Abstract for Grant
The integrative genomics core (IGC) is a shared resource facility within the Beckman Research Institute (BRI) at City of Hope. Partially supported by NCI comprehensive cancer center grant, the goal of the IGC is to provide comprehensive genomic services from pre-experimental consultation, sample processing, data analysis and interpretation to manuscript and grant preparation.
The IGC is committed to providing these services in a cost-effective and timely manner to support basic science, translational, and clinical researchers at City of Hope.
The IGC is equipped with all major state-of-the-art microarray and sequencing platforms for genomic studies, including Illumina’s Hiseq 2500 and Life Technology’s Ion Proton sequencers, Illumina’s Hiscan Beadchip system, Affymetrix’s GeneChip system, and Agilent’s microarray system.
The core also has a state-of-the-art Hitachi AB model 3730 48-capillary DNA Analyzer with the capacity to analyze 4,000 to 8,000 samples per week. These instruments enable a wide range of genetic, epigenetic and gene expression analysis capabilities, and complement each other for different applications, including transcriptomic and miRNA profiling, protein and DNA/RNA interaction, histone modifications, DNA methylation, SNP/indel, copy number variations and other structural variations, genome-wide and customer genotyping. The core also has an ABI Taqman Real-time PCR system, ViiA 7, an excellent technology for expression validation, as well as Nanodrop, Qubit 2.0 and Agilent Bioanalyzer for sample QC.
With a highly experienced team of bioinformaticians integrated within the core, efficient genomic data analysis services will be provided to convert high throughput data into biologically interpretable results. The team has established analysis pipelines for all major sequencing applications, e.g. RNA-seq, miRNA-seq, ChIP-seq, exome-seq, amplicon-seq, etc., and has extensive expertise in utilizing both commercial and open-source software tools for sequencing data analysis. These include but are not limited to R/Bioconductor, IGV, Bowtie, TopHat, Cufflinks, Novoalign, MACS, MEME, Transfac, BWA, GATK, Samtools, Gene Set Enrichment Analysis (GSEA), Ingenuity Pathway Analysis and DAVID.
The core processes over 1500 samples with microarray and sequencing instruments each year and supports bioinformatics analysis on all the data generated. The bioinformatics team is also experienced in mining public domain data, such as GEO, TCGA, and 1000 genome databases. The core also supports depositing the genomic data into NCBI’s GEO and SRA database for data sharing.