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Table 2 Haplotype frequencies in the discovery, replication and combined studies

From: A rare CHD5 haplotype and its interactions with environmental factors predicting hepatocellular carcinoma risk

Haplotypes Case, Control Ratio Countsa Case, Control Frequenciesb Chi Square PAR P corrected c P Permutation d
Discovery study
 Block 1
  GGCA 176.0: 384.0, 171.1: 338.9 0.314, 0.335 0.54 0.4623 0.2970 0.9976
  GACA 176.0: 384.0, 171.1: 338.9 0.314, 0.335 0.54 0.4623 0.2970 0.9976
  AGCG 67.5: 492.5, 61.1: 448.9 0.121, 0.120 0.002 0.9651 0.8263 1
  AACG 67.5: 492.5, 61.1: 448.9 0.121, 0.120 0.002 0.9651 0.8263 1
  AGCA 29.5: 530.5, 20.9: 489.1 0.053, 0.041 0.795 0.3727 0.6037 0.9876
  AACA 29.5: 530.5, 20.9: 489.1 0.053, 0.041 0.795 0.3727 0.6037 0.9876
 Block 2
  CCCG 417.3: 126.7, 375.9: 118.1 0.767, 0.761 0.055 0.8153 0.7749 1
  TTTA 42.0: 502.0, 37.3: 456.7 0.077, 0.076 0.011 0.9171 0.9690 1
  CCTG 36.0: 508.0, 35.5: 458.5 0.066, 0.072 0.128 0.7208 0.8452 1
  TTCA 25.5: 518.5, 25.2: 468.8 0.047, 0.051 0.098 0.7544 0.7805 1
  CCCA 9.5: 534.5, 8.4: 485.6 0.017, 0.017 0.002 0.9622 0.9417 1
  TTTG 7.7: 536.3, 5.8: 488.2 0.014, 0.012 0.121 0.7282 0.7548 1
 Block 3
  AA 324.0: 170.0, 289.0: 151.0 0.656, 0.657 0.001 0.9757 0.8983 1
  GG 143.8: 350.2, 148.8: 291.2 0.291, 0.338 2.399 0.1214 0.1665 0.5747
  AG 26.2: 467.8, 2.2: 437.8 0.053, 0.005 18.248 1.94 × 10− 5 5.73 × 10−5 4.00 × 10−5
Replication study
 Block 3
  AA 630.9: 341.1, 579.0: 309.0 0.649, 0.652 0.018 0.8945 0.8714 8 0.9893
  GG 294.5: 677.5, 303.5: 584.5 0.303, 0.342 3.202 0.0735 0.1069 0.1542
  AG 46.6: 925.4, 5.5: 882.5 0.048, 0.006 29.716 5.038 × 10–8 7.571 × 10- 0.00001
Combined study
 Block 3
  AA 954.9: 511.1, 868.0: 460.0 0.651, 0.654 0.015 0.9012 0.9467 0.9909
  GG 438.3: 1027.7, 452.3:875.7 0.299, 0.341 5.556 0.0184 0.0383 0.0410
  AG 72.7: 1393.3, 7.7: 1320.3 0.050, 0.006 47.941 4.393 × 10−12 5.514 × 10− 11 0.00001
  1. Block 1, rs12037962, rs11587, rs41307753 and rs3810989
  2. Block 2, rs2273041, rs2273040, rs2273038 and rs55930553
  3. Block 3, rs12564469 and rs9434711
  4. aNumber of haplotypes were compared in cases versus controls: Haplotype(1):haplotype(others) cases, Haplotype(1):haplotype(others) controls
  5. bFrequency of the haplotype
  6. cCalculated in logistical regression models with adjustment for age, gender, smoking and drinking status; p < 0.005 means significant value by Bonferroni correction based on the total number of markers genotyped
  7. dEmpirical p-value based on 105 permutations of case-control status using the max(T) procedure. p < 0.05 means significant value