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Table 1 Summary of genotype frequencies and mutation rates for cancer samples analyzed by AluScan and by WGSa

From: Massive interstitial copy-neutral loss-of-heterozygosity as evidence for cancer being a disease of the DNA-damage response

Sampleb

Sex

Totalc (Mb)

Genotype frequency (%)

Mutation ratesd (%)

MM/mm Ratioe

MM

mm (×10−2)

Mm (×10−2)

RMM (×10−3)

RGOH-M (×10−3)

Rmm

RGOH-m

RMm

RLOH

RMm->MM

RMm->mm

Gastric 1

M

16.08

99.978

0.760

1.393

0.616

0.616

1.146

1.146

22.277

21.964

17.723

4.241

4.179

Gastric 2

M

24.50

99.952

2.105

2.698

0.531

0.531

0.737

0.717

0.544

0.423

0.287

0.136

2.111

Gastric 3

M

24.84

99.961

2.040

1.903

0.221

0.221

0.138

0.138

2.813

2.390

1.523

0.867

1.756

Gastric 4

M

18.22

99.969

1.327

1.798

0.297

0.297

0.414

0.414

2.809

2.565

1.924

0.641

3.000

Gastric 5

M

16.67

99.975

0.593

1.920

0.606

0.606

0.910

0.910

3.062

2.999

2.593

0.406

6.385

Glioma 1

F

18.92

99.964

1.236

2.381

0.169

0.169

0.086

0.086

1.421

1.421

1.043

0.377

2.765

Glioma 2

M

9.84

99.960

1.707

2.310

0.468

0.468

0.298

0.298

13.154

9.239

6.863

2.376

2.889

Glioma 3

M

21.08

99.959

1.973

2.118

3.166

3.071

4.257

3.920

24.009

22.307

16.484

5.823

2.831

Glioma 4

F

8.89

99.956

2.197

2.240

7.294

7.249

0.154

0.154

4.671

4.269

2.963

1.306

2.269

Glioma 5

M

10.49

99.964

1.776

1.866

4.749

4.702

10.574

9.662

26.622

26.162

21.564

4.599

4.689

Leukemia 1

F

15.36

99.960

1.650

2.367

0.091

0.085

0.039

0.039

0.303

0.275

0.248

0.028

9.000

Leukemia 2

F

13.00

99.956

1.824

2.604

0.085

0.085

0.000

0.000

0.296

0.266

0.207

0.059

3.500

Leukemia 3

M

21.91

99.954

1.799

2.777

0.059

0.059

0.101

0.101

0.427

0.329

0.279

0.049

5.667

Leukemia 4

F

17.75

99.975

0.712

1.773

0.118

0.118

0.238

0.238

1.208

1.017

0.890

0.127

7.000

Leukemia 5

M

20.98

99.975

0.847

1.689

0.243

0.243

0.675

0.675

1.383

1.185

1.016

0.169

6.000

Liver 1

F

10.85

99.980

0.780

1.237

3.881

3.844

10.520

10.284

27.103

26.731

23.083

3.649

6.327

Liver 2

M

17.73

99.962

1.310

2.511

0.717

0.717

1.421

1.291

13.814

12.736

11.927

0.809

14.750

Liver 3

M

12.04

99.955

1.926

2.574

0.590

0.590

0.862

0.862

6.387

5.226

4.323

0.903

4.786

Liver 4

M

7.93

99.965

1.359

2.122

0.605

0.593

1.763

1.391

16.162

16.102

13.131

2.971

4.420

Liver 5

M

11.08

99.957

1.984

2.274

0.352

0.352

0.227

0.227

7.302

6.587

5.357

1.230

4.355

Lung 1

M

11.94

99.952

1.956

2.821

0.260

0.260

0.899

0.899

6.980

6.920

5.495

1.426

3.854

Lung 2

M

12.96

99.956

2.400

1.963

2.454

2.454

1.479

1.318

11.635

11.439

10.653

0.786

13.553

Lung 3

F

14.23

99.964

1.368

2.207

1.680

1.673

3.236

3.236

7.291

6.495

5.858

0.637

9.200

Lung 4

M

12.49

99.965

1.286

2.234

2.811

2.811

6.476

6.413

5.661

5.410

5.016

0.394

12.727

Lung 5

F

14.46

99.950

2.057

2.896

11.609

10.633

20.134

15.261

49.690

48.161

37.751

10.411

3.626

Lung-Brain 1

M

21.69

99.934

2.688

3.884

0.807

0.807

0.583

0.566

2.125

1.840

1.425

0.416

3.429

Lung-Brain 2

M

21.68

99.943

2.432

3.208

0.858

0.844

0.512

0.493

7.346

6.627

4.572

2.056

2.224

Lung-Brain 3

F

17.04

99.948

1.894

3.302

0.564

0.564

1.209

1.178

1.707

1.120

1.013

0.107

9.500

Lung-Brain 4

M

22.79

99.948

1.886

3.292

0.931

0.917

1.024

1.024

5.052

4.679

3.332

1.346

2.475

Lung-Brain 5

M

21.04

99.937

2.708

3.625

0.528

0.528

0.158

0.140

1.285

0.931

0.695

0.236

2.944

Leukemia Sample Av.f, g

 

17.80 ± 3.74

99.964 ± 0.010

1.366 ± 0.542

2.242 ± 0.490

0.119 ± 0.072 (0.117 ± 0.073)

0.118 ± 0.073 (0.117 ± 0.073)

0.211 ± 0.275 (0.214 ± 0.278)

0.211 ± 0.275 (0.214 ± 0.278)

0.723 ± 0.528 (0.702 ± 0.505)

0.614 ± 0.449 (0.598 ± 0.431)

0.528 ± 0.391 (0.510 ± 0.372)

0.086 ± 0.059 (0.088 ± 0.060)

6.233 ± 2.006 (6.033 ± 1.959)

Leukemia Aggregate Av.h, g

 

17.80

99.964

1.336

2.224

0.124 (0.122)

0.124 (0.122)

0.168 (0.171)

0.168 (0.171)

0.677 (0.661)

0.571 (0.559)

0.490 (0.477)

0.081 (0.082)

6.063 (5.813)

Solid Tumor Sample Av.i, g

 

15.98 ± 5.10

99.958 ± 0.011

1.750 ± 0.571

2.431 ± 0.660

1.871 ± 2.666 (1.817 ± 2.563)

1.821 ± 2.512 (1.766 ± 2.402)

2.769 ± 4.663 (2.756 ± 4.664)

2.481 ± 3.862 (2.476 ± 3.856)

10.837 ± 11.503 (10.704 ± 11.460)

10.190 ± 11.261 (10.183 ± 11.233)

8.264 ± 9.065 (8.278 ± 9.049)

1.926 ± 2.347 (1.905 ± 2.332)

5.242 ± 3.753 (5.365 ± 3.909)

Solid Tumor Aggregate Av.j, g

 

15.98

99.957

1.800

2.516

1.611 (1.572)

1.565 (1.525)

2.244 (2.302)

1.972 (2.024)

8.757 (8.727)

8.160 (8.198)

6.511 (6.564)

1.650 (1.635)

3.947 (4.015)

Glioma Sample Av.k, g

 

13.84 ± 5.70

99.961 ± 0.003

1.778 ± 0.358

2.183 ± 0.202

3.169 ± 2.992 (2.928 ± 2.568)

3.132 ± 2.970 (2.885 ± 2.537)

3.074 ± 4.550 (3.065 ± 4.570)

2.824 ± 4.152 (2.808 ± 4.159)

13.975 ± 11.241 (13.430 ± 11.333)

12.680 ± 10.998 (12.792 ± 10.936)

9.783 ± 8.876 (9.888 ± 8.823)

2.896 ± 2.270 (2.904 ± 2.265)

3.089 ± 0.928 (3.157 ± 0.887)

Glioma Aggregate Av.l, g

 

13.84

99.961

1.733

2.195

2.733 (2.500)

2.691 (2.453)

3.202 (3.445)

2.943 (3.158)

13.488 (13.513)

12.290 (12.786)

9.348 (9.758)

2.943 (3.027)

3.177 (3.224)

All Sample Av.m, g

 

16.28 ± 4.89

99.959 ± 0.011

1.686 ± 0.576

2.400 ± 0.631

1.579 ± 2.515 (1.534 ± 2.419)

1.537 ± 2.374 (1.491 ± 2.273)

2.342 ± 4.352 (2.332 ± 4.352)

2.103 ± 3.619 (2.099 ± 3.613)

9.150 ± 11.147 (9.037 ± 11.095)

8.594 ± 10.870 (8.586 ± 10.847)

6.975 ± 8.753 (6.984 ± 8.744)

1.619 ± 2.246 (1.602 ± 2.231)

5.407 ± 3.514 (5.477 ± 3.639)

All Sample Aggregate Av.n, g

 

16.28

99.958

1.715

2.463

1.340 (1.300)

1.303 (1.262)

1.950 (1.990)

1.716 (1.753)

7.427 (7.370)

6.912 (6.913)

5.520 (5.539)

1.392 (1.373)

3.967 (4.033)

Lung-to-Liver (WGS)g

M

1422.89

99.823

6.391

11.328

0.049 (0.045)

0.049 (0.045)

0.008 (0.008)

0.008 (0.008)

0.167 (0.167)

0.155 (0.155)

0.148 (0.149)

0.007 (0.006)

22.790 (22.952)

Liver (WGS)g

M

2601.55

99.892

4.780

5.992

0.190 (0.194)

0.188 (0.192)

0.016 (0.014)

0.005 (0.003)

0.144 (0.137)

0.121 (0.130)

0.103 (0.115)

0.017 (0.015)

5.974 (7.601)

  1. aSee Additional file 3: Table S1 and Additional file 1: Table S2 for data on individual cancer samples
  2. b‘Sample’ refers in rows 1–38 (not counting row of headings) to 30 tumor-control pairs analyzed by AluScan as described in Methods; refers in row 39 to the lung-to-liver metastatic cancer analyzed by Ju et al. [8] using WGS; and refers in row 40 to the primary liver cancer analyzed by Ouyang et al. [9] using WGS
  3. cOnly nucleotide positions that were captured in both the tumor and the control samples for AluScan sequencing were analyzed and counted
  4. dMutation rates (R) were given in each instance by the ratio [100 % × (number of mutated residues) / (total number of residues analyzed)]. RGOH-M refers to the % of MM residues, and RGOH-m the % of mm residues, that underwent a GOH mutation. RMm refers to the % of Mm residues that underwent a mutation. RLOH refers to the % of Mm residues that underwent an LOH mutation. The rates of LOHs leading to the production of MM residues and mm residues are given by RMm->MM and RMm->mm respectively
  5. eThe ratio between the MM residues and mm residues produced from Mm residues by LOH is expressed by MM/mm
  6. fThe average of the individual values for 5 leukemia samples ± SD
  7. gAll Av. values estimated without removal of CNV-associated LOHs and GOHs are shown without parentheses; all Av. values estimated after removal of CNV-associated LOHs and GOHs are shown inside parentheses
  8. hAggregate Av. for Total (Mb) represents 0.2 × total Mb analyzed in the 5 leukemia samples. Aggregate Av. values for the other columns are obtained directly from dividing by 5 the total figures for the 5 leukemia samples pooled together
  9. i, jSample Av. and Aggregate Av. values are defined as in f and h, but pertain to the 25 solid tumors
  10. k, lSample Av. and Aggregate Av. values are defined as in f and h, but pertain to the 5 glioma tumors
  11. m, nSample Av. and Aggregate Av. values are defined as in f and h, but pertain to all 30 cancer samples
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BMC Medical Genomics

ISSN: 1755-8794

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