120
Views
3
CrossRef citations to date
0
Altmetric
Original Article

Multi-gene biomarker panel for reference free prostate cancer diagnosis: determination and independent validation

, , &
Pages 693-706 | Received 04 Jun 2010, Accepted 25 Jul 2010, Published online: 01 Oct 2010

References

  • Belacel N, Cuperlovic-Culf M, Laflamme M, Ouellette R. (2004). Fuzzy J-Means and VNS methods for clustering genes from microarray data. Bioinformatics20: 1690–701.
  • Belacel N, Cuperlovic-Culf M, Ouellette R. (2007). Molecular methods for diagnosis of prostate cancer. US Patent WO2007030919 - 2007-03-22.
  • Belacel N. (2004). The k-closest resemblance approach for multiple criteria classification problems. In: HoaiLT Tao, PD, eds.Modelling Computation and Optimization in Information Systems and Management Sciences. London: Hermes Science Publishing. p. 525.
  • Belacel N. (2000).Multicriteria assignment method PROAFTN: methodology and medical applications. Eur J Operational Res 125:175–83.
  • Berger R, Feboo PG, Majumder PK et al. (2004). Androgen-induced differentiation and tumorigenicity of human prostate epithelial cells. Cancer Res 64:8867–75.
  • Camp NJ, Cannon-Albright LA, Farnham JM, Baffoe-Bonnie AB, George A et al. (2007). Compelling evidence for a prostate cancer gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics. Human Mol Genet 16:1271–8.
  • Chen Z, Fan Z, McNeal JE, Nolley R et al. (2003).Hepsin and mapsin are inversly expressed in laser capture microdisectioned prostate cancer. J Urol 169:1316–19.
  • Cuperlovic-Culf M, Belacel N, Ouellette R. (2005).Determination of tumour marker genes from gene expression data. Drug Discovery Today 10:42.
  • Dasarathy BV. (1991).Nearest Neighbour (NN). Norms: NN Pattern Classification Technique. Los Alamitos, CA: IEEE Computer Society Press.
  • Dhanasekaran SM, Barrette TR, Ghosh D et al. (2001). Delineation of prognostic biomarkers in prostate cancer. Nature 1412:2169–80.
  • Esserman L, Shieh Y, Thompson I. (2009). Rethinking screening for breast cancer and prostate cancer. JAMA 302:1685–92.
  • Gentleman R, Carey V, Huber W , Irizarry R , Dudoit S (2005).Bioinformatics and Computatonal Biology Solutions Using Bioconductor. Springer.
  • Graif T, Loeb S, Roehl KA et al. (2007).Under diagnosis and over diagnosis of prostate cancer. J Urol 178:88–92.
  • Grutzmann R, Boriss H, Ammerpohl O, et al. (2005). Meta-analysis of microarray data on pancreatic cancer defines a set of commonly dysregulated genes. Oncogene 24:5079–88.
  • Hessels D, van Gils MPMQ, van Hooij O, Jannink SA, Witjes JA, Verhaegh GW, Schalken JA. (2010).Predicitive value of PCA3 in urinary sediments in determining clinico-pathological characteristics of prostate cancer. Prostate 70:10–16.
  • Holzbeierlein J, Lal P, La Tulippe E, Smith A, Satagopan J, et al. (2004). Gene expression analysis of human prostate carcinoma during hormonal therapy identifies androgen-responsive genes and mechanisms of therapy resistance. Am J Pathol 164:217–27.
  • Irizarry RA, Boltstad BM, Collin F, Cope LM, Hobbs B, Speed TP. (2003). Summaries of AffymetrixGeneChip Probe Level Data. Nucl Acids Res 31:e15.
  • Johanneson B, Deutsch K, McIntosh L, Friedrichsen-Karyadi DM, Janer M,Kwon EM, Iwasaki L, Hood L, Ostrander EA, Stanford JL. (2007). Suggestive genetic linkage to chromosome 11p11.2-q12.2 in hereditary prostate cancer families with primary kidney cancer. Prostate 67:732–42.
  • Karan D, Lin M, Johansson SL, Batra SK. (2003). Current status of the molecular genetics of human prostateic adenocarcinomas. Int J Cancer 103:285–93.
  • Lacroix M, Leclercq G. (2004). About GATA3, HNF3A and XBP1,three genes co-expressed with the oestrogen receptor-a gene (ESR1). in breast cancer. Mol Cell Endocrinology 219:1–7.
  • Landers KA, Burger MJ, Tebay MA, Purdie DM, Scells B, Samaratunga H, Lavin MF, Gardiner RA. (2005). Use of multiple biomarkers for a molecular diagnosis of prostate cancer. Int J Cancer 114:950–6.
  • Lapointe J, Li C, Higgins JP et al. (2004). Gene expression profiling identifies clinically relevant subtypes of prostate cancer. ProcNatlAcadSci USA 101:811–16.
  • La Tulippe E, Satagopan J, Smith A, Scher H, Scardino P, Reuter V, Gerald WL. (2002). Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease. Cancer Res 62:4499–506.
  • Li S, Bhamre S, Lapointe J, Pollack JR, Brooks JD.(2006). Application of genomic technologies to human prostate cancer. Omics 10:261–75.
  • Li J, Fine JP. (2008). ROC analysis with multiple tests and multiple classes: methodology and applications in microarray studies. Biostatistics 9:566–76.
  • Luo J, Duggan DJ, Chen Y, et al. (2001). Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. Cancer Res 60:858–63
  • Magee JA, Araki T, Patil S, Ehrig T et al. (2001). Expression profiling reveals hepsin overexpression in prostate cancer. Cancer Res 61:5692–6.
  • Mhawech-Fauceglia P, Zhang S, Terracciano L, Sauter G, Chadhuri A, Herrmann FR, Penetrante R. (2007). Prostate-specific membrane antigen (PSMA).Protein expression in normal and neoplastic tissues and its sensitivity and specificity in prostate adenocarcinoma. Histopathology 50:472–83.
  • Nelson PS. (2004). Predicting prostate cancer behavior using transcript profiles. J Urol 172:828–33.
  • Ogdie A, Li J, Dai L, Yu X, Daiz-Torne, C, Schumacher HR, Pessler F. (2010). Identification of broadly applicable tissue biomarkers of synovitis with binary and multi-category receiver operating characteristic analysis. Biomarkers 15:183–90.
  • Pal P, Kaushal R, Sun G, Jin CH, et al. (2006). Variants in the HEPSIN gene are associated with prostate cancer in men of European origin. Human Genet 120:187–92.
  • Peehl DM. (2005). Primary cell cultures as models of prostate cancer development. EndocrinolRel Cancer 12:19–47.
  • Pfaffl MW. (2001). A new mathematical model for relative quantification in real-time RT PCR. Nucl Acid Res 29:e45.
  • Rhodes DR, Barrette TR, Rubin MA et al. (2002). Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 62:4427–33.
  • Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs BB, Barrette TR, Anstet MJ, Kincead-Beal C, Kulkarni P, Varambally S, Ghosh D, Chinnaiyan AM. (2007). Oncomine 3.0: genespathwaysand networks in a collection of 18 000 cancer gene expression profiles. Neoplasia 9:166–80.
  • Rose A, Xu Y, Chen Z, et al. (2005).Comparative gene and protein expression in primary cultures of epithelialcells from benign prostatic hyperplasia and prostate cancer.Cancer Lett 227:213–22.
  • Singh D, Febbo PG, Ross K, et al. (2002). Gene expression correlates of clinical prostate cancer behaviour. Cancer Cell 2:203–9.
  • Stephen C, Yousef GM, Scorilas A, Jung K, et al. (2004).Hepsin is highly over expressed in and a new candidate for a prognostic indicator in prostate cancer. J Urol 171:187–91.
  • Sterner-Kock A, Thorey IS, Koli K, Wempe F,Otte J, Bangsow T, Kuhlmeier K, Kirchner T, Jin S, Keski-Oja J, von Melchner H. (2002).Disruption of the gene encoding the latent transforming growth factor-beta binding protein 4 (LTBP4). causes abnormal lung development, cardiomyopathy, and colorectal cancer. Genes Dev 16:2264–73.
  • Takahashi S, Suzuki S, Inaguma S, Ikeda Y, et al. (2002). Down-regulation of human X-box binding protein I expression correlates with tumor progression in human prostate cancers. Prostate 50:154–61.
  • Tanguay S. (2000).The role of complexed PSA and percent free PSA in prostate cancer detectionprostate update.The Canadian Prostate Health Council 5.
  • Tomlins SA, Mehra R, Rhodes DR, Cao X et al. (2007). Integrative molecular concept modeling of prostate cancer progression. Nat Genet 39:41–51.
  • Tusher VG, Tibishirani R, Chu G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. ProcNatlAcadSci USA 98:5116–21.
  • Vanaja DK, Cheville JC, Iturria SJ, Young CY. (2003). Transcriptional silencing of zinc finger protein 185 identified by expression profiling is associated with prostate cancer progression. Cancer Res 63:3877–82.
  • Varambally S, Dhanasekharan S, Zhou M, et al. (2002). The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419:624–9.
  • Welsh JB, Sapinosos LM, Su AI, et al. (2001). Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res 61:5974–8.
  • Yu YP, Landsittel D, Jing L, et al. (2004). Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J ClinOncol 22:2790–9.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.