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

Table 2 Results for PedGenie Chi-square statistic and Slager and Schaid Armitage test for trend using GAW12 data¹

SNP ID	MOI²	Minor Allele Freq	D'³	r²	PedGenie Chi-Square p-value: Mean (SD) [Interquartile distance]	Slager & Schaid Trend Test p-value
5782	D	0.092	–	–	<0.001⁴	2.06E-13
5782	R	0.092	–	–	0.232 (0.010) [0.225–0.239]	0.213
5007	D	0.093	1.00	1.00	<0.001⁴	3.42E-13
5007	R	0.093	1.00	1.00	0.232 (0.010) [0.225–0.238]	0.213
4848	D	0.40	1.00	0.064	0.030 (0.004) [0.027–0.033]	0.030
4848	R	0.40	1.00	0.064	0.693 (0.010) [0.687–0.700]	0.688
11146	D	0.029	0.84	0.003	0.219 (0.009) [0.213–0.225]	0.212
11146	R	0.029	0.84	0.003	-⁵	-⁵

¹PedGenie results for the Chi-Square test averaged over 1000 runs are compared to the Slager and Schaid Armitage test for trend [20] using prior coefficient of kinship probabilities in the correlation matrix. The 'answer' in this simulated data set is SNP 5782, dominant model.
²Mode of inheritance. D = dominant R = recessive
³D' and r²: linkage disequilibrium measures, calculated between SNP 5782 and each subsequent SNP
⁴The significance threshold of PedGenie is limited by the number of simulations used to create the empirical null distribution (i.e., 2,000). For this result, all statistics based on observed values were less than the statistics based on simulated values.
⁵Result could not be calculated due to sparse data

ISSN: 1471-2105