The Integrative Genomics Core (IGC) combines the expertise and instrumentation of two NCI-supported facilities—the Functional Genomics/Genomic Sequencing Core and the Bioinformatics Core—to provide an integrated array of services for genomics and informatics. The overall goal of the IGC is to provide comprehensive genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators. The IGC accomplishes this goal using state-of-the-art genome technologies and innovative analytical methods supported by a dedicated team of instrument operators and bioinformaticians.
The IGC is equipped with major instrumentation for genomic analyses, including an Illumina Hiseq2500 sequencer, an Illumina miSeq sequencer, a PacBio Sequel sequencer, a PacBio RSII sequencer, a 10X Genomics Chromium, an Affymetrix GeneChip Analysis System, and an Illumina iScan system. These instruments enable a wide range of genetic, epigenetic, and gene expression analysis capabilities, including miRNA expression (miRNA-seq and miRNA arrays), SNP/indel and copy number variation (whole genome and targeted DNA-seq, copy number arrays), protein and DNA/RNA interaction (ChIP-seq and RIP-seq), DNA methylation (BS-seq and RRBS-seq, EPIC methylation array), genome-wide and custom genotyping (SNP arrays), and single cell transcriptomics. The core also has an ABI ViiA 7 Taqman Real-time PCR system, an excellent technology for library quantification and expression validation, as well as a Nanodrop, Qubit, 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, single cell RNA-seq, miRNA-seq, ChIP-seq, exome-seq, methyl-seq, amplicon-seq, etc., and has extensive expertise in utilizing both commercial and open-source software tools for sequencing data analysis. The core processes over 2500 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.
The IGC recently launched several new services, including single cell RNA-seq, VDJ-seq with Feature barcoding using the 10x Genomics’ Chromium System; BCR/TCR immune profiling and microbiome profiling using the miSeq; and base modification detection, Iso-Seq analysis, and de novo assembly of small to intermediate genomes using the PacBio Sequel and RSII. These new services have enabled COHCCC members to expand the nature, depth, and scope of their genomic investigations.