The overall goal of the Integrative Genomics and Bioinformatics (IGBC) 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 NextSeq 2000 sequencer, an Illumina miSeq sequencer, an Illumina iSeq sequencer, a PacBio Sequel IIe sequencer, a 10X Genomics Chromium X 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 4000 samples with microarray and sequencing instruments each year and also supports bioinformatics analysis on 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, recently launched several new services, including multiOMICS single cell sequencing using a 10x Chromium, spatial transcriptome with 10x’s Visium, cost effective sequencing with the NovaSeq 6000, and improved long read sequencing using a PacBio Sequel IIe. These new services have enabled COHCCC members to expand the nature, depth, and scope of their genomic investigations. The bioinformatics capability has also been enhanced by expanded bioinformaticians at IGC, allowing more efficient and in-depth data analysis support.
Shu Tao
Assistant Research Professor
Ching Ouyang
Assistant Research Professor
Yuqi Zhao
Assistant Research Professor
Supriyo Bhattacharya
Assistant Research Professor
Haiqing Li
Staff Scientist
Hanjun Qin
Staff Scientist
Wei Chen
Staff Scientist
Min-Hsuan Chen
Staff Scientist
Hyejin Cho
Staff Scientist
Tae Hyuk Kang
Staff Scientist
Charles Warden
Bioinformatics Specialist
Rosalina Lonergan
RAII
With a highly experienced team of bioinformaticians integrated within the core, the IGBC provides efficient genomic data analysis services 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, and has extensive expertise in utilizing both commercial and open-source software tools for sequencing data analysis. Each year, the core processes over 2500 samples with microarray and sequencing instruments and supports bioinformatics analysis on all the data generated. In addition, the bioinformatics team has experience 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 IGBC also launched 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 services enable City of Hope's scientists to expand their genomic investigations' nature, depth, and scope.
Sample Submission Guidelines
The 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. However, please note that the actual turnaround time might vary depending on the workload and complexity of the project.
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 major instrumentation for genomic analyses, including an Illumina NovaSeq 6000, an Illumina NextSeq 2000, an Illumina NextSeq 500, an Illumina iSeq 100, two Illumina MiSeqs, a PacBio Sequel IIe, multiple 10X Genomics Chromium instruments, a Mission Bio Tapestri, and an Illumina iScan system. These instruments enable a wide range of genomic capabilities. IGC also has multiple ABI ViiA 7 Real-time PCR systems, an excellent technology for library quantification and expression validation, as well as multiple instruments for sample and library QC (Nanodrop, Qubit, along with Agilent Bioanalyzers). These instruments enable a wide range of genetic, epigenetic and gene expression analysis capabilities, and complement each other for different applications. On single cell level, RNA-seq and VDJ profiling can be done from the same cells using 10x Genomics’ Chromium system, while DNA sequencing can be done using the Tapestri system. We also support the new Visium spatial gene expression platform from 10x Genomics. 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 and DNA-seq, single cell VDJ-seq, single cell ATAC-seq, TCR/BCR-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 500 projects 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, SRA, and dbGap database for data sharing.
Current pricing can be found on iLab Solutions.
This single-cell genomics instrument can help study RNA and DNA on a single-cell level. It has been used for RNA-seq, VDJ-seq, ATAC-seq and more.
This low throughput sequencing can generate 600bp to 1000bp in 48 samples per run. It is used for small-scale sequencing and cell line validation.
This microarray platform is used primarily for gene expression applications. Many arrays with different throughputs are available.
This instrument is used to provide quality control and quantification of DNA and RNA samples.
This instrument provide quantification of DNA or RNA samples up to 96 samples at a time.
The LE220 reproducibly shears DNA to desired lengths in a multi-sample parallel-processing mode.
This liquid handling instrument provides an automation solution for smaller-scale applications, such as beads purification and PCR assays.
This liquid handling instrument provides an automation solution for NGS library preparation, which can speed up the process and ensure better consistency of the results.
This microarray platform is used primarily for GWAS and DNA methylation applications. Many arrays with different throughputs are available.
This high throughput sequencer generates 20M to 25M reads with lengths up to 300bp.
This instrument is used to provide quality control and quantification of DNA and RNA samples.
This sequencer generates 4 million HiFi reads with average length up to 30-40kb. This can be used for small genome de novo assembly, microbiome profiling, RNA isoform sequencing, and other applications that need long reads.
This sequencer generates one million reads with an average length of up to 30kb to 40kb. It can be used for small genome de novo assembly, microbiome profiling, RNA isoform sequencing, and other applications that need long reads.
This instrument is used to provide quantification of DNA samples.
In a given year, City of Hope conducts more than 400 clinical trials enrolling more than 6,000 patients.
Zhao, Z. M., Yost, S. E., Hutchinson, K. E., Li, S. M., Yuan, Y. C., Noorbakhsh, J., Liu, Z., Warden, C., Johnson, R. M., Wu, X., Chuang, J. H., & Yuan, Y.
Ding, Y. C., Steele, L., Warden, C., Wilczynski, S., Mortimer, J., Yuan, Y., & Neuhausen, S. L.
Slavin, T. P., Teh, J. B., Weitzel, J. N., Peng, K., Wong, F. L., Qin, H., Wang, J., Wu, X., Mei, M., Pillai, R., Wang, Y., Tsang, K. K., Pozhitkov, A., Krishnan, A., Forman, S. J., & Armenian, S. H.
Song, A., Dai, W., Jang, M. J., Medrano, L., Li, Z., Zhao, H., Shao, M., Tan, J., Li, A., Ning, T., Miller, M. M., Armstrong, B., Huss, J. M., Zhu, Y., Liu, Y., Gradinaru, V., Wu, X., Jiang, L., Scherer, P. E., & Wang, Q. A.
Yoon, S., Wu, X., Armstrong, B., Habib, N., & Rossi, J. J.
City of Hope is focused on basic and clinical research in cancer, diabetes and other life-threatening diseases.
