Affymetrix® Cancer Community
Affymetrix is dedicated to providing innovative genomic analysis tools and educational resources for the cancer research community. Learn from peers how our unique solutions are applied in cancer research today from discovery to clinical research and validation.
- View presentations from leading cancer researchers
- Learn more about Affymetrix solutions for cancer research
- Browse the list of useful documents on cancer research
European translational cancer research seminar series:
Unlock the full potential inside your FFPE samples
Affymetrix hosted a series of translational cancer research seminars at some of the most prestigious academic cancer centers in Europe. The seminars focused on the challenges associated with successfully obtaining genomic profiles from formalin-fixed paraffin embedded (FFPE) tissue – an important but challenging sample source for clinical cancer researchers. View the presentations to understand how Affymetrix solutions are used for FFPE tissue analyses and:
- Enabled leading oncologists to uncover genome-wide copy number aberrations in rare pediatric cancers (Joshua Schiffman, MD, University of Utah, USA)
- Helped identify novel prognostic biomarkers in solid and hematologic malignancies by SNP based copy number analysis (Eugène Verwiel, Radboud University Nijmegen Medical Center, Netherlands)
- Used gene expression arrays to classify different diffuse large B-cell lymphoma subtypes with FFPE samples (Kim Linton, PhD, University of Manchester, UK)
- Discovered a complex gene expression signature de novo from FFPE samples to differentiate between different cancer types (John Hall, PhD, Paterson Institute for Cancer Research, UK)
- Advanced the discovery of novel biomarkers using cancer-specific gene expression microarray-based tests (Austin Tanney, PhD, Almac Diagnostics Ltd, UK)
- Led to the acceleration of target validation using a unique in situ RNA assay that allows the visualization of a single mRNA copy in single cells (Paul Turner, PhD, Affymetrix UK Ltd)
- Enabled the development of intuitive data analysis solutions for DNA copy number aberration detection (Zhiwei Che, PhD, BioDiscovery Inc, USA)
"For Research Use Only. Not for use in diagnostic procedures."
Keynote speakers and presentations
360 degree tumour profiling
Phenotypic identification of subclones in multiple myeloma with different genomic profile, clonogenic potential and drug sensitivity (presentation only)
Use of Affymetrix Arrays (GeneChip® Human Transcriptome 2.0 Array and Cytoscan® HD Array) in haematological malignancy studies (presentation only)
DNA copy number analysis
From trials evaluating drugs to trials evaluating treatment algorithms – Focus on the SHIVA trial (presentation only)
Christophe Le Tourneau, MD, PhD
Medical Oncologist, Head of the Phase I Program, Institut Curie, France
Identifying genomic biomarkers for translation in pediatric cancer using OncoScan® FFPE Express
Assistant Professor of Pediatric Hematology and Oncology, University of Utah, USA
Gene expression and miRNA analysis
Gene expression profiling of breast cancer for prognosis and prediction
Professor of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas
Expression profiling of archival FFPE samples
Research Associate, Paterson Institute of Cancer Research, Manchester, UK
Microarray-based biomarker discovery: a new trick for old tissues?
Senior Lecturer, School of Cancer and Enabling Sciences, University of Manchester, UK
Protein analysis
For information on IHC, visit our knowledge center
View abstract sheet from Translational cancer research seminar series
"For Research Use Only. Not for use in diagnostic procedures."
Learn more about our cancer research solutions
Affymetrix offers a comprehensive suite of cancer research solutions for studying an extensive range of genomic parameters at wide levels of complexity from the whole-genome to the single gene. Our various tools can also be applied at each stage of a basic or translational workflow from discovery to functional characterization or test development.
Genomic biomarker discovery solutions: whole-genome analysis tools
DNA copy number analysis:
- Complete solution for solid tumor FFPE DNA whole-genome copy number analysis, LOH and key somatic mutations: NEW OncoScan® FFPE Assay Kit*
- Fresh frozen solid tumors and hematological malignancies whole-genome copy number, allelic information, and LOH analysis: CytoScan® HD Array*
Gene expression profiling:
- Optimized biomarker discovery from cancer FFPE samples: Almac Xcel™ Array
- Discovery of transcript isoforms and lncRNA in FFPE samples: GeneChip® Gene 2.0 ST Arrays
- Optimized reagent kits for expression profiling from 10+ year-old FFPE samples: SensationPlus™ FFPE Reagent Kits
- Gene regulation profiling: GeneChip® miRNA 3.0 Array*
Technical and clinical validation solutions: tools for the analysis of 100's to single genes
- Multiplex, straight-from-sample gene expression assays: QuantiGene® Plex 2.0 Assay*
- RNA in situ hybridization assays for visualization of single-molecule RNA in single cells: QuantiGene® ViewRNA Assays*
- Gene regulation profiling: QuantiGene® miRNA 2.0 Assay*
- Flexible, fast mode qRT-PCR reagents: VeriQuest® Real-time PCR Master Mixes*
Cytokine profiling solutions:
- Multiplex quantitative immuno-cytokine assays: Procarta® Cytokine and Chemokine Assays*
Diagnostic test development solutions:
- Molecular diagnostic test development tools for complex diseases: Gene profiling arrays* for expression analysis, IVD-cleared reagents and IVD-cleared instrumentation solutions
*"For Research Use Only. Not for use in diagnostic procedures."
Publications
View publications on the unmet need for reliable copy number data from FFPE
- Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis Hosein A. N., et al. Laboratory Investigation; a Journal of Technical Methods and Pathology 93(6):701-710, 2013
- Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells? Sadanandam A., et al. Breast Cancer Research and Treatment 136(3):693-703, 2012
- Chromosome copy number changes carry prognostic information independent of KIT/PDGFRA point mutations in gastrointestinal stromal tumors Silva M., et al. BMC Medicine doi: 10.1186/1741-7015-8-26
View publications from leading cancer researchers on applications of copy number data in solid tumors
- Identification of Nine Genomic Regions of Amplification in Urothelial Carcinoma, Correlation with Stage, and Potential Prognostic and Therapeutic Value Chekaluk Y., et al. PLoS ONE 8(4):e60927, 2013
- Differentiation of malignant melanoma from benign nevus using a novel genomic microarray with low specimen requirements Chandler W. M., et al. Archives of Pathology & Laboratory Medicine 136(8):947-955, 2012
- A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations Xie T., et al. PLoS One 7(7):e42001, 2012
- Loss-of-heterozygosity on chromosome 19q in early-stage serous ovarian cancer is associated with recurrent disease Skirnisdottir I., et al. BMC Cancer 12(1):407. doi: 10.1186/1471-2407-12-407
Other publications
- Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma Sausen, M.; Leary, R. J.; Jones, S.; Wu, J.; Reynolds, C. P.; Liu, X. Y.; Blackford, A.; Parmigiani, G.; Diaz, L. A.; Papadopoulos, N.; Vogelstein, B.; Kinzler, K. W.; Velculescu, V. E.; Hogarty, M. D. Nature Genetics 45(1), NPG, 2013
- CellLineNavigator: a workbench for cancer cell line analysis Krupp, M.; Itzel, T.; Maass, T.; Hildebrandt, A.; Galle, P. R.; Teufel, A. Nucleic Acids Research 41(D1), D942-8, 2013
- Mammalian cells acquire epigenetic hallmarks of human cancer during immortalization Tommasi, S.; Zheng, A.; Weninger, A.; Bates, S. E.; Li, X. A.; Wu, X. W.; Hollstein, M.; Besaratinia, A. Nucleic Acids Research 41(1), 182-95, 2013
- Targeting the Phosphoinositide 3-Kinase p110-alpha Isoform Impairs Cell Proliferation, Survival, and Tumor Growth in Small Cell Lung Cancer Wojtalla, A.; Fischer, B.; Kotelevets, N.; Mauri, F. A.; Sobek, J.; Rehrauer, H.; Wotzkow, C.; Tschan, M. P.; Seckl, M. J.; Zangemeister-Wittke, U.; Arcaro, A. Clinical Cancer Research 19(1), 96-105, 2013
- Constitutive HER2 Signaling Promotes Breast Cancer Metastasis through Cellular Senescence Angelini, P. D.; Fluck, M. F. Z.; Pedersen, K.; Parra-Palau, J. L.; Guiu, M.; Morales, C. B.; Vicario, R.; Luque-Garca, A.; Navalpotro, N. P.; Giralt, J.; Canals, F.; Gomis, R. R.; Tabernero, J.; Baselga, J.; Villanueva, J.; Arribas, J. Cancer Research 73(1), 450-8, 2013
Scientist Spotlights
- Peter Ambros's work studying pediatric solid tumors Using CytoScan® HD Array helps unravel the complexities of the cancer genome to guide patient-tailored treatment strategies
- Joshua Schiffman's research on copy number changes in pediatric cancers MIP technology reveals important copy number changes in pediatric cancer
- Austin Tanney's work with FFPE tissue Discovering and developing clinically applicable expression biomarkers using archived FFPE tissue samples
Brochures
- OncoScan® FFPE Express brochure Genome-wide copy number in 48 hours
- QuantiGene® ViewRNA Assays brochure RNA in situ hybridization assays for visualization of single-molecule RNA in single cells.
- FFPE Applications Solutions brochure A Platform of comprehensive genomics solutions for analyzing FFPE archival tissues from whole-genome to single molecules
- Solutions for Personalized Medicine brochure From bedside to bench and back again
Application Notes
- QuantiGene® Assays for cancer and disease research application note Multi- and single-plex gene expression quantitation and in situ hybridization assays in cancer research.
Product Spotlight
- Affymetrix® Gene Profiling Array and Reagents product spotlight The only cGMP-manufactured gene expression clinical microarray toolkit for rapid and cost-effective diagnostic test development
"For Research Use Only. Not for use in diagnostic procedures."
Scientific Communities
Archived Webinars +
Clinical Validation of Cancer Biomarker Signatures using Array Technology Webinar
Cancer Genomics Webinar
Circulating Tumor Cells Webinar
Warning! The earliest signals for cancer - miRNA regulation
