Affymetrix - Clinical Research and Trials


Clinical researchers are using the Affymetrix GeneChip® system to more rapidly discover RNA and DNA patterns which can better classify disease, understand mechanism-of-action, and predict response to therapy in a number of disease areas.
•		In drug development, pharmaceutical companies are using the Affymetrix GeneChip platform to increase certainty in drug development via improved target identification, a better understanding of mechanism-of-action, and predicting which subset of patients will respond to a particular drug. Using this technology, researchers’ may employ strategies to rescue drugs that demonstrate low efficacy rates in later-stage clinical trials.
•		Academic researchers, using either tissue or blood, may also discover genomic patterns to facilitate understanding of heterogeneity of disease, patients and targets to ultimately improve patient survival and quality of life.
•		The flexibility and reproducibility of GeneChip brand microarrays enables a number of different formats for follow-up and confirmation of clinically useful RNA expression patterns.
•		Affymetrix GeneChip DNA analysis products for whole genome SNP mapping, custom SNP analysis, and resequencing are also enabling discovery of new kinds of genetic biomarkers signatures

KEY REFERENCES

Numerous peer-reviewed papers have been issued which cite the use of GeneChip technology in clinical research. Here are a few key references across several different therapeutic areas.

Oncology

Breast Cancer
Classification of Human Breast Cancer Using Gene Expression Profiling as a Component of the Survivor Predictor Algorithm Glinsky, G.V., et al.Clinical Cancer Research 10: 2272-2283 (2004)

Myeloid Leukemia
Prognostically Useful Gene-Expression Profiles in Acute Myeloid Leukemia.
Valk, P., et al. New England Journal of Medicine 350: 1617-1628 (2004)

Use of Gene-Expression Profiling to Identify Prognostic Subclasses in Adult Acute Myeloid Leukemia
Bullinger, L., et al. New England Journal of Medicine 350: 1605-1616 (2004)

Gastrointestinal Cancer
Gene Expression in Gastrointestinal Stromal Tumors is Distinguished by KIT genotype and anatomic site. Antonescu, C. R,. et al. Clinical Cancer Research 10: 3282-3290 (2004)

Inflammation

Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood.
Bennett, L., et al. Journal of Experimental Medicine 197: 711-723 (2003).

Metabolic Disease

Gene Expression profile in Skeletal Muscle of Type 2 Diabetes and the Effect of Insulin Treatment.
Sreekumar, R., et al. Diabetes 51: 1913-1920 (2002).

PGC-1Alpha- responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
Mootha, V.K., et al. Nature Genetics 34: 267-273 (2003).

Transplantation

Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes. Flechner, S. M., et al. American Journal of Transplantation on line version (2004)

Search for publications in your disease area.

PRODUCTS AND APPLICATIONS

Learn more about our products for use in your clinical research and clinical trial applications.

Scan the human genome to identify patterns whose expression levels (either upregulated or downregulated) correlate with a clinical response and/or an adverse event using GeneChip Human Genome U133 Plus 2.0 Arrays.

The GeneChip Human X3P Array was designed specifically for whole-genome expression profiling of formalin-fixed paraffin-embedded (FFPE) samples and is available via the GeneChip Made-to-Order Program.

Validate your biomarker pattern in larger studies with the cost effective GeneChip CustomExpress Arrays. Follow-up the results from your HG-U133 experiments and seamlessly study previously identified subsets of biomarkers.

For whole-genome association studies, the GeneChip Mapping 100K Set is the first in a family of products for these types of studies. The Mapping 100K Set can be used for cancer genetics, linkage disequilibrium studies, family-based association studies and chromosome copy number change analysis.

Our GeneChip Mapping 10K 2.0 Arrays enable measurement of more than 10,000 genotypes in a single experiment and are cost comparable with microsatellite analysis. Cancer genetics applications using these arrays include detection of chromosomal amplification, deletions and genotypes, requiring only 250 ng of genomic DNA per sample.

To better understand target heterogeneity and the potential impact of this on patient drug response, use CustomSeq® Resequencing Arrays for comparative sequence analysis projects. Efficiently and reliably resequence up to 30Kb of double stranded sequence in a single experiment.

SUPPORT MATERIALS

Affymetrix Solutions for Cancer Analysis (pdf, 362 KB) describes use of the GeneChip Mapping 10K 2.0 Array, Mapping 100K Set, the Mitochondrial Resequencing Array, and the Human X3P Array for cancer applications. Some of the applications include chromosomal amplification, deletion, and loss of heterozygosity (LOH) analysis (pdf, 376 KB), resequencing mitochondrial DNA, and gene expression analysis on whole genome arrays including formalin-fixed, paraffin-embedded samples.

Several key clinical studies using GeneChip microarrays are reviewed in Advances in Clinical Research with Affymetrix GeneChip RNA Expression and DNA Analysis Arrays (pdf, 1.8 MB) . These key studies span several different therapeutic areas including leukemia, inflammatory disease and diabetes and describe use of GeneChip arrays for gene expression and DNA analyses.

AFFYMETRIX SERVICE PROVIDERS

Several Affymetrix service providers have been certified by the FDA's Good Laboratory Practice Standards compliance monitoring program.

REGULATORY


To fully move array technology into the clinical marketplace requires the establishment of best practices, standard controls and standardized methods. Learn more about how Affymetrix is participating in consortia associated with the development of Standard Controls and Best Practices. The FDA is expected to release a guidance document titled ‘Guidance for Industry: Pharmacogeomics Data Submissions’ by the end of the summer. This document is anticipated to focus on providing information related to voluntary submission of genomic data as part of the drug approval process. Stay tuned…