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Table 3 NGS data quality

From: Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

   ID #1 ID #2 ID #3 ID #4 ID #5 ID #6 ID #7 ID #8 ID #9 ID #10 ID #11
A N°Amplicons ≥500x 322 318 320 317 324 313 331 318 225 302 295
% Amplicons ≥500x 93.9 92.7 93.3 92.4 94.5 91.3 96.5 92.7 65.6 88.0 86.0
N°Amplicons ≥200x 337 334 332 336 334 331 338 335 240 327 328
% Amplicons ≥200x 98.3 97.4 96.8 98.0 97.4 96.5 98.5 97.7 70.0 95.3 95.6
N°Amplicons <100x 4 6 6 5 4 10 5 5 91 6 8
% Amplicons <100X 1.2 1,7 1,7 1,5 1,2 2,9 1,5 1,5 26,5 1,7 2,3
Average amplicon coverage 3,93 4002 3375 3,26 3522 3126 4083 3302 3714 2146 1737
Uniformity (%) 90.1 89.8 88.2 91.15 91.44 82.3 92.5 90.7 65.1 91.1 91.8
B N°Amplicons ≥500x 337 340 340 338 341 290 289 294 338 302 254
% Amplicons ≥500x 98.3 99.1 99.1 98.5 99.4 84.5 84.3 85.7 98.5 88.0 74.1
N°Amplicons ≥200x 342 342 342 342 343 330 332 338 339 331 324
% Amplicons ≥200x 99.7 99.7 99.7 99.7 100.0 96.2 96.8 98.5 98.8 97.1 94.5
N°Amplicons <100x 0 0 0 0 0 6 3 4 3 5 7
% Amplicons <100x 0.0 0.0 0.0 0.0 0.0 1.7 0.9 1.2 0.9 1.5 2.0
Average amplicon coverage 9,75 15,009 12,239 11,254 14,842 967 1137 1102 1647 1308 1083
Uniformity (%) 94.7 92.7 93.9 96.2 93.9 95.6 96.0 97.1 92.0 95.7 93.8
C N°Amplicons ≥500x 307 277 307 306 321 240 310 310 209 310 339
% Amplicons ≥500x 89.5 80.8 89.5 89.2 93.6 70.0 90.4 90.4 60.9 90.4 98.8
N°Amplicons ≥200x 336 326 336 335 337 300 336 334 286 334 340
% Amplicons ≥200x 98.0 95.0 98.0 97.7 98.3 87.5 98.0 97.4 83.4 97.4 99.1
N°Amplicons <100x 3 11 4 4 4 23 4 6 26 2 2
% Amplicons <100x 0.9 3.2 1.2 1.2 1.2 6,7 1,2 1,7 7,6 0,6 0,6
Average amplicon coverage 1,91 1267 1825 1617 2016 1531 2085 2292 1217 1387 3,73
Uniformity (%) 93.9 93.3 93.0 94.2 95.6 81.2 92.7 91.3 80.5 94.2 96.2
  1. The table shows for each NGS platforms ((A) PGM™ platform, (B) Proton™ platform, and (C) MiSeq™ Illumina platform) data quality for the eleven tumor samples in terms of uniformity (the percentage of bases in all target regions covered by at least 20% of the average base coverage depth reads), average amplicon coverage depth and number (%) of amplicons at different coverage