TABLE 3.
Concordance between LD relations and tag SNP selection in five genes for three ethnic populations
| Japanese
|
African Americans
|
Caucasians
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Gene name | No. of SNPs testeda |
Average value of pairwise LDb |
Threshold value of LD groupingc |
No. of tag SNPs/no. of polymorphic SNPsd (%) |
Average value of pairwise LD |
Threshold value of LD groupingc |
No. of tag SNPs/no. of polymorphic SNPsd (%) |
Average value of pairwise LD |
Threshold value of LD groupingc |
No. of tag SNPs/no. of polymorphic SNPsd (%) |
| ABCA1 | 37 | 0.12 | 0.4 | 19/37 (51) | 0.05 | 0.2 | 24/37 (64) | 0.08 | 0.5 | 17/37 (45) |
| ADPRT | 29 | 0.38 | 0.4 | 7/29 (24) | 0.26 | 0.6 | 10/28 (35) | 0.32 | 0.2 | 7/28 (25) |
| F5 | 41 | 0.25 | 0.7 | 12/41 (29) | 0.18 | 0.6 | 15/41 (36) | 0.22 | 0.2 | 10/40 (25) |
| LPL | 25 | 0.31 | 0.5 | 9/23 (39) | 0.14 | 0.5 | 17/25 (68) | 0.23 | 0.4 | 12/25 (48) |
| SLC12A3 | 25 | 0.14 | 0.3 | 10/25 (40) | 0.05 | 0.2 | 19/25 (76) | 0.10 | 0.3 | 11/25 (44) |
ABCA1, ATP-binding cassette, subfamily A (ABC1), member 1; ADPRT, poly (ADP-ribose) polymerase family, member 1; F5, coagulation factor V; SLC12A3, solute carrier family 12 (sodium/chloride transporters), member 3.
a
From exons, 5′-UTRs, and 3′-UTRs of each gene, SNPs with MAF of at least 5% in any of three populations were tested.
b
The LD by coefficient r2 was averaged over all possible pairs of polymorphic SNPs.
c
The optimal r2 threshold for defining LD groups of SNPs was chosen automatically within our algorithm (see the minimum value, t, in step 7).
d
This ratio indicates the efficiency of tag SNP selection (see results).