquartile range	0.860–0.870	0.583–0.599	0.619–0.648	0.735–0.763	0.878–0.886	0.891–0.902	0.981–0.985	0.112–0.122	0.083–0.091	0.113–0.123	0.074–0.082
95% CI Empirical (Mean values)	-	-	0.846–1.107	0.685–1.314	-	-	-	-	-	-	-

¹For each statistical test, PedGenie was run 1,000 times to compute the average, standard deviation, and interquartile distance (1^st and 3^rd quartile values). The standard distribution is the standard distribution used for the particular statistical test (e.g., the p-value reported for the Chi-square test is from the Chi-square distribution). HOM = homozygous for minor allele, HET = heterozygous, WT = wild type.
²Test run using 2,000 independent, unrelated cases and 2000 independent, unrelated controls
³Test run using 4,000 independent nuclear families, composed of either trios (2 parents and one affected offspring), sib-pairs (one affected and one unaffected sib), or for the combined analysis, a combination of both trios (2,000) and sib-pairs (2,000).
⁴QTDT analysis run using method of Monks et al.[11]

ISSN: 1471-2105