Our Science Initiatives – Microarray Technology
The CCR microarray technology enterprise has three components. Two complementary DNA (cDNA) microarray core facilities—the Laboratory of Molecular Technology’s Microarray Group and the Microarray Facility, which is part of the Advanced Technology Center in Gaithersburg, MD—oversee the development of new microarray platforms. Researchers from these laboratories are working together to evaluate oligonucleotide arrays in anticipation of the expected transition from cDNA to oligonucleotide-based technology.
The third component, the Tissue Array Research Program (TARP), produces multitumor microarray slides for high-throughput screening of multiple tumor tissues using immunohistochemical, in situ, and FISH analyses. Because large numbers of tissues can be placed on a single slide, multi-tissue arrays are ideal tools for tissue surveys of the incidence or prevalence of proteins or for transcripts in particular tumors or tissues.
One Human Genome: One Slide
Thanks to the human genome map, researchers can study the expression and
function of every gene in the body. But how can they simultaneously analyze
the expression of 30,000–50,000 genes? The answer lies in microarray
technologies. A microarray is a miniaturized gene hybridization and detection
assay. Instead of measuring signals in assays at the macro level, individual
microarray assays are measured in microns. It is now possible to place
the entire human gene complement on one slide. DNA microarrays are a pivotal
and powerful research tool; findings made possible by this tool will lead
to more effective and radically new ways to treat and cure cancer. One
day, microarrays will be diagnostic and prognostic tools; each patient
will have personalized or tumor-specific therapies.
Molecular Signatures from Multiple Hosts
Unlike traditional tissue-analysis tools that allow scientists to examine
only a few tissue samples at a time or other types of microarrays that
contain DNA, tissue microarrays allow scientists to examine hundreds of
tumor samples at once. This technology has the potential to accelerate
research by stepping up the process of identifying the unique characteristics
of cancer cells—information vital to advances in the detection, diagnosis,
and development of targeted therapies.
Microtechnology News
Universal RNA Standards Developed for All Microarray Platforms
Microarrays are the most common method of studying global gene expression and may soon enter the realm of FDA-approved clinical/diagnostic testing of cancer and other diseases. However, the acceptance of array data has been made difficult by the proliferation of widely different array platforms with gene probes ranging in size from 25–70 bases (oligonucleotides) to several kilobases (cDNAs). In addition, there is a total lack of universally accepted standards for use among the different platforms and even within the same array types. To overcome this problem, the NCI Microarray Facility has been participating in studies designed to develop universally accepted RNA standards and protocols for microarray and quantitative PCR technologies. The National Institute of Standards and Technology (NIST) and the Food and Drug Administration (FDA) are sponsoring these large studies.
The NIST group, designated the External RNA Controls Consortium (ERCC), has nearly completed the development of a set of RNA standards that will be used in more than 10 microarray and PCR platforms. The commercial, academic, and government members of the consortium have agreed to include these standards in their platforms so that all microarray and PCR studies will have exactly the same standards. Success in this endeavor will go a long way toward ending the confusion in interpreting data from expression profiling experiments. The FDA-sponsored consortium, MicroArray Quality Control (MAQC) Project, is attempting to determine the factors/metrics required for acceptable quality control in the various microarray platforms, and more than 50 academic, government, and commercial organizations are participating in this study.
The group has just completed an experiment in which more than 35 laboratories (with 10 different array platforms) used the same RNA samples to analyze gene expression. The goals here are to determine how closely the results from all the laboratories match and to pinpoint the problem areas where improvement is required before data can be deemed acceptable. Results from both the NIST and FDA studies will be made publicly available and, hopefully, will have a major impact on the reliability of microarray technologies.
Recent NCI Microarray Articles/Projects
The External RNA Controls Consortium: a progress report. Nat Methods 2: 731–4, 2005. The NCI is one of the founding members of a NIST-sponsored international group composed of more than 100 organizations from academic, government, and commercial laboratories. The goal of the ERCC is to develop RNA standards that will be used in all microarray and quantitative PCR platforms.
External RNA Controls Consortium. Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6:150, 2005. This article describes how the ERCC will validate the RNA controls to be used in all microarray and quantitative PCR platforms.
Irizarry RA, et al. Multiple-laboratory comparison of microarray platforms. Nat Methods 2:345–50, 2005. The NCI Microarray Facility participated in a Johns Hopkins University study that compared array results from several labs using different platforms.
Petersen D, et al. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 6:63, 2005. The NCI Microarray Facility conducted an independent study to demonstrate that data from short (25-mer) oligonucleotide, long (70-mer) oligonucleotide, and cDNA array platforms were directly comparable.
The MAQC Project: calibrated RNA samples, reference datasets, and QC metrics/thresholds for microarray quality control. The NCI is one of the main participants in this FDA-sponsored project involving more than 50 microarray and quantitative PCR labs and companies. The results from this study will help the FDA in its analysis and acceptance of array data in clinical studies, drug development, and diagnostics.
Useful websites for further information on the ERCC and MAQC:
National Institute of Standards and Technology (NIST) - type “ERCC” in the search engine.
