Table 2 Overall cost per patient (in Euro) of the NGS applications for targeted genes panel in eight germline oncogenetics laboratories
Laboratories | Lab1 | Lab2 | Lab3 | Lab4 | Lab5 | Lab6 | Lab7 | Lab8 | |
|---|---|---|---|---|---|---|---|---|---|
Protocol | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |
Procedure | 5–50 gene tumor panel | ||||||||
Indications | Colon cancer (Lynch syndrome) | Breast ovary | Breast ovary | Breast | Breast | Onco genetic endocrinal | Colon cancer | Breast | |
Enrichment technic | Ampliseq | Surselect | Multiplicom | Multiplicom | Nextera | Haloplex | Surselect | Multiplicom | |
Sequencing platform | PGM | Miseq | PGM | Miseq | Miseq | Miseq | GAIIx | Miseq | |
Number of patients/run | 18 | 20 | 30 | 40 | 45 | 48 | 80 | 96 | |
Cost per process step (in €) | Mean | ||||||||
0. DNA extraction | 12€ | 12€ | 12€ | 12€ | 12€ | 12€ | 12€ | 12€ | 12€ |
1. Enrichment | 145€ | 175€ | 333€ | 184€ | 70€ | 178€ | 253€ | 174€ | 189€ (34%) |
Part of consumablesa (%) | 92 | 77 | 93 | 95 | 81 | 94 | 88 | 90 | |
Part of equipment (%) | 1.4 | 13.1 | 2.4 | 1.6 | 5.7 | 0.6 | 0.8 | 3.4 | |
Part of labor (%) | 6.2 | 10.3 | 4.2 | 3.3 | 12.9 | 5.1 | 11.1 | 6.3 | |
2. Sequencing | 48€ | 114€ | 38€ | 47€ | 38€ | 24€ | 78€ | 18€ | 51€ (9%) |
Part of consumablesa (%) | 67 | 79 | 79 | 66 | 87 | 79 | 19 | 72 | |
Part of equipment (%) | 16.7 | 16.7 | 13.2 | 17.0 | 10.5 | 16.7 | 20.5 | 22.2 | |
Part of labor (%) | 12.5 | 4.4 | 7.9 | 17.0 | 2.6 | 4.2 | 60.3 | 5.6 | |
3. Bioinformatics analysis | 49€ | 34€ | 62€ | 39€ | 36€ | 46€ | 31€ | 35€ | 42€ (8%) |
Part of equipment & software (%) | 63 | 91 | 50 | 79 | 86 | 67 | 100 | 89 | |
Part of labor (%) | 37 | 9 | 50 | 21 | 14 | 33 | 0 | 11 | |
4. Technical validation | 68€ | 47€ | 26€ | 10€ | 19€ | 20€ | 48€ | 13€ | 31€ (6%) |
Part of consumables (%) | 26 | 55 | 42 | 0 | 58 | 55 | 42 | 54 | |
Part of equipment (%) | 10 | 6 | 11 | 20 | 10 | 5 | 0 | 15 | |
Part of labor (%) | 63 | 38 | 46 | 80 | 32 | 45 | 58 | 31 | |
5. Biological validation | 105€ | 36€ | 40€ | 26€ | 42€ | 78€ | 45€ | 61€ | 54€ (10%) |
NGS production cost (0+1+2+3+4+5) | 427€ | 382€ | 511€ | 318€ | 217€ | 358€ | 467€ | 313€ | |
6. Cost of time not directly linked to NGS activity | 57€ | 14€ | 24€ | 17€ | 20€ | 34€ | 52€ | 27€ | 31€ (6%) |
7. Overhead cost | 131€ | 107€ | 144€ | 90€ | 64€ | 106€ | 140€ | 92€ | 109€ (20%) |
8. Other additional costb | 42€ | 36€ | 48€ | 30€ | 21€ | 36€ | 48€ | 30€ | 36€ (6%) |
Total cost per patient (0+1+2+3+4+5+6+7+8) | 657€ | 539€ | 727€ | 455€ | 322€ | 534€ | 707€ | 462€ | 555€ |
