BMC Genomics

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The molecular portraits of breast tumors are conserved across microarray platforms

Zhiyuan Hu, Cheng Fan, Daniel S Oh, JS Marron, Xiaping He, Bahjat F Qaqish, Chad Livasy, Lisa A Carey, Evangeline Reynolds, Lynn Dressler, Andrew Nobel, Joel Parker, Matthew G Ewend, Lynda R Sawyer, Junyuan Wu, Yudong Liu, Rita Nanda, Maria Tretiakova, Alejandra R Orrico, Donna Dreher, Juan P Palazzo, Laurent Perreard, Edward Nelson, Mary Mone, Heidi Hansen, Michael Mullins, John F Quackenbush, Matthew J Ellis, Olufunmilayo I Olopade, Philip S Bernard and Charles M Perou*

BMC Genomics 2006, 7:96 doi:10.1186/1471-2164-7-96

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DNA methylation signatures for breast cancer classification and prognosis

Moshe Szyf Genome Medicine 2012, 4:26 (30 March 2012)

Moshe Szyf reviews recent progress in identifying DNA methylation in breast cancer genomes, and discusses the prospects for classifying subtypes and predicting outcome using DNA methylation markers.

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Gene expression in extratumoral microenvironment predicts clinical outcome in breast cancer patients

Erick Román-Pérez, Patricia Casbas-Hernández, Jason R Pirone, Jessica Rein, Lisa A Carey, Ronald A Lubet, Sendurai A Mani, Keith D Amos, Melissa A Troester Breast Cancer Research 2012, 14:R51 (19 March 2012)

Research article   Open Access

Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker

Ida Johansson, Cecilia Nilsson, Pontus Berglund, Martin Lauss, Markus Ringnér, Håkan Olsson, Lena Luts, Edith Sim, Sten Thorstensson, Marie-Louise Fjällskog, Ingrid Hedenfalk Breast Cancer Research 2012, 14:R31 (14 February 2012)

Research article   Open Access

Molecular profiling of patient-derived breast cancer xenografts

Fabien Reyal, Charlotte Guyader, Charles Decraene, Carlo Lucchesi, Nathalie Auger, Franck Assayag, Ludmilla De Plater, David Gentien, Marie-France Poupon, Paul Cottu, Patricia De Cremoux, Pierre Gestraud, Anne Vincent-Salomon, Jean-Jacques Fontaine, Sergio Roman-Roman, Olivier Delattre, Didier Decaudin, Elisabetta Marangoni Breast Cancer Research 2012, 14:R11 (16 January 2012)

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Empirical comparison of cross-platform normalization methods for gene expression data

Jason Rudy, Faramarz Valafar BMC Bioinformatics 2011, 12:467 (7 December 2011)

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Luminal-B breast cancer and novel therapeutic targets

Ben Tran, Philippe L Bedard Breast Cancer Research 2011, 13:221 (30 November 2011)

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The breast cancer genome - a key for better oncology

Hans Vollan, Carlos Caldas BMC Cancer 2011, 11:501 (30 November 2011)

This article is part of a collection on BMC Cancer's 10th...

Methodology article   Open Access

DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference

Yan Jiao, Katherine Lawler, Gargi S Patel, Arnie Purushotham, Annette F Jones, Anita Grigoriadis, Andrew Tutt, Tony Ng, Andrew E Teschendorff BMC Bioinformatics 2011, 12:403 (19 October 2011)

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A clinically relevant gene signature in triple negative and basal-like breast cancer

Achim Rody, Thomas Karn, Cornelia Liedtke, Lajos Pusztai, Eugen Ruckhaeberle, Lars Hanker, Regine Gaetje, Christine Solbach, Andre Ahr, Dirk Metzler, Marcus Schmidt, Volkmar Müller, Uwe Holtrich, Manfred Kaufmann Breast Cancer Research 2011, 13:R97 (6 October 2011)

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CD44 isoforms are heterogeneously expressed in breast cancer and correlate with tumor subtypes and cancer stem cell markers

Eleonor Olsson, Gabriella Honeth, Pär-Ola Bendahl, Lao H Saal, Sofia Gruvberger-Saal, Markus Ringnér, Johan Vallon-Christersson, Göran Jönsson, Karolina Holm, Kristina Lövgren, Mårten Fernö, Dorthe Grabau, Åke Borg, Cecilia Hegardt BMC Cancer 2011, 11:418 (29 September 2011)

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Breast tumors from CHEK2 1100delC-mutation carriers: genomic landscape and clinical implications

Taru A Muranen, Dario Greco, Rainer Fagerholm, Outi Kilpivaara, Kati Kämpjärvi, Kristiina Aittomäki, Carl Blomqvist, Päivi Heikkilä, Åke Borg, Heli Nevanlinna Breast Cancer Research 2011, 13:R90 (20 September 2011)

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Murine mammary tumor cells with a claudin-low genotype

Craig I Campbell, Devan E Thompson, Megan D Siwicky, Roger A Moorehead Cancer Cell International 2011, 11:28 (16 August 2011)

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Kinome expression profiling and prognosis of basal breast cancers

Renaud Sabatier, Pascal Finetti, Emilie Mamessier, Stéphane Raynaud, Nathalie Cervera, Eric Lambaudie, Jocelyne Jacquemier, Patrice Viens, Daniel Birnbaum, François Bertucci Molecular Cancer 2011, 10:86 (21 July 2011)

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Nottingham Prognostic Index in Triple-Negative Breast Cancer: a reliable prognostic tool?

André Albergaria, Sara Ricardo, Fernanda Milanezi, Vítor Carneiro, Isabel Amendoeira, Daniella Vieira, Jorge Cameselle-Teijeiro, Fernando Schmitt BMC Cancer 2011, 11:299 (15 July 2011)

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Functional proteomics can define prognosis and predict pathologic complete response in patients with breast cancer

Ana M Gonzalez-Angulo, Bryan T Hennessy, Funda Meric-Bernstam, Aysegul Sahin, Wenbin Liu, Zhenlin Ju, Mark S Carey, Simen Myhre, Corey Speers, Lei Deng, Russell Broaddus, Ana Lluch, Sam Aparicio, Powel Brown, Lajos Pusztai, W Symmans, Jan Alsner, Jens Overgaard, Anne-Lise Borresen-Dale, Gabriel N Hortobagyi, Kevin R Coombes, Gordon B Mills Clinical Proteomics 2011, 8:11 (8 July 2011)

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Microarrays in the 2010s: the contribution of microarray-based gene expression profiling to breast cancer classification, prognostication and prediction

Pierre-Emmanuel Colombo, Fernanda Milanezi, Britta Weigelt, Jorge S Reis-Filho Breast Cancer Research 2011, 13:212 (27 June 2011)

In this review, the authors examine the clinical relevance of microarray-based profiling of breast cancer and discuss its impact on patient management.

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Molecular profiling currently offers no more than tumour morphology and basic immunohistochemistry

Britta Weigelt, Jorge S Reis-Filho Breast Cancer Research 2010, 12(Suppl 4):S5 (20 December 2010)

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Basal-like breast cancers: the phenotypic disparity between the cancer-initiating cells and tumor histology

Afshin Raouf Breast Cancer Research 2010, 12:316 (16 December 2010)

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Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics

Göran Jönsson, Johan Staaf, Johan Vallon-Christersson, Markus Ringnér, Karolina Holm, Cecilia Hegardt, Haukur Gunnarsson, Rainer Fagerholm, Carina Strand, Bjarni A Agnarsson, Outi Kilpivaara, Lena Luts, Päivi Heikkilä, Kristiina Aittomäki, Carl Blomqvist, Niklas Loman, Per Malmström, Håkan Olsson, Oskar Th Johannsson, Adalgeir Arason, Heli Nevanlinna, Rosa B Barkardottir, Åke Borg Breast Cancer Research 2010, 12:R42 (24 June 2010)

The identification of six subtypes of breast cancer - differing in biology, genomic alterations and patient outcome - may prove useful for understanding tumor development and for prognostic and treatment prediction purposes.

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High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer

Johan Staaf, Göran Jönsson, Markus Ringnér, Johan Vallon-Christersson, Dorthe Grabau, Adalgeir Arason, Haukur Gunnarsson, Bjarni A Agnarsson, Per-Olof Malmström, Oskar Johannsson, Niklas Loman, Rosa B Barkardottir, Åke Borg Breast Cancer Research 2010, 12:R25 (6 May 2010)

A survey of copy number alterations in HER2+ breast tumors using a combination of array comparative genomic hybridization and gene expression analyses pinpoints significant genomic aberrations, including potentially novel therapeutic targets.

Method   Open Access

A fuzzy gene expression-based computational approach improves breast cancer prognostication

Benjamin Haibe-Kains, Christine Desmedt, Françoise Rothé, Martine Piccart, Christos Sotiriou, Gianluca Bontempi Genome Biology 2010, 11:R18 (15 February 2010)

A fuzzy computational approach that takes into account several molecular subtypes in order to provide more accurate breast cancer prognosis

Research   Open Access

Bimodal gene expression patterns in breast cancer

Marina Bessarabova, Eugene Kirillov, Weiwei Shi, Andrej Bugrim, Yuri Nikolsky, Tatiana Nikolskaya BMC Genomics 2010, 11(Suppl 1):S8 (10 February 2010)

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Molecular-based tumour subtypes of canine mammary carcinomas assessed by immunohistochemistry

Francesco Sassi, Cinzia Benazzi, Gastone Castellani, Giuseppe Sarli BMC Veterinary Research 2010, 6:5 (28 January 2010)

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Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4A as likely candidate target genes

Lorenzo Melchor, Laura Paula Saucedo-Cuevas, Iván Muñoz-Repeto, Socorro María Rodríguez-Pinilla, Emiliano Honrado, Alfredo Campoverde, Jose Palacios, Katherine L Nathanson, María José García, Javier Benítez Breast Cancer Research 2009, 11:R86 (8 December 2009)

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Impact of biospecimens handling on biomarker research in breast cancer

Loris De Cecco, Valeria Musella, Silvia Veneroni, Vera Cappelletti, Italia Bongarzone, Maurizio Callari, Barbara Valeri, Marco A Pierotti, Maria Daidone BMC Cancer 2009, 9:409 (24 November 2009)

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BRCA1-deficient mammary tumor cells are dependent on EZH2 expression and sensitive to Polycomb Repressive Complex 2-inhibitor 3-deazaneplanocin A

Julian Puppe, Rinske Drost, Xiaoling Liu, Simon A Joosse, Bastiaan Evers, Paulien Cornelissen-Steijger, Petra Nederlof, Qiang Yu, Jos Jonkers, Maarten van Lohuizen, Alexandra M Pietersen Breast Cancer Research 2009, 11:R63 (26 August 2009)

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An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer

Andrea H Bild, Joel S Parker, Adam M Gustafson, Chaitanya R Acharya, Katherine A Hoadley, Carey Anders, P Kelly Marcom, Lisa A Carey, Anil Potti, Joseph R Nevins, Charles M Perou Breast Cancer Research 2009, 11:R55 (28 July 2009)

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A compact VEGF signature associated with distant metastases and poor outcomes

Zhiyuan Hu, Cheng Fan, Chad Livasy, Xiaping He, Daniel S Oh, Matthew G Ewend, Lisa A Carey, Subbaya Subramanian, Robert West, Francis Ikpatt, Olufunmilayo I Olopade, Matt van de Rijn, Charles M Perou BMC Medicine 2009, 7:9 (16 March 2009)

Expression of the 13-gene VEGF (vascular endothelial growth factor) profile occurs in distant cancer metastases and is predictive of poor outcome, but may help to target anti-angiogenesis therapies.

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Selecting control genes for RT-QPCR using public microarray data

Vlad Popovici, Darlene R Goldstein, Janine Antonov, Rolf Jaggi, Mauro Delorenzi, Pratyaksha Wirapati BMC Bioinformatics 2009, 10:42 (2 February 2009)

Research   Open Access

Knowledge driven decomposition of tumor expression profiles

Martin H van Vliet, Lodewyk FA Wessels, Marcel JT Reinders BMC Bioinformatics 2009, 10(Suppl 1):S20 (30 January 2009)

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A resampling-based meta-analysis for detection of differential gene expression in breast cancer

Bala Gur-Dedeoglu, Ozlen Konu, Serkan Kir, Ahmet Ozturk, Betul Bozkurt, Gulusan Ergul, Isik G Yulug BMC Cancer 2008, 8:396 (30 December 2008)

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EZH2 and BMI1 inversely correlate with prognosis and TP53 mutation in breast cancer

Alexandra M Pietersen, Hugo M Horlings, Michael Hauptmann, Anita Langerød, Abderrahim Ajouaou, Paulien Cornelissen-Steijger, Lodewijk F Wessels, Jos Jonkers, Marc Vijver, Maarten van Lohuizen Breast Cancer Research 2008, 10:R109 (19 December 2008)

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Frequent PTEN genomic alterations and activated phosphatidylinositol 3-kinase pathway in basal-like breast cancer cells

Bérengère Marty, Virginie Maire, Eléonore Gravier, Guillem Rigaill, Anne Vincent-Salomon, Marion Kappler, Ingrid Lebigot, Fathia Djelti, Audrey Tourdès, Pierre Gestraud, Philippe Hupé, Emmanuel Barillot, Francisco Cruzalegui, Gordon C Tucker, Marc-Henri Stern, Jean-Paul Thiery, John A Hickman, Thierry Dubois Breast Cancer Research 2008, 10:R101 (3 December 2008)

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A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the Proliferation, Immune response and RNA splicing modules in breast cancer

Fabien Reyal, Martin H van Vliet, Nicola J Armstrong, Hugo M Horlings, Karin E de Visser, Marlen Kok, Andrew E Teschendorff, Stella Mook, Laura van 't Veer, Carlos Caldas, Remy J Salmon, Marc Vijver, Lodewyk FA Wessels Breast Cancer Research 2008, 10:R93 (13 November 2008)

Methodology article   Open Access

A method for analyzing censored survival phenotype with gene expression data

Tongtong Wu, Wei Sun, Shinsheng Yuan, Chun-Houh Chen, Ker-Chau Li BMC Bioinformatics 2008, 9:417 (6 October 2008)

Research article   Open Access

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis

Andrew H Sims, Graeme J Smethurst, Yvonne Hey, Michal J Okoniewski, Stuart D Pepper, Anthony Howell, Crispin J Miller, Robert B Clarke BMC Medical Genomics 2008, 1:42 (21 September 2008)

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The functional loss of the retinoblastoma tumour suppressor is a common event in basal-like and luminal B breast carcinomas

Jason I Herschkowitz, Xiaping He, Cheng Fan, Charles M Perou Breast Cancer Research 2008, 10:R75 (9 September 2008)

The functional loss of the retinoblastoma tumour suppressor, RB1, is common in basal-like tumours and may play a key role in their aggressive biology and unique therapeutic responses.

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A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancer

Andrew E Teschendorff, Carlos Caldas Breast Cancer Research 2008, 10:R73 (28 August 2008)

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Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures

Pratyaksha Wirapati, Christos Sotiriou, Susanne Kunkel, Pierre Farmer, Sylvain Pradervand, Benjamin Haibe-Kains, Christine Desmedt, Michail Ignatiadis, Thierry Sengstag, Frédéric Schütz, Darlene R Goldstein, Martine Piccart, Mauro Delorenzi Breast Cancer Research 2008, 10:R65 (28 July 2008)

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Genes responsive to both oxidant stress and loss of estrogen receptor function identify a poor prognosis group of estrogen receptor positive primary breast cancers

Christina Yau, Christopher C Benz Breast Cancer Research 2008, 10:R61 (17 July 2008)

An investigation into the effect of oxidative stress on estrogen and estrogen receptor-regulated gene expression identified a subset of oxidant-sensitive genes associated with poor prognosis in ER+ primary breast cancer.

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PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes

Anna Git, Inmaculada Spiteri, Cherie Blenkiron, Mark J Dunning, Jessica CM Pole, Suet-Feung Chin, Yanzhong Wang, James Smith, Frederick J Livesey, Carlos Caldas Breast Cancer Research 2008, 10:R54 (27 June 2008)

Breast cancer cell line PMC42 is a good model for normal breast epithelium, providing a unique biological tool to study breast differentiation and the function of key miRNAs typically lost in cancer.

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The CD44+/CD24- phenotype is enriched in basal-like breast tumors

Gabriella Honeth, Pär-Ola Bendahl, Markus Ringnér, Lao H Saal, Sofia K Gruvberger-Saal, Kristina Lövgren, Dorthe Grabau, Mårten Fernö, Åke Borg, Cecilia Hegardt Breast Cancer Research 2008, 10:R53 (17 June 2008)

Basal-like and particularly BRCA1 hereditary breast cancer are associated with CD44+/CD24- cells, however tumorigenicity may not be confined to cells of this phenotype as they are found in very few HER2+ tumours.

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Cell cycle correlated genes dictate the prognostic power of breast cancer gene lists

Jonathan D Mosley, Ruth A Keri BMC Medical Genomics 2008, 1:11 (25 April 2008)

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DNMT3b overexpression contributes to a hypermethylator phenotype in human breast cancer cell lines

J Devon Roll, Ashley G Rivenbark, Wendell D Jones, William B Coleman Molecular Cancer 2008, 7:15 (25 January 2008)

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Can clinically relevant prognostic subsets of breast cancer patients with four or more involved axillary lymph nodes be identified through immunohistochemical biomarkers? A tissue microarray feasibility study

Simon J Crabb, Chris D Bajdik, Samuel Leung, Caroline H Speers, Hagen Kennecke, David G Huntsman, Karen A Gelmon Breast Cancer Research 2008, 10:R6 (14 January 2008)

Letter   Free

Are triple-negative tumours and basal-like breast cancer synonymous? Authors' response

Bas Kreike, Marc J van de Vijver Breast Cancer Research 2007, 9:405 (17 December 2007)

Research article   Open Access

CD40 signaling predicts response to preoperative trastuzumab and concomitant paclitaxel followed by 5-fluorouracil, epirubicin, and cyclophosphamide in HER-2-overexpressing breast cancer

Francisco J Esteva, Jing Wang, Feng Lin, Jaime A Mejia, Kai Yan, Kadri Altundag, Vicente Valero, Aman U Buzdar, Gabriel N Hortobagyi, W Fraser Symmans, Lajos Pusztai Breast Cancer Research 2007, 9:R87 (17 December 2007)

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Are triple-negative tumours and basal-like breast cancer synonymous?

Emad A Rakha, David SP Tan, William D Foulkes, Ian O Ellis, Andrew Tutt, Torsten O Nielsen, Jorge S Reis-Filho Breast Cancer Research 2007, 9:404 (30 November 2007)

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MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype

Cherie Blenkiron, Leonard D Goldstein, Natalie P Thorne, Inmaculada Spiteri, Suet-Feung Chin, Mark J Dunning, Nuno L Barbosa-Morais, Andrew E Teschendorff, Andrew R Green, Ian O Ellis, Simon Tavaré, Carlos Caldas, Eric A Miska Genome Biology 2007, 8:R214 (8 October 2007)

Integrated analysis of miRNA expression and genomic changes in human breast tumors allows the classification of tumor subtypes.

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High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

Suet F Chin, Andrew E Teschendorff, John C Marioni, Yanzhong Wang, Nuno L Barbosa-Morais, Natalie P Thorne, Jose L Costa, Sarah E Pinder, Mark A van de Wiel, Andrew R Green, Ian O Ellis, Peggy L Porter, Simon Tavaré, James D Brenton, Bauke Ylstra, Carlos Caldas Genome Biology 2007, 8:R215 (7 October 2007)

High resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer, and provides a genome-wide list of common copy number alterations associated with aberrant expression and poor prognosis.

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Gene expression profiling and histopathological characterization of triple-negative/basal-like breast carcinomas

Bas Kreike, Marieke van Kouwenhove, Hugo Horlings, Britta Weigelt, Hans Peterse, Harry Bartelink, Marc J van de Vijver Breast Cancer Research 2007, 9:R65 (2 October 2007)

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Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer

Martin Buess, Dimitry SA Nuyten, Trevor Hastie, Torsten Nielsen, Robert Pesich, Patrick O Brown Genome Biology 2007, 8:R191 (14 September 2007)

In an effort to deconvolute global gene-expression profiles, an interaction between some breast cancer cells and stromal fibroblasts was found to induce an interferon response, which may be associated with a greater propensity for tumor progression.

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An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer

Andrew E Teschendorff, Ahmad Miremadi, Sarah E Pinder, Ian O Ellis, Carlos Caldas Genome Biology 2007, 8:R157 (2 August 2007)

A feature selection method was used in an analysis of three major microarray expression datasets to identify molecular subclasses and prognostic markers in estrogen receptor-negative breast cancer, showing that it is a heterogeneous disease with at least four main subtypes.

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EGFR associated expression profiles vary with breast tumor subtype

Katherine A Hoadley, Victor J Weigman, Cheng Fan, Lynda R Sawyer, Xiaping He, Melissa A Troester, Carolyn I Sartor, Thais Rieger-House, Philip S Bernard, Lisa A Carey, Charles M Perou BMC Genomics 2007, 8:258 (31 July 2007)

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Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors

Jason I Herschkowitz, Karl Simin, Victor J Weigman, Igor Mikaelian, Jerry Usary, Zhiyuan Hu, Karen E Rasmussen, Laundette P Jones, Shahin Assefnia, Subhashini Chandrasekharan, Michael G Backlund, Yuzhi Yin, Andrey I Khramtsov, Roy Bastein, John Quackenbush, Robert I Glazer, Powel H Brown, Jeffrey E Green, Levy Kopelovich, Priscilla A Furth, Juan P Palazzo, Olufunmilayo I Olopade, Philip S Bernard, Gary A Churchill, Terry Van Dyke, Charles M Perou Genome Biology 2007, 8:R76 (10 May 2007)

Comparison of mammary tumor gene-expression profiles from thirteen murine models using microarrays and with that of human breast tumors showed that many of the defining characteristics of human subtypes were conserved among mouse models.

Research   Open Access

Integrative analysis of a cancer somatic mutome

Pilar Hernández, Xavier Solé, Joan Valls, Víctor Moreno, Gabriel Capellá, Ander Urruticoechea, Miguel Pujana Molecular Cancer 2007, 6:13 (5 February 2007)

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A consensus prognostic gene expression classifier for ER positive breast cancer

Andrew E Teschendorff, Ali Naderi, Nuno L Barbosa-Morais, Sarah E Pinder, Ian O Ellis, Sam Aparicio, James D Brenton, Carlos Caldas Genome Biology 2006, 7:R101 (31 October 2006)

A consensus prognostic classifier for estrogen receptor positive breast tumors has been developed and shown to be valid in nearly 900 samples across different microarray platforms.

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High-throughput genomic technology in research and clinical management of breast cancer. Exploiting the potential of gene expression profiling: is it ready for the clinic?

Andrew H Sims, Kai Ong, Robert B Clarke, Anthony Howell Breast Cancer Research 2006, 8:214 (11 October 2006)

This article is part of a collection on High-throughput genomic...