Table 1.
Cell Counts for the Specific Language Impairment 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 | |||
| 5 | rs10447141 | 39852924 | 16 | 6 | 10 | 10 | 1.99 | 8.01 | 4 | 3.02 | 0.98 | 0.326 | 0.494 | 1.29 × 10−7 | 6.18 × 10−5 |
| 5 | rs980306 | 39852592 | 14 | 6 | 8 | 9 | 1.99 | 7.01 | 4 | 3.02 | 0.98 | 0.334 | 0.487 | 4.28 × 10−7 | 7.53 × 10−5 |
| 5 | rs17194068 | 39857074 | 14 | 6 | 8 | 9 | 1.99 | 7.01 | 4 | 3.02 | 0.98 | 0.336 | 0.487 | 4.91 × 10−7 | 7.53 × 10−5 |
| 5 | rs6895329 | 39861497 | 15 | 6 | 9 | 11 | 2.99 | 8.01 | 4 | 3.02 | 0.98 | 0.343 | 0.497 | 1.12 × 10−6 | 1.10 × 10−4 |
| 5 | rs1994882 | 39841921 | 7 | 7 | 0 | 13 | 1.99 | 11.01 | 2 | 1.02 | 0.98 | 2.388 | 2.013 | 2.70 × 10−6 | 5.57 × 10−5 |
| 14 | rs4280164 | 23841124 | 10 | 5 | 5 | 12 | 1.01 | 10.99 | 1 | 1.00 | 0.00 | 0.254 | 0.317 | 2.29 × 10−8 | 1.32 × 10−7 |
| 14 | rs11158632 | 23839502 | 10 | 5 | 5 | 12 | 1.01 | 10.99 | 1 | 1.00 | 0.00 | 0.256 | 0.320 | 2.83 × 10−8 | 1.70 × 10−7 |
| 14 | rs2144494 | 23843226 | 10 | 5 | 5 | 12 | 1.01 | 10.99 | 1 | 1.00 | 0.00 | 0.256 | 0.317 | 3.03 × 10−8 | 1.31 × 10−7 |
| 14 | rs2281472 | 23845685 | 12 | 6 | 6 | 10 | 1.02 | 8.98 | 2 | 2.00 | 0.00 | 0.299 | 0.364 | 2.12 × 10−7 | 6.96 × 10−7 |
| 14 | rs3181384 | 23856815 | 11 | 5 | 6 | 11 | 1.02 | 9.98 | 1 | 1.00 | 0.00 | 0.326 | 0.376 | 1.02 × 10−6 | 2.21 × 10−6 |
Shown are the results at the five SNPs on chromosomes 5 and 14 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 as 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 5 and 14 were tested for maternally and paternally inherited imprinting effects, respectively.