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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