Table I. Details of tag SNPs selection for cell cycle genes.
| Gene | Size (kb) | Data | Percentage of gene re-sequenced by EGP |
No. of common variants |
No. of tag SNPs genotyped |
Additional SNPs genotypeda |
Common variants tagged rp2 > 0.8 |
Common variants tagged rp2 > 0.5 |
Common variants tagged rs2 > 0.8 |
LD blocks |
|---|---|---|---|---|---|---|---|---|---|---|
| CCND1 | 16 | EGP | 100 | 13b | 5 | 2 | 10 (76.9%) | 10 (76.9%) | 10 (76.9%) | 1 |
| CCND2 | 32 (40 kb file)c | HapMap | NA | 30 | 14 | 0 | 19 (63.3%) | 25 (83.3%) | 23 (76.7%) | 2 |
| CCND3 | 9 | EGP | 88 | 13 | 7 | 0 | 12 (92.3%) | 12 (92.3%) | 12 (92.3%) | 1 |
| CCNE1 | 13.5 | EGP | 84 | 12d | 3 | 1 | 5 (41.7%) | 7 (58.3%) | 5 (41.7%) | 1 |
| CDK2 | 7.6 | EGP | 98 | 6 | 2 | 0 | 2 (33.3%) | 2 (33.3%) | 2 (33.3%) | 1 |
| CDK4 | 6.7 | EGP | 96 | 5 | 2 | 0 | 4 (80%) | 4 (80%) | 4 (80%) | 1 |
| CDK6 | 220.8 | HapMap | NA | 88 | 13 | 0 | 68 (77.3%) | 83 (94.3%) | 76 (86.4%) | 3 |
| CDKN1A | 10.9 | EGP | 85 | 27 | 9e | 1 | 17 (63.0%) | 22 (81.5%) | 17 (63.0%) | 3 |
| CDKN1B | 5.7 (10 kb file)c | HapMap | 100 | 7 | 7 | 1 | 7 (100%) | 7 (100%) | 7 (100%) | 1 |
| CDKN2A (2B)f | 28.8 (13.3) | EGP | 81 (94) | 33 | 13 | 3 | 32 (97%) | 32 (97%) | 32 (97%) | 1 |
| CDKN2C | 8.9 | EGP/HapMap | 87 | 3 | 2 | 0 | 3 (100%) | 3 (100%) | 3 (100%) | 1 |
| CDKN2D | 4.1 | EGP | 63 | 3 | 2 | 0 | 3 (100%) | 3 (100%) | 3 (100%) | 1 |
NA, not applicable.
a
Additional SNPs genotyped that were not common in the data set used for tagging. These SNPs do not contribute to the estimates of tagging efficiency
b
One common SNP in EGP (rs3212867) was monomorphic in the CEU HapMap population.
c
File size actually used for tagging process.
d
Eleven SNPs in LD in EGP had a MAF of 0 in the CEU HapMap population, so were not considered in our population.
e
Assay for rs3176359 was too rare in our population (MAF 5 0.002).
f
Genes CDKN2A and CDKN2B were considered together as they lie in a single LD block on 9p21.