A genome wide association study on Newfoundland colorectal cancer patients’ survival outcomes

Biomarker Research

Table 2 SNPs identified from six models with nominal significance (p < 1.0x10 ⁻⁶ )

Group/Outcome	Gene	SNP	Chr	Position	MAF	HWE-p	genotype	p-value	HR	CI_low	CI_high
MSS/MSI-L-DFS	LINC01121	rs6720296	2	45408269	0.4026	0.48	150 215 66	5.46E-07	1.74	1.40	2.16
MSS/MSI-L-DFS	n/a (intergenic)	rs1407508	9	101644538	0.0580	0.65	383 46 2	8.51E-07	2.53	1.75	3.66
colon-OS	n/a (intergenic)	rs4812219	20	59422971	0.0823	1.00	281 51 2	7.41E-07	3.27	2.05	5.23
colon-DFS	n/a (intergenic)	rs17280262	14	97053924	0.0629	0.13	295 36 3	1.33E-07	3.02	2.00	4.55
rectum-OS	n/a (intergenic)	rs17026425	4	150672514	0.0439	0.27	157 13 1	6.65E-07	5.06	2.67	9.60
rectum-OS	n/a (intergenic)	rs6854845	4	75746665	0.1082	0.70	135 35 1	9.46E-07	4.12	2.34	7.26
rectum-DFS	n/a (intergenic)	rs1570271	10	115288501	0.0882	1.00	141 28 1	1.47E-07	3.66	2.26	5.94
rectum-DFS	AC011343.1	rs17057166	5	159248014	0.0468	1.00	155 16 0	2.11E-07	5.56	2.91	10.64
rectum-DFS	n/a (intergenic)	rs4868304	5	173131457	0.1550	0.25	124 41 6	2.52E-07	2.91	1.94	4.37
rectum-DFS	n/a (intergenic)	rs6854845	4	75746665	0.1082	0.70	135 35 1	6.16E-07	3.31	2.07	5.30

Chr: chromosome, CI_high: higher bound of the 95% confidence interval for the HR estimate, CI_low: lower bound of 95% confidence interval for the HR estimate; DFS: disease-free survival, HWE-p: p-value for the Hardy-Weinberg Equilibrium test, HR: hazards ratio, MAF: minor allele frequency, MSS: microsatellite stable, MSI-L: microsatellite instability-low, OS: overall survival, SNP: single nucleotide polymorphism. Please note that the genotyping platform also contain other types of genetic markers, such as small insertions/deletions. For simplicity, all genetic markers are annotated as SNPs throughout this manuscript; interested readers may check the dbSNP database ([24]) for further information on these SNPs. Gene information as noted in the dbSNP database for each of the SNPs.

ISSN: 2050-7771