An NCI-designated Comprehensive Cancer Center
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. 

Meet the Team

Research Professor
Manager, Integrative Genomics

Sample Submission Guidelines

Typical turnaround time for microarray service is one to two weeks, three to four weeks for sequencing, and one to four weeks for data analysis. Please note that actual turnaround time might vary depending on the workload and complexity of the project.
 

Abstract for Grants

The Integrative Genomics Core (IGC) is a shared resource facility within the Beckman Research Institute (BRI) at City of Hope. Partially supported by an 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 sequencing and microarray platforms for genomic studies, including Illumina’s Hiseq 2500 and miSeq, and Pacific Bioscience’s Sequel and RSII sequencer, 10x Genomics Chromium single cell platforms, Illumina’s iScan Beadchip system and Affymetrix’s GeneChip system for microarray. Through TGEN integration, we also have access to the newest Illumina NovaSeq sequencer. The core also has a 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 (RNA-seq) 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, de novo assembly, microbiome, and immune repertoire sequencing. On single cell level, RNA-seq and VDJ profiling can be done from the same cells using 10x Genomics’ Chromium system. 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, scRNA-seq, TCR-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. The core processes over 3500 samples each year and supports bioinformatics analysis on all the data generated from these samples. The bioinformatics staffs are also very experienced in mining public domain data, such as GEO, TCGA, and 1000 genome databases. The core also supports data sharing and depositing of the genomic data into NCBI’s GEO and SRA database for data sharing.  
 
The Integrative Genomics Core (IGC) is equipped with all major state-of-the-art microarray and sequencing platforms for genomic studies including: an Illumina Hiseq2500 sequencer, an Illumina miSeq sequencer, a PacBio RSII sequencer, a Fluidigm C1, a 10X Genomics Chromium, an Affymetrix GeneChip Analysis System, an Agilent scanner/microarray system, and an Illumina HiScan system. The core also has a 48-capillary DNA analyzer (Hitachi AB model 3730), PCR systems (ABI Taqman Real-time PCR System, ViiA 7 Real-Time PCR System); ultrasonicator (Covaris LE220), spectrophotometer (Nanodrop); fluorometer (Qubit 2.0); and bioanalyzer (Agilent Bioanalyzer). The bioinformatics team within IGC 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.
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CCNE1 amplification is associated with poor prognosis in patients with triple negative breast cancer.
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Molecular subtypes of triple-negative breast cancer in women of different race and ethnicity.
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Association between Clonal Hematopoiesis and Late Nonrelapse Mortality after Autologous Hematopoietic Cell Transplantation.
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Low- and high-thermogenic brown adipocyte subpopulations coexist in murine adipose tissue.
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An RNA Aptamer Targeting the Receptor Tyrosine Kinase PDGFRalpha Induces Anti-tumor Effects through STAT3 and p53 in Glioblastoma.