Table 2 Overall cost per patient (in Euro) of the NGS applications for targeted genes panel in eight germline oncogenetics laboratories

From: Correction: Cost of cancer diagnosis using next-generation sequencing targeted gene panels in routine practice: a nationwide French study

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€
  1. a Failure include
  2. b Quality cost, R&D cost, and others fees