Analytical validation of a practical molecular assay prognostic of survival in nonsquamous non-small cell lung cancer

Diagnostic Molecular Pathology

Volumn 22, Issue 2, 2013, Pages 65-69

  Kratz, Johannes R ^a   Tham, Patrick T ^a   Mulvihill, Michael S ^a   Ziaei, Fatemeh ^b   Ray, Mahashweta Roshni ^a   Hurst, Jerry W ^b   Segal, Mark R ^a   Berryman, David M ^b   Chu, Wenjiang ^b   He, Biao ^a   Jablons, David M ^a   Mann, Michael J ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Pinpoint Genomics   (United States)

^c Division of Cardiothoracic Surgery   (United States)

Author keywords

Analytical validation; Lung cancer; PCR; Prognostic assay

Indexed keywords

BAG 1 PROTEIN; BRCA1 PROTEIN; CELL CYCLE PROTEIN 6; COMPLEMENTARY DNA; EPIDERMAL GROWTH FACTOR RECEPTOR 3; FORMALDEHYDE; INTERLEUKIN 11; TRANSCRIPTION FACTOR YAP1; WNT3A PROTEIN;

ARTICLE; BIOASSAY; CANCER PROGNOSIS; CANCER SURVIVAL; DNA MICROARRAY; GENE EXPRESSION; HUMAN; HUMAN TISSUE; LUNG NON SMALL CELL CANCER; MAJOR CLINICAL STUDY; MOLECULAR PROGNOSTIC ASSAY; NONSQUAMOUS LUNG NON SMALL CELL CANCER; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; RNA EXTRACTION; VALIDATION STUDY;

CARCINOMA, NON-SMALL-CELL LUNG; DNA PRIMERS; FORMALDEHYDE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; LINEAR MODELS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARAFFIN EMBEDDING; POLYMERASE CHAIN REACTION; PROGNOSIS; REPRODUCIBILITY OF RESULTS; RNA, NEOPLASM;

EID: 84879908932     PISSN: 10529551     EISSN: 15334066     Source Type: Journal    
DOI: 10.1097/PDM.0b013e318273fb61     Document Type: Article

References (31)

1. Jemal A, Bray F, Center MM, et al. Global cancer statistics. CA Cancer J Clin. 2011;61:69-90.
2. Jemal A, Siegel R, Xu J, et al. Cancer statistics, 2010. CA Cancer J Clin. 2010;60:277-300.
3. Herbst RS, Heymach JV, Lippman SM. Lung cancer. N Engl JMed. 2008;359:1367-1380.
4. Goldstraw P, Ball D, Jett JR, et al. Non-small-cell lung cancer. Lancet. 2011;378:1727-1740.
5. Detterbeck FC, Boffa DJ, Tanoue LT. The new lung cancer staging system. Chest. 2009;136:260-271.
6. Subramanian J, Simon R. Gene expression-based prognostic signatures in lung cancer: ready for clinical use? J Natl Cancer Inst. 2010;102:464-474.
7. Kratz JR, Jablons DM. Genomic prognostic models in early-stage lung cancer. Clin Lung Cancer. 2009;10:151-157.
8. Kratz JR, He J, Van Den Eeden SK, et al. A practical molecular assay to predict survival in resected non-squamous, non-small-cell lung cancer: development and international validation studies. Lancet. 2012;379:823-832.
9. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3:1101-1108.
10. NCCLS. Evaluation of the Linearity of Quantitative Measurement Procedures: a Statistical Approach; Approved Guideline. NCCLS Document EP6-A. 2003. ISBN 1-56238-498-8. Wayne, PA: NCCLS.
11. Bustin SA. A-Z of Quantitative PCR. La Jolla CA: International University Line; 2004.
12. NCCLS. Protocols for Determination of Limits of Detection and Limits of Quantitation; Approved Guideline. NCCLS Document EP17-A. 2004. Wayne, PA: NCCLS.
13. Cronin M, Sangli C, Liu ML, et al. Analytical validation of the oncotype DX genomic diagnostic test for recurrence prognosis and therapeutic response prediction in node-negative, estrogen receptorpositive breast cancer. Clin Chem. 2007;53:1084-1091.
14. Roepman P, Jassem J, Smit EF, et al. An immune response enriched 72-gene prognostic profile for early-stage non-small-cell lung cancer. Clin Cancer Res. 2009;15:284-290.
15. Boutros PC, Lau SK, Pintilie M, et al. Prognostic gene signatures for non-small-cell lung cancer. Proc Natl Acad Sci U S A. 2009; 106:2824-2828.
16. Sun Z, Wigle DA, Yang P. Non-overlapping and non-cell-typespecific gene expression signatures predict lung cancer survival. J Clin Oncol. 2008;26:877-883.
17. Skrzypski M, Jassem E, Taron M, et al. Three-gene expression signature predicts survival in early-stage squamous cell carcinoma of the lung. Clin Cancer Res. 2008;14:4794-4799.
18. Shedden K, Taylor JM, Enkemann SA, et al. Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med. 2008;14:822-827.
19. Raz DJ, Ray MR, Kim JY, et al. A multigene assay is prognostic of survival in patients with early-stage lung adenocarcinoma. Clin Cancer Res. 2008;14:5565-5570.
20. Lau SK, Boutros PC, Pintilie M, et al. Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol. 2007;25:5562-5569.
21. Larsen JE, Pavey SJ, Passmore LH, et al. Gene expression signature predicts recurrence in lung adenocarcinoma. Clin Cancer Res. 2007;13:2946-2954.
22. Larsen JE, Pavey SJ, Passmore LH, et al. Expression profiling defines a recurrence signature in lung squamous cell carcinoma. Carcinogenesis. 2007;28:760-766.
23. Chen HY, Yu SL, Chen CH, et al. A five-gene signature and clinical outcome in non-small-cell lung cancer. N Engl JMed. 2007;356:11-20.
24. Raponi M, Zhang Y, Yu J, et al. Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res. 2006;66:7466-7472.
25. Lu Y, Lemon W, Liu PY, et al. A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med. 2006;3:e467.
26. Guo L, Ma Y, Ward R, et al. Constructing molecular classifiers for the accurate prognosis of lung adenocarcinoma. Clin Cancer Res. 2006;12:3344-3354.
27. Tomida S, Koshikawa K, Yatabe Y, et al. Gene expression-based, individualized outcome prediction for surgically treated lung cancer patients. Oncogene. 2004;23:5360-5370.
28. Beer DG, Kardia SL, Huang CC, et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med. 2002;8:816-824.
29. Xu JZ, Wong CW. Hunting for robust gene signature from cancer profiling data: sources of variability, different interpretations, and recent methodological developments. Cancer Lett. 2010;296:9-16.
30. Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst. 2007;99:147-157.
31. von Ahlfen S, Missel A, Bendrat K, et al. Determinants of RNA quality from FFPE samples. PLoS One. 2007;2:e1261.