TumorCheck™ Human Tumor Tissue Characterization
Cancer is characterized by a multi-step process of acquired genetic changes that can involve alterations in the genome, transcriptome, and epigenome. Sensitive tools are now available to identify and characterize these genetic changes for development of tumor signatures which may have diagnostic, prognostic, and predictive clinical value. TumorCheck™ is a comprehensive menu of molecular tools now available to the cancer research community…
• Clinical Trials: Advanced Genomics has the tools, expertise and bioinformatics resources to collaborate with the drug development industry to identify and validate biomarkers for cancer diagnostic, prognostic, and patient stratification studies.
•Molecular Karyotyping: These assays detect aneuploidy, deletions, duplications and gene amplification using a variety of high density microarrays by Illumina with a median marker spacing as low as 1.5 kb. The arrays also detect copy-neutral allelic aberrations such as segmental uniparental disomy.
•Genotyping:
o Whole-Genome SNP Arrays: A wide variety of high density, whole-genome microarrays are available for genetic association studies.
o Cancer SNP Panel: This array contains >1,400 SNPs derived from 400 genes selected from the National Cancer Institute’s Cancer Genome Anatomy Project SNP500 Cancer Database. The SNPs represent genes involved in important cancer pathways such as apoptosis, oncogenesis, tumor suppression, and G-protein coupled receptor protein signaling.
•Methylation Profiling:
o Whole-Genome: The Illumina genome-wide methylation arrays quantitatively analyze over 27,000 CpG loci covering more than 14,000 genes.
o Cancer Panel: This array targets 1,505 CpG loci from 807 genes representing tumor suppressor genes, oncogenes, DNA repair genes, and genes involved in cell cycle control, differentiation, apoptosis, and imprinting. All the genes targeted in this array are also found in the Illumina Human WG-6 v 2.0 Expression array to permit comparisons to gene expression data.
•Gene Expression Analysis:
o Whole-Genome Arrays: Two whole-genome arrays are available. One array allows analysis of over 48,000 transcripts and the other targets approximately 24,500 well annotated RefSeq transcripts.
o Human Cancer Panel: This array targets 502 genes selected from ten publicly available cancer gene lists. The assay is designed and optimized to work well on sub-optimal samples such as found in FFPE specimens.
o Focused Gene Expression Arrays: These arrays can query groups of up to 1,400 genes consisting of either standard or custom probe content.
•MicroRNA Expression Profiling: As many as 30% of mammalian genes may be regulated by miRNAs. The Illumina microRNA expression profiling assay quantifies levels of miRNA described in the Sanger Institute miRBase database.
•DNA and RNA Isolation: Preparation of high quality DNA and RNA for use in downstream genomic and gene expression studies.
• Cell line Identification and Signature: This panel uses sixteen loci (15 STRs and amelogenin), recognized by major standardization bodies throughout the world, for the identification of tissue culture cell lines. These studies will establish the molecular signature of cell lines to authenticate their origin.