Table 2.

Cell Counts for the Tetralogy of Fallot Data

Chromosome	SNP	Base-Pair Position	Cell Counts in Case-Parent Trios			Cell Counts in Case-Mother Duos			Cell Counts in Case-Father Duos			EMIM Odds Ratio with Parent of Origin		EMIM p Value with Parent of Origin
9	9a	9b	4	4a	4b	4	4a	4b	Unknown	Estimated	Unknown	Estimated
12	rs11065987	110556807	28	13	15	12	1.993	10.007	3	1.976	1.024	1.662	1.555	2.10 × 10−8	4.16 × 10−7
12	rs11066188	111095097	30	13	17	13	2.996	10.004	4	2.976	1.024	1.591	1.489	3.38 × 10−7	5.02 × 10−6
12	rs3184504	110368991	30	14	16	11	9.942	1.058	3	0.987	2.013	0.622	0.662	3.43 × 10−7	3.35 × 10−6
12	rs17696736	110971201	29	13	16	12	1.987	10.013	4	2.977	1.023	1.582	1.481	4.63 × 10−7	6.84 × 10−6
12	rs653178	110492139	30	14	16	11	9.943	1.057	3	0.987	2.013	0.627	0.666	4.82 × 10−7	4.50 × 10−6
13	rs7982677	91786324	19	10	9	6	3.016	2.984	4	4.000	0.000	1.577	1.504	9.54 × 10−7	6.97 × 10−6
13	rs7318834	108710500	11	5	6	6	1.006	4.994	1	0.987	0.013	1.667	1.640	5.87 × 10−6	8.40 × 10−6
13	rs4771856	91792510	18	9	9	6	3.016	2.984	3	2.998	0.002	1.519	1.461	1.12 × 10−5	4.79 × 10−5
13	rs7994141	47672251	42	24	18	4	2.008	1.992	4	2.007	1.993	0.656	0.668	1.41 × 10−5	1.13 × 10−5
13	rs7995410	47651319	42	24	18	4	2.008	1.992	4	2.007	1.993	0.656	0.668	1.43 × 10−5	1.14 × 10−5

Shown are the results at the five SNPs on chromosomes 12 and 13 with the lowest p values, when using EMIM with and without haplotype estimation. Cell counts are shown for the ambiguous scenarios in which all individuals are heterozygous: cell 9 for case-parent trios and cell 4 for case-mother duos and case-father duos. The estimated number of trios and duos in which the risk allele is inherited from the father is given as cells 9a and 4a, respectively, and the estimated number in which the risk allele is inherited from the mother is given as cells 9b and 4b, respectively. Cell counts estimated from duos need not be integers given that they incorporate the adjustment described in Appendix B. The odds ratios and p values given by EMIM, with and without haplotype estimation, are shown. Chromosomes 12 and 13 were tested for paternally and maternally inherited imprinting effects, respectively.