Cancer Research UK Grants & Research

Selected Publications

Ahmed AA, Mills AD, Ibrahim AEK, Temple J, Blenkiron C, Vias M, Massie CE, Iyer NG, McGeoch A, Crawford R, Nicke B, Downward J, Swanton C, Bell SD, Earl HM, Laskey RA, Caldas C, Brenton JD. The extracellular matrix protein TGFBI induces microtubule stabilization and sensitizes ovarian cancers to paclitaxel. Cancer Cell 2007; 12(6): 514-527. Full text article

Brenton JD, Carey LA, Ahmed AA and Caldas C. Molecular classification and molecular forecasting of breast cancer: ready for clinical application? J Clin Oncol 2005; 23: 7350-7360. PubMed

Garcia MJ, Pole JCM, Chin S-F, Teschendorff A, Naderi A, Ozdag H, Vias M, Kranjac T, Subkhankulova T, Paish C, Ellis I, Brenton JD, Edwards PAW and Caldas C. A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene 2005; 24: 5235-5245. PubMed

Ahmed AA, Vias M, Iyer G, Caldas C and Brenton JD. Microarray segmentation methods significantly influence data precision. Nucl Acids Res 2004; 32: e50 (7pp). PubMed

Haq R, Brenton JD, Takahashi M, Finan D, Rottapel R and Zanke B. Constitutive p38HOG mitogen-activated protein kinase activation induces permanent cell cycle arrest and senescence. Cancer Res 2002; 62: 5076-5082. PubMed

Bayani J, Brenton JD, Macgregor PF, Beheshti B, Albert M, Nallainathan D, Karaskova J, Rosen B, Murphy J, Laframboise S, Zanke B and Squire JA. Parallel analysis of sporadic primary ovarian carcinomas by spectral karyotyping, comparative genomic hybridization, and expression microarrays. Cancer Res 2002; 62: 3466-3476. PubMed

Primary Research Publications

2008

Ito Y, Koessler T, Ibrahim AE, Rai S, Vowler SL, Abu-Amero S, Silva AL, Maia A-T, Huddleston JE, Uribe-Lewis S, Woodfine K, Jagodic M, Nativio R, Dunning A, Moore G, Klenova E, Bingham S, Pharoah PD, Brenton JD, Beck S, Sandhu MS, Murrell A. Somatically acquired hypomethylation of IGF2 in breast and colorectal Cancer. Human Molecular Genetics. 2008; 17:2633-43

Swanton C, Szallasi Z, Brenton JD, Downward J. Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer. Breast Cancer Research 2008; 10:214

Zahra MA, Tan LT, Priest AN, Graves MJ, Arends M, Crawford RA, Brenton JD, Lomas DJ, Sala E. Semiquantitative and quantitative dynamic contrast-enhanced magnetic resonance imaging measurements predict radiation response in cervix cancer. International Journal of Radiation Oncology, Biology, Physics 2008; Nov 17 [Epub ahead of print]

2007

Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, De Wiel MAV, Green AR, Ellis IO, Porter PL, Tavaré S, Brenton JD, Ylstra B, Caldas C. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 2007; 8(10):Article R215

Chin SF, Wang Y, Thorne NP, Teschendorff AE, Pinder SE, Vias M, Naderi A, Roberts I, Barbosa-Morais NL, Garcia MJ, Iyer NG, Kranjac T, Robertson JFR, Aparicio S, Tavaré S, Ellis I, Brenton JD, Caldas C. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene 2007; 26(13):1959-1970

Krypuy M, Ahmed AA, Etemadmoghadam D, Hyland SJ, deFazio A, Fox SB, Brenton JD, Bowtell DD, Dobrovic A, Australian Ovarian Canc Study Grp. High resolution melting for mutation scanning of TP53 exons 5-8. BMC Cancer 2007; 7:Article 168

Melchor L, Garcia MJ, Honrado E, Pole JCM, Alvarez S, Edwards PAW, CaldaS C, Brenton JD, Benitez J. Genomic analysis of the 8p11-12 amplicon in familial breast cancer. Int J Cancer 2007; 120(3):714-717

Naderi A, Teschendorff AE, Barbosa-Morais NI, Pinder SE, Green AR, Powe DG, Robertson JFR, Aparicio S, Ellis IO, Brenton JD, Caldas C. A gene-expression signature to predict survival in breast cancer across independent data sets. Oncogene 2007; 26(10):1507-1516

Naderi A, Teschendorff AE, Beigel J, Cariati M, Ellis IO, Brenton JD, Caldas C. BEX2 is overexpressed in a subset of primary breast cancers and mediates nerve growth factor/nuclear factor-kappa B inhibition of apoptosis in breast cancer cell lines. Cancer Res 2007; 67(14):6725-6736

Swanton C, Marani M, Pardo O, Warne PH, Kelly G, Sahai E, Elustondo F, Chang J, Temple J, Ahmed AA, Brenton JD, Downward J, Nicke B. Regulators of mitotic arrest and ceramide metabolism are determinants of sensitivity to paclitaxel and other chemotherapeutic drugs. Cancer Cell 2007; 11(6):498-512

2006

Bundy JG, Iyer NG, Gentile MS, Hu DE, Kettunen M, Maia AT, Thorne NP, Brenton JD, Caldas C, Brindle KM. Metabolic consequences of p300 gene deletion in human colon cancer cells. Cancer Res 2006; 66(15):7606-7614

Ibrahim AEK, Thorne NP, Baird K, Barbosa-Morais NL, Tavaré S, Collins VP, Wyllie AH, Arends MJ, Brenton JD. MMASS: an optimized array-based method for assessing CpG island methylation. Nucleic Acids Res 2006; 34(20):Article e136

Krubasik D, Iyer NG, English WR, Ahmed AA, Vias M, Roskelley C, Brenton JD, Caldas C, Murphy G. Absence of p300 induces cellular phenotypic changes characteristic of epithelial to mesenchyme transition. Br J Cancer 2006; 94(9):1326-1332

Ozdag H, Teschendorff AE, Ahmed AA, Hyland SJ, Blenkiron C, Bobrow L, Veerakumarasivam A, Burtt G, Subkhankulova T, Arends MJ, Collins VP, Bowtell D, Kouzarides T, Brenton JD, Caldas C. Differential expression of selected histone modifier genes in human solid cancers. BMC Genomics 2006; 7:Article 90

Teschendorff AE, Naderi A, Barbosa-Morais NL, Pinder SE, Ellis IO, Aparicio S, Brenton JD, Caldas C. A consensus prognostic gene expression classifier for ER positive breast cancer. Genome Biol 2006; 7(10):Article R101

2005

Garcia MJ, Pole JCM, Chin SF, Teschendorff A, Naderi A, Ozdag H, Vias M, Kranjac T, Subkhankulova T, Paish C, Ellis I, Brenton JD, Edwards PAW, Caldas C. A 1Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene 2005; 24(33):5235-5245

Naderi A, Ahmed AA, Wang YZ, Brenton JD, Caldas C. Optimal amounts of fluorescent dye improve expression microarray results in tumor specimens. Mol Biotechnol 2005; 30(2):151-154

Reid LH, Lucas AB, Kopf-Sill AR, Chen B, Bromley B, Foy C, Hinkel CS, Boysen C, Liu CM, Ranamukha-arachchi D, Wagar E, Kawasaki ES, Goodsaid FM, Wilmer F, Fischer G, Kiser GL, Causton HC, Fuscoe JC, Brenton JD, Warrington JA, Soriano J, Coller J, Burrill JD, Rhodes K, Kerr KF, Zoon KC, Lee K, Shi LM, Salit M, Satterfield M, Marton M, Cronin M, Conley MP, Williams M, Fero M, Wilson M, Novoradovskaya N, Gilles P, Wolber PK, Ikonomi P, Puri R, Beyer RP, Shippy R, Setterquist R, Elespuru RK, Baker SC, Chervitz SA, Bauer SR, Russell S, Kaysser-Kranich T, Bammler TK, Ryder TB, Sendera TJ, Scherf U, Gao XL, Wu XN, Guo X, Liu ZL, External RNA Controls Consortium. Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 2005; 6:Article 150

Teschendorff AE, Wang YZ, Barbosa-Morais NL, Brenton JD, Caldas C. A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data. Bioinformatics 2005; 21(13):3025-3033

2004

Ahmed AA, Vias M, Iyer NG, Caldas C, Brenton JD. Microarray segmentation methods significantly influence data precision. Nucleic Acids Res 2004; 32(5):Article e5

Naderi A, Ahmed AA, Barbosa-Morais NL, Aparicio S, Brenton JD, Caldas C. Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling. BMC Genomics 2004; 5:Article 9

2002

Bayani J, Brenton JD, MacGregor PF, Beheshti B, Albert M, Nallainathan D, Karaskova J, Rosen B, Murphy J, Laframboise S, Zanke B, Squire JA. Parallel analysis of sporadic primary ovarian carcinomas by spectral karyotyping, comparative genomic hybridization, and expression microarrays. Cancer Res 2002; 62(12):3466-3476

Drewell RA, Arney KL, Arima T, Barton SC, Brenton JD, Surani MA. Novel conserved elements upstream of the H19 gene are transcribed and act as mesodermal enhancers. Development 2002; 129(5):1205-1213

Haq R, Brenton JD, Takahashi M, Finan D, Rottapel R, Zanke B. Constitutive p38HOG mitogen-activated protein kinase activation induces permanent cell cycle arrest and senescence. Cancer Res 2002; 62(17):5076-5082

Other Publications

Brenton JD, Ahmed AA, Caldas C. Molecular forecasting of breast cancer: Time to move forward with clinical testing - In reply. J Clin Oncol 2006; 24(4):722-723

Ahmed AA, Brenton JD. Microarrays and breast cancer clinical studies: forgetting what we have not yet learnt. Breast Cancer Res 2005; 7(3):96-99

Baker SC, Bauer SR, Beyer RP, Brenton JD, Bromley B, Burrill J, Causton H, Conley MP, Elespuru R, Fero M, Foy C, Fuscoe J, Gao XL, Gerhold DL, Gilles P, Goodsaid F, Guo X, Hackett J, Hockett RD, Ikonomi P, Irizarry RA, Kawasaki ES, Kaysser-Kranich T, Kerr K, Kiser G, Koch WH, Lee KY, Liu CM, Liu ZL, Lucas A, Manohar CF, Miyada G, Modrusan Z, Parkes H, Puri RK, Reid L, Ryder TB, Salit M, Samaha RR, Scherf U, Sendera TJ, Setterquist RA, Shi LM, Shippy R, Soriano JV, Wagar EA, Warrington JA, Williams M, Wilmer F, Wilson M, Wolber PK, Wu XN, Zadro R, External RNA Controls Consortium. The external RNA controls consortium: a progress report. Nat Methods 2005; 2(10):731-734

Brenton JD, Carey LA, Ahmed AA, Caldas C. Molecular classification and molecular forecasting of breast cancer: Ready for clinical application? J Clin Oncol 2005; 23(29):7350-7360

Caldas C, Brenton JD. Sizing up miRNAs as cancer genes. Nat Med 2005; 11(7):712-714

Brenton JD, Caldas C. Predictive cancer genomics - what do we need? Lancet 2003; 362(9381):340-341