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Table 4 Comparison of extremes of phenotypic subgroups

From: The influence of genetic variation in 30 selected genes on the clinical characteristics of early onset breast cancer

Phenotype Gene SNP Risk allele Frequency Trend test Genotypic P value
     ER positive ER negative P value OR (95% CI)  
ER (+/-) FGFR2 rs2981582 A 0.478 0.3608 0.000003* 1.62 (1.32 to 2.00) 0.000014
  FGFR2 rs1219648 G 0.4861 0.3736 0.000008* 1.59 (1.29 to 1.95) 0.000039
  ATM rs1801516 A 0.1085 0.1776 0.000273* 0.56 (0.42 to 0.75) 0.000402
  TOX3 rs1420546 C 0.3655 0.2865 0.002135 1.44 (1.15 to 1.79) 0.003002
  ATM rs3092991 G 0.1248 0.1813 0.002561 0.64 (0.49 to 0.85) 0.00212
Grade (1/3) ESR1 rs2228480 A 0.2178 0.1032 0.002962 2.42 (1.34 to 4.38) NA
  ESR1 rs3798577 C 0.5088 0.373 0.004411 1.74 (1.19 to 2.55) 0.002136
  IGF1 rs2373721 G 0.25 0.1406 0.007009 2.04 (1.21 to 3.42) NA
  LSP1 rs661348 C 0.3694 0.4921 0.009682 0.60 (0.42 to 0.88) 0.01541
  1. The genotypic test is not performed if at least one of the cells has a frequency less than 5 which is represented by NA. *Significant SNPs after correcting for 82 independent tests. CI, confidence interval; ER, oestrogen receptor; OR, odds ratio; SNP, single nuceotide polymorphism.