Standard controls are necessary in clinical applications, aid in
data exchange, and help drive acceptance and facilitate regulatory
approval. To fully move array technology into the clinical marketplace
requires the establishment of best practices, standard controls
and standardized methods, including easily accessible quality controlled
standardized kits with controls.
To this end, Affymetrix is participating in consortia on standards
development with industry, academic and national institutes.
Current Activities
Review Affymetrix current activities in establishing array standards
and standardized methodologies.
Organization for Economic Co-operation and Development (OECD) Biotechnology Industry Advisory Committee , Working Party on Biotechnology, Steering Group on Pharmacogenetics and Working Group on Genetic Testing, Directorate for Science Technology and Industry, Committee Scientific and Technology Policy
MAQC Consortium. (2006) The Microarray Quality Control (MAQC) project shows inter- and intra platform reproducibility of gene expression measurements. Nature Biotechnology 24(9):1151-1161..
Shippy, R., Fulmer-Smentek S, Jensen R.V., Jones W.D., Wolber P.K., Johnson C.D., Pine P.S., Boysen C., Guo X., Chudin E., Sun Y.A., Willey J.C., Thierry-Mieg J., Thierry-Mieg D., Setterquist R.A., Wilson M., Bergstrom Lucas A., Novoradovskaya N., Papallo A., Turpaz Y., Baker S., Warrington J.A., Shi L., Herman D. (2006). Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nature Biotechnology 24(9):1123-1131.
Tong W., Berstrom Lucas A., Shippy R., Fan X., Fang H., Hong H., Orr M.S., Chu T-M., Guo X., Collins P.J., Sun Y.A., Wang S-J., Bao W., Wolfinger R.D., Shchgrova S., Guo L., Warrington J.A., Shi L. (2006). Evaluation of external RNA controls for the assessment of microarray performance. Nature Biotechnology 24(9):1132-1139.
The External RNA Controls Consortium, Warrington J.A. communicating author. (2005)
The External RNA Controls Consortium: A progress report, Nature Methods 2(10):731-734.
The External RNA Controls Consortium (2005). Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6:150.
Mutter G., Zahrieh D., Liu C., Neuberg D., Finkelstein D., Baker H., Warrington J.A. (2004). Comparison of solid tissue storage methods for RNA expression microarrays. BMC Genomics 5:88-93.
Hoffman, E, Awad T, Spira A, Palma J, Webster T, Wright G, Buckley J, Davis R, Hubbell E, Jones W, Tibshirani R, Tompkins R, Triche T, Xiao W, West M, Warrington J.A. (2004). Expression profiling- best practices for data generation and interpretation in clinical trials. Nature Reviews Genetics 5:229-232.
Intellectual Property
Affymetrix has an extensive portfolio of patents and patent applications. As a result, Affymetrix may own intellectual property rights that may be relevant to one or more of the array standards and standardized methodologies that are being discussed or may eventually become designated as a recommended standard array control or best practice method or standardized kits that may result. The community is urged to review Affymetrix patents to determine how they may be related to standard controls and best practices.
