Skip to main content

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
Back to article page

BMC Cancer

ISSN: 1471-2407

Contact us