A highly standardized, robust, and cost-effective method for genome-wide transcriptome analysis of peripheral blood applicable to large-scale clinical trials

Genomics

Volumn 87, Issue 5, 2006, Pages 653-664

  Debey, Svenja ^a   Zander, Thomas ^a   Brors, Benedikt ^b   Popov, Alexey ^a   Eils, Roland ^b   Schultze, Joachim L ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

Gene expression profiling; Peripheral blood; Peripheral blood mononuclear cells; Transcriptome

Indexed keywords

GLOBIN; TRANSCRIPTOME;

ARTICLE; BLOOD SAMPLING; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DNA MICROARRAY; FEMALE; GENE EXPRESSION; GENOME ANALYSIS; HUMAN; MALE; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; OUTCOME ASSESSMENT; PREDICTION; PRIORITY JOURNAL; RNA ANALYSIS; RNA STABILITY; STATISTICAL SIGNIFICANCE; TREATMENT OUTCOME;

BLOOD CELLS; BLOOD SPECIMEN COLLECTION; CLINICAL TRIALS; COST-BENEFIT ANALYSIS; FEMALE; GENDER IDENTITY; GENE EXPRESSION PROFILING; GENOME, HUMAN; GLOBINS; HUMANS; LEUKOCYTES, MONONUCLEAR; MALE; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SENSITIVITY AND SPECIFICITY;

EID: 33646087412     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2005.11.010     Document Type: Article

References (35)

1. Branca M. Genetics and medicine: putting gene arrays to the test. Science 300 (2003) 238
2. Schubert C.M. Microarray to be used as routine clinical screen. Nat. Med. 9 (2003) 9
3. Golub T.R., et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286 (1999) 531-537
4. Alizadeh A.A., et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403 (2000) 503-511
5. Bittner M., et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406 (2000) 536-540
6. Armstrong S.A., et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat. Genet. 30 (2002) 41-47
7. van de Vijver M.J., et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347 (2002) 1999-2009
8. Shipp M.A., et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat. Med. 8 (2002) 68-74
9. Rosenwald A., et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346 (2002) 1937-1947
10. Bullinger L., et al. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N. Engl. J. Med. 350 (2004) 1605-1616
11. Valk P.J., et al. Prognostically useful gene-expression profiles in acute myeloid leukemia. N. Engl. J. Med. 350 (2004) 1617-1628
12. Gerhold D.L., Jensen R.V., and Gullans S.R. Better therapeutics through microarrays. Nat. Genet. 32 (2002) 547-551 (Suppl)
13. Scherf U., et al. A gene expression database for the molecular pharmacology of cancer. Nat. Genet. 24 (2000) 236-244
14. Gunther E.C., et al. Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro. Proc. Natl. Acad. Sci. USA 100 (2003) 9608-9613
15. Bennett L., et al. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J. Exp. Med. 197 (2003) 711-723
16. Palucka A.K., et al. Cross-regulation of TNF and IFN-alpha in autoimmune diseases. Proc. Natl. Acad. Sci. USA 102 (2005) 3372-3377
17. Pascual V., et al. Role of interleukin-1 (IL-1) in the pathogenesis of systemic onset juvenile idiopathic arthritis and clinical response to IL-1 blockade. J. Exp. Med. 201 (2005) 1479-1486
18. Burczynski M.E., et al. Transcriptional profiles in peripheral blood mononuclear cells prognostic of clinical outcomes in patients with advanced renal cell carcinoma. Clin. Cancer Res. 11 (2005) 1181-1189
19. Brazma A., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29 (2001) 365-371
20. Bammler T., et al. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods 2 (2005) 351-356
21. Irizarry R.A., et al. Multiple-laboratory comparison of microarray platforms. Nat. Methods 2 (2005) 345-350
22. Larkin J.E., et al. Independence and reproducibility across microarray platforms. Nat. Methods 2 (2005) 337-344
23. Debey S., et al. Comparison of different isolation techniques prior to gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell types. Pharmacogenom. J. 4 (2004) 193-207
24. Rainen L., et al. Stabilization of mRNA expression in whole blood samples. Clin. Chem. 48 (2002) 1883-1890
25. Cobb J.P., et al. Application of genome-wide expression analysis to human health and disease. Proc. Natl. Acad. Sci. USA 102 (2005) 4801-4806
26. Feezor R.J., et al. Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol. Genom. 19 (2004) 247-254
27. Tibshirani R., et al. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl. Acad. Sci. USA 99 (2002) 6567-6572
28. Whitney A.R., et al. Individuality and variation in gene expression patterns in human blood. Proc. Natl. Acad. Sci. USA 100 (2003) 1896-1901
29. Kuhn K., et al. A novel, high-performance random array platform for quantitative gene expression profiling. Genome Res. 14 (2004) 2347-2356
30. J. Bell, Predicting disease using genomics, 429 (2004) 453-456.
31. Affymetrix Technical Note, Globin reduction protocol: a method for processing whole blood RNA samples for improved array results (2003).
32. Li C., and Wong W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98 (2001) 31-36
33. Galinsky V.L. Automatic registration of microarray images: II. Hexagonal grid. Bioinformatics 19 (2003) 1832-1836
34. Fan J.B., et al. A versatile assay for high-throughput gene expression profiling on universal array matrices. Genome Res. 14 (2004) 878-885
35. Ruschhaupt M., et al. A compendium to ensure computational reproducibility in high-dimensional classification tasks. Stat. Appl. Genet. Mol. Biol. 3 (2004) 37