Table 2.
Overview of Genetic Analyses and Results for the 10 Candidate Genes Hypothesized to Influence Risk of Secondary Lymphedema Following Breast Cancer Treatment
| Gene | Gene regiona | Sizeb(kilobases) | # tagSNPs to cover HapMap SNPs in gene regionc | # tagSNPs testedd | Trend test p<0.05 (# of tagSNPs) | Genotype-specific ORe>2.0 or <0.5 (# of tagSNPs) | Mendelian patternfof ‘extreme’ ORs (# tagSNPs) |
|---|---|---|---|---|---|---|---|
| VEGFC | chr4:177718895.177599691 | 119.2 kb | 17 tagSNPs to capture 126 SNPs | 17 | 0 | 5 | 4 |
| VEGFR2 | chr4:55939427.55996762 | 57.3 kb | 29 tagSNPs to capture 55 SNPs | 24 | 1 | 12 | 11 |
| VEGFR3 | chr5:180023507.180081624 | 58.1 kb | 33 tagSNPs to capture 52 SNPs | 32 | 3 | 14 | 13 |
| RORC | chr1:151773548.151809348 | 35.8 kb | 23 tagSNPs to capture 39 SNPs | 22 | 1 | 9 | 8 |
| VEGFD | chrX:15358718.15407577 | 48.9 kb | 7 tagSNPs to capture 36 SNPs | 7 | 0 | 4 | 2 |
| PROX1 | chr1:214156860.214214761 | 57.9 kb | 13 tagSNPs to capture 35 SNPs | 11 | 0 | 5 | 2 |
| LYVE1 | chr11:10574413.10595365 | 20.9kb | 11 tagSNPs to capture 25 SNPs | 8 | 0 | 4 | 3 |
| ADM | chr11:10321642.10333924 | 12.3 kb | 8 tagSNPs to capture 11 SNPs | 7 | 0 | 1 | 1 |
| SOX18 | chr20:62674081.62685979 | 11.9 kb | 3 tagSNPs to capture 3 SNPs | 3+ 3SNPsd | 0 | 3 | 0 |
| FOXC2 | chr16:86595857.86607536 | 11.7 kb | 2 tagSNPs to capture 2 SNPs | 2 | 0 | 0 | 0 |
Co-ordinates from NCBI37 assembly; bAn extra 5 kb on each end of the genetic locus was included for TagSNP selection; cAs determined by Haploview version 4.2 using HapMap data release 24/phaseII, November 2008, on NCBI B36 assembly, dbSNP 126; dDifferences in # tagSNPs from # SNPs tested are due to failures in design or genotyping (16 of 152 total SNPs attempted). Additional SNPs were chosen to capture genetic variation in the SOX18 gene more completely; eOdds ratio (OR) reveals at least a doubling or halving of lymphedema risk for women who are heterozygous and/or homozygous for the rare allele; fPattern of odds ratios across the three genotypes conforms with co-dominant, dominant, or recessive mode of inheritance.