Background
Methods
Study Participants and Genotyping
Web based search for putative splice-variants
In silicoPromoter and SNP analysis
Cell culture, RT PCR and sequencing of KLK15putative promoter region
Statistical Analysis
Results
Analysis of KLK15transcripts
In silicopromoter analysis to prioritize regions for sequencing and SNP modeling
SNP information and prediction of functional effects
Gene
Promoter
Promoter sequencing of cancer cell lines and aggressive cancer patients
LD mapping and SNPs selection for survival studies
SNP no | Name | Rationale | Position | ObsHET | PredHET | HWpval | MAF |
---|---|---|---|---|---|---|---|
1 |
rs2659058
|
Tagged SNP from HapMap | 56017918 | 0.421 | 0.443 | 0.0869 | 0.331 |
2 |
rs3212810
|
Tagged SNP from HapMap and predicted to fall in miRNA binding site | 56020548 | 0.364 | 0.369 | 0.6072 | 0.244 |
3 | rs3212853 | Ploymorphic miRNA target site | 56020606 | 0.044 | 0.041 | 0.2863 | 0.037 |
4 | rs3212852 | Exon-Intron boundary | 56021941 | 0.038 | 0.038 | 1 | 0.019 |
5 |
rs3745522
|
Tagged SNP from HapMap | 56022744 | 0.349 | 0.383 | 0.0013 | 0.259 |
6 |
rs2659056
|
Tagged SNP from HapMap | 56027755 | 0.383 | 0.382 | 1 | 0.257 |
7 |
rs266851
|
Tagged SNP from HapMap | 56028151 | 0.297 | 0.306 | 0.2742 | 0.189 |
8 | rs16987576 | 2 bp 3' of exon B, Imp for splicing | 56028165 | 0.003 | 0.003 | 1 | 0.001 |
9 |
rs2659055
| Predicted in silico to affect HRE | 56029044 | 0.485 | 0.5 | 0.3033 | 0.49 |
10 | rs2163861 |
Tagged SNP from HapMap | 56029204 | 0.485 | 0.5 | 0.2841 | 0.489 |
11 | rs266853 | Predicted in silico to affect TFBS and HRE | 56029520 | 0.001 | 0.001 | 1 | 0.001 |
12 | rs266854 | Predicted in silico to affect HRE | 56029630 | 0.004 | 0.004 | 1 | 0.002 |
13 |
rs190552
| Predicted in silico to affect TFBS and HRE | 56030005 | 0.333 | 0.346 | 0.1823 | 0.222 |
14 |
rs266855
| Predicted in silico to affect HRE | 56030196 | 0.396 | 0.413 | 0.1259 | 0.292 |
15 | rs266856 |
Tagged SNP from HapMap | 56030318 | 0.333 | 0.349 | 0.1131 | 0.225 |
16 |
rs2739442
| Predicted in silico to affect TFBS and HRE | 56030985 | 0.479 | 0.493 | 0.2975 | 0.442 |
17 | rs2033496 | Predicted in silico to affect TFBS and HRE | 56031019 | 0.49 | 0.493 | 0.8309 | 0.442 |
18 | rs12978902 | Predicted in silico to affect HRE | 56031056 | 0 | 0 | 1 | 0 |
19 |
rs2659053
| Predicted in silico to affect TFBS and HRE | 56032606 | 0.449 | 0.472 | 0.0722 | 0.382 |
20 |
rs2569746
| Predicted in silico to affect TFBS and HRE | 56032727 | 0.462 | 0.487 | 0.0638 | 0.42 |
21 |
rs35711205
| Novel SNP (reported later in NCBI) | 56032818 | 0.296 | 0.309 | 0.1212 | 0.191 |
22 | rs2569747 | Predicted in silico to affect TFBS and HRE | 56032875 | 0.459 | 0.487 | 0.0346 | 0.419 |
Association with ovarian cancer survival
Australian dataset | UK GWAS dataset | TCGA dataset | |
---|---|---|---|
n* (%) | n* (%) | n* (%) | |
Age group
| |||
<40 | 21 (7) | 97 (5) | 7 (2) |
40-49 | 51 (16) | 316 (17) | 74 (19) |
50-59 | 85 (26) | 653 (36) | 123 (31) |
60-69 | 99 (31) | 594 (33) | 97 (24) |
70+ | 63 (20) | 155 (9) | 96 (24) |
FIGO stage
| |||
I | 54 (18) | 586 (44) | 8 (2) |
II | 35 (11) | 162 (12) | 12 (3) |
III | 192 (63) | 507 (38) | 312 (79) |
IV | 26 (8) | 80 (6) | 65 (16) |
Histological grade
| |||
well differentiated | 41 (14) | 239 (18) | 2 (1) |
moderately differentiated | 94 (32) | 418 (32) | 44 (11) |
poor/undifferentiated | 156 (54) | 643 (50) | 344 (88) |
Histological subtype
| |||
serous | 199 (64) | 867 (54) | 397 (100) |
endometrioid | 35 (11) | 200 (13) | |
mucinuous | 23 (8) | 320 (20) | |
clear cell | 21 (7) | 173 (11) | |
other | 32 (10) | 40 (2) |
KLK15 | n | n censored | Adjusted* HR (95% CI) | p value (trend) |
---|---|---|---|---|
rs2659058
| ||||
TT | 123 | 74 | 1.0 | |
CT | 138 | 88 | 1.13 (0.82-1.55) | 0.75 |
CC | 50 | 26 | 1.20 (0.75-1.91) | |
rs3212810
| ||||
CC | 207 | 122 | 1.0 | |
TC | 87 | 51 | 1.01 (0.72-1.41) | 0.29 |
TT | 18 | 14 | 1.46 (0.82-2.62) | |
rs3745522
| ||||
GG | 187 | 106 | 1.0 | |
GT | 81 | 48 | 0.97 (0.68-1.39) | 0.15 |
TT | 18 | 13 | 1.73 (0.93-3.24) | |
rs266851
| ||||
CC | 222 | 128 | 1.0 | |
CT | 89 | 55 |
1.43 (1.02-2.00)
| |
TT | 7 | 5 | 1.26 (0.49-3.24) |
0.01
|
CT/TT | 96 | 60 |
1.42 (1.02-1.96)
| |
rs2659055
| ||||
TT | 84 | 52 | 1.0 | 0.23 |
TC | 144 | 87 | 0.86 (0.60-1.23) | |
CC | 67 | 36 | 0.74 (0.47-1.17) | |
rs190552
| ||||
TT | 178 | 109 | 1.0 | 0.79 |
CT | 114 | 65 | 1.04 (0.76-1.42) | |
CC | 19 | 13 | 1.21 (0.67-2.17) | |
rs2739442
| ||||
GG | 92 | 55 | 1.0 | 0.99 |
GA | 133 | 76 | 1.09 (0.75-1.58) | |
AA | 89 | 54 | 1.08 (0.73-1.62) | |
rs2659053
| ||||
GG | 129 | 79 | 1.0 | 0.2 |
GA | 118 | 73 | 0.93 (0.66-1.29) | |
AA | 63 | 34 | 0.95 (0.63-1.44) | |
rs2569746
| ||||
AA | 111 | 65 | 1.0 | 0.43 |
TA | 119 | 74 | 0.90 (0.64-1.27) | |
TT | 57 | 36 | 1.12 (0.74-1.69) |
KLK15rs266851 | n | n censored | Adjusted* HR (95% CI)*
|
---|---|---|---|
Australian
| |||
CC | 222 | 128 | 1.0 |
CT/TT | 96 | 60 | 1.42 (1.02-1.96) |
UK GWAS**
| |||
CC | 1139 | 390 | 1.0 |
CT/TT | 676 | 221 | 1.07 (0.94-1.24) |
TCGA***
| |||
CC | 280 | 135 | 1.0 |
CT/TT | 133 | 76 | 1.20 (0.90-1.61) |
Combined Analysis
| |||
CC | 1641 | 653 | 1.0 |
CT/TT | 905 | 357 | 1.16 (1.00-1.34) |