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Table 2 Accuracy, FPR and FNR of prediction between DMD and BMD in DMD patients of TREAT-NMD, Flanigan’s and GHCPAPF

From: DMDtoolkit: a tool for visualizing the mutated dystrophin protein and predicting the clinical severity in DMD

Population

Mutation type

Reading-frame rule

Length of potential protein

Number of potential stop-gains

Joint prediction (Rules)

Joint prediction (Rules & patterns)

TREAT-NMD DMD patients

large deletions/duplications

5161/5681 = 90.8%

NA

520/5681 = 9.2%

5283/5681 = 93.0%

NA

398/5681 = 7.0%

5180/5681 = 91.2%

NA

501/5681 = 8.8%

5419/5681 = 95.4%

NA

262/5681 = 4.6%

5463/5681 = 96.2%

NA

218/5681 = 3.8%

small deletions/duplications

475/483 = 98.3%

NA

8/483 = 1.7%

408/483 = 84.5%

NA

75/483 = 15.5%

476/483 = 98.6%

NA

7/483 = 1.4%

476/483 = 98.6%

NA

7/483 = 1.4%

476/483 = 98.6%

NA

7/483 = 1.4%

splice sites

155/198 = 78.3%

NA

43/198 = 21.7%

99/198 = 50.0%

NA

99/198 = 50.0%

155/198 = 78.3%

NA

43/198 = 21.7%

155/198 = 78.3%

NA

43/198 = 21.7%

155/198 = 78.3%

NA

43/198 = 21.7%

total

5791/6362 = 91.0%

NA

571/6362 = 9.0%

5790/6362 = 91.0%

NA

572/6362 = 9.0%

5811/6362 = 91.3%

NA

551/6362 = 8.7%

6050/6362 = 95.1%

NA

312/6362 = 4.9%

6094/6362 = 96.8%

NA

268/6362 = 4.2%

nonsense

 

598/726 = 82.4%

NA

128/726 = 17.6%

725/726 = 99.9%

NA

1/726 = 0.1%

725/726 = 99.9%

NA

1/726 = 0.1%

725/726 = 99.9%

NA

1/726 = 0.1%

Flanigan’s DMD patients

large deletions/duplications

369/435 = 84.8%

23/435 = 5.3%

43/435 = 9.8%

374/435 = 86.0%

31/435 = 7.1%

30/435 = 6.9%

370/435 = 85.1%

24/435 = 5.5%

41/435 = 9.4%

386/435 = 88.7%

31/435 = 7.1%

18/435 = 4.1%

389/435 = 89.4%

32/435 = 7.4%

14/435 = 3.2%

small deletions/duplications

69/78 = 88.5%

7/78 = 9.0%

2/78 = 2.6%

59/78 = 75.6%

4/78 = 5.1%

15/78 = 19.2%

69/78 = 88.5%

7/78 = 9.0%

2/78 = 2.6%

69/78 = 88.5%

7/78 = 9.0%

2/78 = 2.6%

69/78 = 88.5%

7/78 = 9.0%

2/78 = 2.6%

splice sites

17/22 = 77.3%

1/22 = 4.5%

4/22 = 18.2%

12/22 = 54.5%

1/22 = 4.5%

9/22 = 40.9%

17/22 = 77.3%

1/22 = 4.5%

4/22 = 18.2%

17/22 = 77.3%

1/22 = 4.5%

4/22 = 18.2%

17/22 = 77.3%

1/22 = 4.5%

4/22 = 18.2%

total

455/535 = 85.0%

31/535 = 5.8%

49/533 = 9.2%

445/535 = 83.2%

36/535 = 6.7%

54/535 = 10.1%

456/535 = 85.2%

32/535 = 6.0%

47/535 = 8.8%

472/535 = 88.2%

39/535 = 7.3%

24/535 = 4.5%

475/535 = 88.8%

40/535 = 7.5%

20/535 = 3.7%

nonsense

 

146/206 = 70.9%

31/206 = 15.0%

29/206 = 14.1%

176/206 = 85.4%

0/206 = 0%

30/206 = 14.6%

176/206 = 85.4%

0/206 = 0%

30/206 = 14.6%

176/206 = 85.4%

0/206 = 0%

30/206 = 14.6%

GHCPAPF DMD patients

large deletions/duplications

213/231 = 92.2%

0/231 = 0%

18/231 = 7.8%

217/231 = 93.9%

5/231 = 2.2%

9/231 = 3.9%

217/231 = 93.9%

0/231 = 0%

14/231 = 6.1%

218/231 = 94.4%

5/231 = 2.2%

8/231 = 3.5%

218/231 = 94.4%

6/231 = 2.6%

7/231 = 3.0%

small deletions/duplications

15/17 = 88.2%

1/17 = 5.9%

1/17 = 5.9%

13/17 = 76.5%

1/17 = 5.9%

3/17 = 17.6%

15/17 = 88.2%

1/17 = 5.9%

1/17 = 5.9%

15/17 = 88.2%

1/17 = 5.9%

1/17 = 5.9%

15/17 = 88.2%

1/17 = 5.9%

1/17 = 5.9%

splice sites

1/1 = 100.0%

0/1 = 0%

0/1 = 0%

1/1 = 100.0%

0/1 = 0%

0/1 = 0%

1/1 = 100.0%

0/1 = 0%

0/1 = 0%

1/1 = 100.0%

0/1 = 0%

0/1 = 0%

1/1 = 100.0%

0/1 = 0%

0/1 = 0%

total

229/249 = 92.0%

1/249 = 0.4%

19/249 = 7.6%

231/249 = 92.8%

6/249 = 2.4%

12/249 = 4.8%

233/249 = 93.6%

1/249 = 0.4%

15/249 = 6.0%

234/249 = 94.0%

6/249 = 2.4%

9/249 = 3.6%

234/249 = 94.0%

7/249 = 2.8%

8/249 = 3.2%

nonsense

 

18/19 = 94.7%

1/19 = 5.3%

0/19 = 0%

19/19 = 100.0%

0/19 = 0%

0/19 = 0%

19/19 = 100.0%

0/19 = 0%

0/19 = 0%

19/19 = 100.0%

0/19 = 0%

0/19 = 0%

  1. This table shows the statistics for large deletions/duplications, small deletions/duplications, splice sites, as well as nonsense mutations for TREAT-NMD, Flanigan’s and GHCPAPF data. FPR, false positive rate. FNR, false negative rate. Joint prediction (Rules): the joint prediction used the three rules, i.e., reading-frame rule, length of potential protein, number of potential stop-gains, and If any one is a positive judgment, the result is positive. Joint prediction (Rules & patterns): the joint prediction used the three rules and supplemental patterns on location of mutations