Functional Genomics/Genomic Sequencing

项目总结(见说明)； 功能基因组学/基因组测序核心(FGC)的总体目标是向COHCCC研究人员提供最先进的癌症基因组学仪器和专家科学技术建议。FGC配备了主要的基因组学仪器，如Affymetrix基因芯片�分析系统、安捷伦扫描仪/微阵列系统、罗氏NimbleGen MS200微阵列扫描仪/系统、llLumina HiScanSQ、HiSeq2000、GA LLX和罗氏454FLX。CORE还拥有用于微阵列验证的下一代ABI Taqman实时聚合酶链式反应系统VIIa 7。FGC提供全面的基因组支持，包括通过微阵列和RNA-Seq/smRNA-Seq、ChlP-Chip/ChlPSeq、DNA甲基化、DNA-Seq(包括全基因组和靶基因组测序)、微阵列全基因组和定制基因分型、SNP/CNV、aCGH、RNAi和qRT-PCR进行转录和mlRNA/smRNA分析。FGC最近建立了许多新的基因组技术和分析，包括使用困难的临床福尔马林固定石蜡包埋(FFPE)RNA样本的微阵列耦合全基因组基因表达谱，使用FFPE衍生样品的smRNASeq和RNA-Seq，微流控芯片和微阵列耦合的单细胞全基因组基因表达谱。此外，FGC还实施了基于NimbleGen阵列的全面高通量相对甲基化(CHAME)阵列、Affymetrix DMET和全基因组人类SNP 6.0阵列基因分型，以及以单核苷酸分辨率询问整个人类基因组超过450,000个甲基化位点的LLumina Infinium Human Mylation450珠芯片。FGC支持了许多NIH/NCI项目，产生了影响很大的出版物。总之，FGC中的先进基因组工具使COHCCC的研究人员能够：1)高通量地识别癌症基因突变；2)绘制癌症基因组、转录和表观基因组指纹图谱，以识别癌症早期检测和诊断的基因组生物标记物；3)确定针对癌症的新治疗靶点；以及4)预测治疗反应。

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.