Functional Genomics/Genomic Sequencing

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PROJECT SUMMARY (See instructions); The overall goal of the Functional Genomics/Genomic Sequencing Core (FGC) is to provide state-of-the-art instruments, and expert scientific and technical advice in cancer genomics to COHCCC investigators. The FGC is equipped with major genomics instrumentation such as Affymetrix GeneChip¿ Analysis System, Agilent scanner/microarray system, Roche NimbleGen MS200 microarray scanner/system, lllumina HiScanSQ, HiSeq2000, GA llx and Roche 454 FLX. The core also has a next-generation ABI Taqman Realtime PCR system ViiA 7 for microarray validation. FGC provides comprehensive genomic support including transcriptomic and mlRNA/smRNA profiling by,microarrays and RNA-Seq/smRNA-Seq, ChlP-Chip/ChlPSeq, DNA methylation, DNA-Seq including whole genome and target genome sequencing, microarray genome-wide and custom genotyping, SNP/CNV, aCGH, RNAi and qRT-PCR. The FGC has recently set up numerous new genomic technologies and assays including microarray-coupled genome-wide gene expression profiling using difficult clinical formalin-fixed paraffin-embedded (FFPE) RNA samples, smRNASeq and RNA-Seq using FFPE-derived samples, microfluidic chip- and microarray-coupled single-cell genome-wide gene expression profiling. In addition, the FGC has implemented NimbleGen array-based comprehensive high-throughput arrays for relative methylation (CHARM), Affymetrix DMET and genomewide human SNP 6.0 array genotyping, and lllumina Infinium HumanMethylation450 BeadChip that interrogates more than 450,000 methylation sites across the whole human genome at single-nucleotide resolution. The FGC has supported numerous NIH/NCI projects resulting in high impact publications. In summary, the advanced genomic tools in the FGC allow COHCCC investigators to: 1) identify cancer gene mutations at high-throughput rates; 2) map cancer genomic, transcriptomic and epigenomic fingerprints to identify genomic biomarkers for cancer early detection and diagnosis; 3) identify novel therapeutic targets against cancers; and 4) predict responses to therapy.