Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue

Publication Name: PLOS ONE

Author(s): Lorenza Mittempergher, Jorma J. de Ronde, Marja Nieuwland, Ron M. Kerkhoven, Iris Simon,Emiel J. Th. Rutgers, Lodewyk F. A. Wessels, Laura J. Van't Veer

Background and Methods: Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, … Continued

TSPYL5 suppresses p53 levels and function by physical interaction with USP7

Publication Name: Nature Cell Biology

Author(s): Mirjam T. Epping, Lars A.T. Meijer, Oscar Krijgsman, Johannes L. Bos, Pier Paolo Pandolfi and René Bernards

We have previously reported a gene expression signature that is a powerful predictor of poor clinical outcome in breast cancer1. Among the seventy genes in this expression profile is a gene of unknown function: TSPYL5 (TSPY-like 5, also known as … Continued

Microarray-Based Determination of Estrogen Receptor, Progesterone Receptor, and HER2 Receptor Status in Breast Cancer

Publication Name: Clinical Cancer Research

Author(s): Paul Roepman, Hugo M. Horlings, Oscar Krijgsman, Marleen Kok, Jolien M. Bueno-de-Mesquita, Richard Bender, Sabine C. Linn, Annuska M. Glas and Marc J. van de Vijver

Purpose: The level of estrogen receptor (ER), progesterone receptor (PR), and HER2 aids in the determination of prognosis and treatment of breast cancer. Immunohistochemistry is currently the predominant method for assessment, but differences in methods and interpretation can substantially affect … Continued

Robust interlaboratory reproducibility of a gene expression signature measurement consistent with the needs of a new generation of diagnostic tools

Publication Name: BMC Genomics

Author(s): Robert A Ach, Arno Floore, Bo Curry, Vladimir Lazar, Annuska M Glas, Rob Pover, Anya Tsalenko, Hugues Ripoche, Fatima Cardoso, Mahasti Saghatchian d'Assignies, Laurakay Bruhn and Laura J Van't Veer

Background: The increasing use of DNA microarrays in biomedical research, toxicogenomics, pharmaceutical development, and diagnostics has focused attention on the reproducibility and reliability of microarray measurements. While the reproducibility of microarray gene expression measurements has been the subject of several … Continued

Converting a breast cancer microarray signature into a high-throughput diagnostic test.

Publication Name: BMC Genomics

Author(s): Glas AM, Floore A, Delahaye LJMJ et al.

Background: A 70-gene tumor expression profile was established as a powerful predictor of disease outcome in young breast cancer patients. This profile, however, was generated on microarrays containing 25,000 60-mer oligonucleotides that are not designed for processing of many samples … Continued

Molecular Portraits and 70-Gene Prognosis Signature Are Preserved throughout the Metastatic Process of Breast Cancer

Publication Name: The Journal of Cancer Research

Author(s): Britta Weigelt, Zhiyuan Hu, Xiaping He, Chad Livasy, Lisa A. Carey, Matthew G. Ewend, Annuska M. Glas, Charles M. Perou and Laura J. van't Veer

Microarray analysis has been shown to improve risk stratification of breast cancer. Breast tumors analyzed by hierarchical clustering of expression patterns of “intrinsic” genes have been reported to subdivide into at least four molecular subtypes that are associated with distinct … Continued

A Gene-Expression Signature as a Predictor of Survival in Breast Cancer.

Publication Name: New England Journal of Medicine

Author(s): Marc J. van de Vijver, M.D., Ph.D., Yudong D. He, Ph.D., Laura J. van 't Veer, Ph.D., Hongyue Dai, Ph.D., Augustinus A.M. Hart, M.Sc., Dorien W. Voskuil, Ph.D., George J. Schreiber, M.Sc., Johannes L. Peterse, M.D., Chris Roberts, Ph.D., Matthew J. Marton, Ph.D., Mark Parrish, Douwe Atsma, Anke Witteveen, Annuska Glas, Ph.D., Leonie Delahaye, Tony van der Velde, Harry Bartelink, M.D., Ph.D., Sjoerd Rodenhuis, M.D., Ph.D., Emiel T. Rutgers, M.D., Ph.D., Stephen H. Friend, M.D., Ph.D., and René Bernards, Ph.D.

Background: A more accurate means of prognostication in breast cancer will improve the selection of patients for adjuvant systemic therapy. Methods: Using microarray analysis to evaluate our previously established 70-gene prognosis profile, we classified a series of 295 consecutive patients … Continued

Gene expression profiling predicts clinical outcome of breast cancer

Publication Name: Nature

Author(s): Laura J. van 't Veer, Hongyue Dai, Marc J. van de Vijver, Yudong D. He, Augustinus A. M. Hart, Mao Mao, Hans L. Peterse, Karin van der Kooy, Matthew J. Marton, Anke T. Witteveen, George J. Schreiber, Ron M. Kerkhoven, Chris Roberts, Peter S. Linsley, René Bernards & Stephen H. Friend

Breast cancer patients with the same stage of disease can have markedly different treatment responses and overall outcome. The strongest predictors for metastases (for example, lymph node status and histological grade) fail to classify accurately breast tumors according to their … Continued