Universal reference RNA is not a representative normal sample for oligonucleotide microarray studies

Pathology and Oncology Research

Volumn 14, Issue 3, 2008, Pages 243-251

  Mojica, Wilfrido D ^a   Stein, Leighton ^b   Hawthorn, Lesleyann ^b  

^a UNIVERSITY AT BUFFALO   (United States)

^b ROSWELL PARK CANCER INSTITUTE   (United States)

Author keywords

Experimental bias; Oligonucleotide expression microarray; Reference RNA

Indexed keywords

ARTICLE; COLON CANCER; COLON MUCOSA; CONTROLLED STUDY; DNA MICROARRAY; EPITHELIUM CELL; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; REFERENCE DATABASE; RNA TRANSLATION; STANDARDIZATION;

CELL LINE, TUMOR; COLON; COLONIC NEOPLASMS; EPITHELIAL CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REFERENCE STANDARDS; RNA; RNA, NEOPLASM;

EID: 58549099468     PISSN: 12194956     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12253-008-9068-2     Document Type: Article

References (21)

1. LJ van't Veer S Paik DF Hayes 2005 Gene expression profiling of breast cancer: a new tumor marker J Clin Oncol 23 8 1631 1635
2. M Cronin K Ghosh F Sistare J Quakenbush V Vilker C O'Connell 2004 Universal RNA reference materials for gene expression Clin Chem 50 1464 1471
3. JK Cowell L Hawthorn 2007 The application of microarray technology to the analysis of the cancer genome Curr Mol Med 7 1 103 120
4. N Novoradovskaya ML Whitfield LS Basehore 2005 Universal reference RNA as a standard for microarray experiments BMC Genom 5 20
5. NF Schlecht RD Burk L Adrien 2007 Gene expression profiles in HPV-infected head and neck cancer J Pathol 213 283 293
6. JE Larsen SJ Pavey LH Passmore 2007 Expression profiling defines a recurrence signature in lung squamous cell carcinoma Carcinogenesis 28 3 760 766
7. F Bianchi J Hu G Pelosi 2004 Lung cancers detected by screening with spiral computed tomography have a malignant phenotype when analyzed by cDNA microarray Clin Cancer Res 10 6023 6028
8. GC Warner PP Reis I Jurisica 2004 Molecular classification of oral cancer by cDNA microarrays identifies overexpressed genes correlated with nodal metastasis Int J Cancer 110 857 868
9. WD Mojica A Arshad S Sharma 2006 Manual exfoliation plus immunomagnetic bead separation as an initial step toward translational studies Arch Pathol Lab Med 130 1 74 79
10. WD Mojica L Stein L Hawthorn 2007 An exfoliation and enrichment strategy results in improved transcriptional profiles when compared to matched formalin fixed samples BMC Clin Pathol 7 7
11. L Hawthorn L Stein J Panzarella 2006 Characterization of cell-type specific profiles in tissues and isolated cells from squamous cell carcinomas of the lung Lung Cancer 53 2 129 142
12. RA Irizarry B Hobbs F Collin 2003 Exploration, normalization, and summaries of high-density oligonucleotide array probe level data Biostatistics 4 249 264
13. AA Alizadeh MB Eisen RE Davis 2000 Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Nature 403 6769 503 511
14. AW Burgess 1998 Growth control mechanisms in normal and transformed intestinal cells Philos Tran R Soc Lond B Biol Sci 353 903 909
15. M Pinto S Robine-Leon MD Appay 1983 Enterocyte like differentiation and polarization of the human colon carcinoma cell line Caco-2 in culture Bio Cell 47 323 330
16. SV Allander PB Illei Y Chen 2002 Expression profiling of synovial sarcoma by cDNA microarrays Am J Pathol 161 5 1587 1595
17. TO Nielssen RB West SC Linn 2002 Molecular characterization of soft tissue tumours: a gene expression study Lancet 359 1301 1307
18. RAF MacLeod WG Dirks Y Matsui 1999 Widespread intraspecies cross-contamination of human tumor cells arising at source Int J Cancer 83 555 563
19. F Demichelis H Gruelich JA Macoska 2007 SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines Mod Pathol 20 S2 346A
20. A Celis HH Rasmussen P Celis 1999 Short term culturing of low grade superficial bladder transitional cell carcinoma leads to changes in the expression levels of several proteins involved in key cellular activities Electrophoresis 20 355 361
21. M Somel P Khaitovich S Bahn 2006 Gene expression becomes heterogeneous with age Curr Biol 16 10 R359 360