Table 3. Analysis of allele-specific imbalance in discovery, validation, and combined sample sets.

SNP	Sample Set	Risk Allele	Non-risk Allele	Risk Allele Lost*	Non-risk Allele Lost†	Total Imbalance§	P-value‡	Adjusted P-value∞
rs7136702
	Discovery	T	C	12 (16%)	5 (7%)	17/75 (23%)	0.09	1.00
	Validation	T	C	6 (5%)	8 (6%)	14/133 (11%)	0.59	1.00
	Combined	T	C	18 (9%)	13 (6%)	31/208 (15%)	0.37	1.00
rs16892766
	Discovery	C	A	6 (22%)	1 (4%)	7/27 (26%)	0.06	0.96
	Validation	C	A	3 (8%)	3 (8%)	6/38 (16%)	1.00	1.00
	Combined	C	A	9 (14%)	4 (6%)	13/65 (20%)	0.17	0.51
rs6983267
	Discovery	G	T	6 (9%)	14 (21%)	20/67 (30%)	0.07	1.00
	Validation	G	T	9 (7%)	19 (15%)	28/125 (22%)	0.06	0.18
	Combined	G	T	15 (8%)	33 (17%)	48/192 (25%)	0.01	0.03

^* Risk Allele Lost refers to relative loss of risk allele compared to non-risk allele. Number in parentheses indicates percentage of total heterozygous samples showing relative loss of risk allele.

^† Non-risk Allele Lost refers to relative loss of non-risk allele compared to risk allele. Number in parentheses indicates percentage of total heterozygous samples showing relative loss of non-risk allele.

^§Total number of tumors with imbalance/total heterozygous samples (% of heterozygotes showing imbalance).

^‡Chi-squared statistical test, df = 1.

^∞Bonferroni correction for 16 multiple comparisons (original) or 3 multiple comparisons (validation, combined).