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Table 2 Sequencing metrics

From: The use of whole exome sequencing and murine patient derived xenografts as a method of chemosensitivity testing in sarcoma

Diagnosis Depth Reads (M) % on-target reads Somatic mutations Synonymous Non-synonymous INDEL Frame-shift Stop gain/loss
Osteosarcoma
 Germline 88.1 75 89.1       
 Tumour 153.2 134 81.5 479 144 290 12 24 9
 PDX 282.7 141 53.9 96,393 79,080 15,354 440 1334 139
Dedifferentiated liposarcoma
 Germline 74.7 71 89.8       
 Tumour 148.5 123 79.4 458 154 250 14 28 12
Leiomyosarcoma
 Germline 94.9 778 79.0       
 Tumour 145.7 116 81.1 384 118 218 15 26 7
Osteosarcoma
 Germline 72.1 613 74.7       
 Tumour 175.2 148 79.0 575 179 331 18 30 17
 PDX 142.1 123 80.2 288,522 232,825 48,320 1496 5307 477
Synovial sarcoma
 Germline 71.5 784 58.3       
 Tumour 159.6 134 79.5 471 169 245 13 32 12
Ewing’s sarcoma
 Germline 65.8 730 58.4       
 Tumour 122.7 128 61.0 529 191 262 21 45 10
 PDX 141.7 125 75.5 7089 3399 3416 115 105 53
Undifferentiated pleomorphic sarcoma
 Germline 77.1 677 75.4       
 Tumour 139.6 132 72.5 522 202 271 15 26 7
 PDX 168 137 79.4 118,641 97,602 18,574 568 1651 207
Alveolar rhabdo-myosarcoma
 Germline 83.1 727 86.6       
 Tumour 152.6 132 86.3 591 187 325 25 39 12
 PDX 187.3 159 76.7 24,851 12,266 10,617 121 331 117
Leiomyosarcoma
 Germline 98.8 880 76.7       
 Tumour 166 147 80.2 368 112 220 5 20 11
 PDX 159.8 134 77.9 34,442 28,019 5701 183 470 67
Chordoma
 Germline 70.7 617 77.5       
 Tumour 145.8 141 78.9 440 147 247 7 31 8
Metastatic angiosarcoma
 Germline 72 632 76.1       
 Tumour 202.2 176 78.2 489 177 249 17 36 10
 PDX 147 121 77.7 10,376 7892 2238 42 148 52
Undifferentiated pleomorphic sarcoma
 Germline 78.6 692 82.4       
 Tumour 146 119 82.6 405 147 210 16 25 7