Skip to main content

Table 3 Nominally significant rare-variant tests for breast cancer overall and by estrogen receptor status, across all ethnicities

From: Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities

Outcome Gene Chromosome: index SNP Number of variants CP Significant test(s) p value OR (95 % CI)
Breast cancer overall ORAOV1 Chr11: rs614367 43 4.80 % SKAT 0.004 0.8 (0.6–1.1)
  GTPBP3 Chr19: rs8170 48 3.50 % SKAT 0.01 1.3 (0.9–1.8)
  GLT25D1 Chr19: rs8170 55 2.50 % SKAT 0.015 0.9 (0.7–1.4)
  DDA1 - p2 Chr19: rs8170 1 <1.0 % SKAT 0.046 2.0 (0.9–4.1)
  NSMCE4A Chr10: rs2981579 17 0.70 % BURDEN 0.023 0.4 (0.2–0.9)
  ANO8 - p2 Chr19: rs8170 8 <1.7 % BURDEN 0.034 5.3 (1.1–24.2)
ER+ GTPBP3 Chr19: rs8170 48 3.50 % SKAT 0.007 1.4 (1.0–2.1)
  TMEM221 - p2 Chr19: rs8170 5 <2.1 % SKAT 0.013 0.4 (0.2–1.0)
  GLT25D1 Chr19: rs8170 55 2.50 % SKAT 0.018 0.8 (0.5–1.3)
  ZNF365 - p2 Chr10: rs10995190 8 <2.0 % SKAT, BURDEN 0.019 2.5 (1.0–5.9)
  ORAOV1 Chr11: rs614367 43 4.80 % SKAT 0.024 0.8 (0.6–1.1)
  TMEM221 Chr19: rs8170 24 2.10 % SKAT 0.028 0.6 (0.4–1.1)
  ZFYVE26 Chr14: rs999737 126 5.70 % SKAT 0.041 1.2 (0.9–1.5)
  MAP1S - p2 Chr19: rs8170 22 <4.9 % SKAT 0.045 0.9 (0.6–1.5)
  GLT25D1 - p2 Chr19: rs8170 15 <2.5 % SKAT 0.049 0.9 (0.4–1.9)
  ZNF365 Chr10: rs10995190 38 2.00 % BURDEN 0.013 1.8 (1.1–2.9)
  PLVAP Chr19: rs8170 31 1.80 % BURDEN 0.016 1.8 (1.1–3.0)
  FGFR2 Chr10: rs2981579 41 1.50 % BURDEN 0.016 2.0 (1.1–3.4)
  C6orf211 Chr6: rs2046210 34 2.70 % BURDEN 0.044 0.6 (0.4–1.0)
ER ORAOV1 Chr11: rs614367 43 4.80 % SKAT 0.028 0.9 (0.5–1.4)
  ANO8 - p2 Chr19: rs8170 8 <1.7 % SKAT 0.028 4.4 (0.3–74.5)
  FAM129C Chr19: rs8170 62 6.80 % SKAT 0.035 0.9 (0.6–1.3)
  BABAM1 Chr19: rs8170 24 1.40 % SKAT 0.041 2.1 (0.9–5.1)
  ORAOV1 - p2 Chr11: rs614367 2 <4.8 % SKAT 0.042 3.3E + 06 (0.0– > 1E50)
  UNC13A Chr19: rs8170 69 3.70 % SKAT 0.045 1.5 (0.9–2.5)
  ZFYVE26 Chr14: rs999737 126 5.70 % SKAT 0.049 1.5 (1.0–2.3)
  USE1 Chr19: rs8170 14 0.40 % BURDEN, SKAT 0.022 7.2 (1.3–38.8)
  ABHD8 Chr19: rs8170 19 1.30 % BURDEN 0.026 2.4 (1.1–5.0)
  TMEM221 Chr19: rs8170 24 2.10 % BURDEN 0.029 2.1 (1.1–3.9)
  ZFYVE26 - p2 Chr14: rs999737 29 <5.7 % BURDEN 0.031 2.5 (1.1–5.7)
  1. Abbreviations: SNP Single-nucleotide polymorphism, p2 Subset of variants within gene predicted to be potentially or possibly damaging by Polymorphism Phenotyping version 2, CP Carrier proportion or proportion of subjects who carry at least one rare, nonsynonymous variant in gene, BURDEN Inverse-variance-weighted burden test, SKAT Meta-analysis of sequence kernel association test assuming the effect of each variant is homogeneous, regardless of ethnicity
  2. Underlining = lowest p value if more than one significant test
\