Table 2.
Significant Association in the SLIC Cohort with the Follow-up Panel
| SNP | Chromosome Position (bp – B36) | Gene | Alleles (A1/A2) | A1 CEPH Frequency | Typed Strand | P Quant | Effect Size | Heritability | p Emp QTDT | p Case-Cont | Frequency of A1 Cases | Frequency of A1 Controls | Odds Ratio (95% CI) | p Emp PLINK |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs6564903 | 80,211,158 | CMIP | C∗/T | 0.48 | + | 0.1279 | −0.37 ± 0.10 | 0.038 | 0.1225 | 5 × 10−7∗ | 0.79 | 0.38 | 3.5 (2.1–5.9) | 1 × 10−6∗ |
| rs3935802 | 80,219,068 | CMIP | G∗/C | 0.46 | − | 0.2667 | −0.31 ± 0.10 | 0.025 | 0.2486 | 0.0003∗ | 0.71 | 0.49 | 2.5 (1.5–4.2) | 0.0006∗ |
| rs16955705 | 80,230,851 | CMIP | C/A∗ | 0.50 | + | 0.3916 | −0.25 ± 0.10 | 0.017 | 0.3627 | 0.0003∗ | 0.31 | 0.54 | 2.6 (1.5–4.4) | 0.0003∗ |
| rs4243209 | 80,247,592 | CMIP | C/T∗ | 0.22 | + | 0.0065∗ | −0.42 ± 0.12 | 0.027 | 0.0043∗ | 0.0007∗ | 0.11 | 0.26 | 3.0 (1.6–5.8) | 0.0012∗ |
| rs12149426 | 83,022,607 | ATP2C2 | A/C∗ | 0.26 | + | 0.0064∗ | −0.31 ± 0.12 | 0.017 | 0.0082∗ | 0.0082∗ | 0.14 | 0.27 | 2.3 (1.2–4.2) | 0.0039∗ |
Of the 105 SNPs analyzed in the follow-up panel, 16 lay in CMIP, 76 lay in the ATP2C2 gene, and the remaining 13 lay in other regions that had shown association in the screen (see Table 1). Eight SNPs were genotyped in both the screen and follow-up panels. All of these markers showed some evidence of association in the screen phase (p < 0.01) but had genotype success rates of <95%, and none lay within CMIP or ATP2C2. Each of the duplicated SNPs showed increased success rates and decreased association levels in the follow-up panel. SNP alleles are given with the minor allele in the SLIC sample first. Putative risk alleles are marked with an asterisk. p Quant gives the p value for the quantitative, family-based analysis. p case-cont gives the p value for the case-control analysis. p values <0.01 are shown in bold. The odds ratios indicate the ratio of case/control odds for each additional copy of the putative risk allele. Odds ratios were calculated within PLINK. The effect size is the estimated effect of each risk allele on the nonword-repetition score (in SD ± SE). Effect sizes were calculated with MERLIN. Heritability gives the proportion of total variance explained by the SNP. Heritability estimates were calculated with MERLIN. The p Emp column gives empirical p values for the given SNP; these values were derived from permutations within QTDT or PLINK.