A Kallikrein 15 (KLK15) single nucleotide polymorphism located close to a novel exon shows evidence of association with poor ovarian cancer survival

Batra, Jyotsna; Nagle, Christina M; O'Mara, Tracy; Higgins, Melanie; Dong, Ying; Tan, Olivia L; Lose, Felicity; Skeie, Lene Marie; Srinivasan, Srilakshmi; Bolton, Kelly L; Song, Honglin; Ramus, Susan J; Gayther, Simon A; Pharoah, Paul DP; Kedda, Mary-Anne; Spurdle, Amanda B; Clements, Judith A

doi:10.1186/1471-2407-11-119

Table 1 SNP selection for the survival studies.

From: A Kallikrein 15 (KLK15) single nucleotide polymorphism located close to a novel exon shows evidence of association with poor ovarian cancer survival

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

ObsHet: Observed heterozygous alleles; PredHET: Predicted heterozygous alleles; HWpval: Hardy-Weinberg equilibrium p value; MAF: Minor allele frequency; HRE: Hormone Response Element; TFBS: Transcription Factor Binding Site
SNPs in the KLK15 gene derived from the HapMap database and those by in silico prediction methods were genotyped in control individuals, and the minor allele frequency (MAF) and HWE were calculated using Haploview 4.2. SNPs in bold were shortlisted for genotyping and survival analysis on the basis on LD calculations.

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ISSN: 1471-2407

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