Integrative Genomics and Bioinformatics Core Shared Resource ABSTRACT The Integrative Genomics and Bioinformatics Core (IGBC) 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 IGBC is to provide comprehensive genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators. The IGBC 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 IGBC is equipped with major instrumentation for genomic analyses, 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. These instruments enable a wide range of genetic, epigenetic, and gene expression analysis capabilities (whole genome and exome sequencing and microarray), 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. The IGBC recently launched several new services, including single cell RNA-seq and DNA-seq using a Fluidigm C1 Single Cell Prep System; BCR/TCR sequencing and microbiome profiling using miSeq; and base modification detection, Iso-Seq analysis, and de novo assembly of small to intermediate genomes using a PacBio RSII. These new services have enabled COHCCC members to expand the nature, depth, and scope of their genomic investigations. The core is co-directed by Drs. Xiwei Wu and Yate-Ching Yuan, with oversight by an interdisciplinary faculty Advisory Committee. User feedback is provided annually through user surveys. Since the last competitive renewal the IGBC contributed to 135 publications by COHCCC members. Over the past five years, the IGBC was used by 146 investigators, including 100 CC members representing all five Programs. Of the 100 CC members, 81 (81%) had peer-reviewed funding.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA033572-37
Application #
9849201
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2019-12-01
Budget End
2020-11-30
Support Year
37
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Beckman Research Institute/City of Hope
Department
Type
DUNS #
027176833
City
Duarte
State
CA
Country
United States
Zip Code
91010
Slavin, Thomas P; Banks, Kimberly C; Chudova, Darya et al. (2018) Identification of Incidental Germline Mutations in Patients With Advanced Solid Tumors Who Underwent Cell-Free Circulating Tumor DNA Sequencing. J Clin Oncol :JCO1800328
Yun, Xinwei; Zhang, Keqiang; Wang, Jinhui et al. (2018) Targeting USP22 Suppresses Tumorigenicity and Enhances Cisplatin Sensitivity Through ALDH1A3 Downregulation in Cancer-Initiating Cells from Lung Adenocarcinoma. Mol Cancer Res 16:1161-1171
Herrera, Alex F; Rodig, Scott J; Song, Joo Y et al. (2018) Outcomes after Allogeneic Stem Cell Transplantation in Patients with Double-Hit and Double-Expressor Lymphoma. Biol Blood Marrow Transplant 24:514-520
Oh, Eunjin; Ahn, Miwon; Afelik, Solomon et al. (2018) Syntaxin 4 Expression in Pancreatic ?-Cells Promotes Islet Function and Protects Functional ?-Cell Mass. Diabetes 67:2626-2639
Shahin, Sophia A; Wang, Ruining; Simargi, Shirleen I et al. (2018) Hyaluronic acid conjugated nanoparticle delivery of siRNA against TWIST reduces tumor burden and enhances sensitivity to cisplatin in ovarian cancer. Nanomedicine 14:1381-1394
Wittenberg, Elaine; Ferrell, Betty; Koczywas, Marianna et al. (2018) Pilot Study of a Communication Coaching Telephone Intervention for Lung Cancer Caregivers. Cancer Nurs 41:506-512
Zhang, Keqiang; Wang, Jinhui; Yang, Lu et al. (2018) Targeting histone methyltransferase G9a inhibits growth and Wnt signaling pathway by epigenetically regulating HP1? and APC2 gene expression in non-small cell lung cancer. Mol Cancer 17:153
Zhang, Bin; Nguyen, Le Xuan Truong; Li, Ling et al. (2018) Bone marrow niche trafficking of miR-126 controls the self-renewal of leukemia stem cells in chronic myelogenous leukemia. Nat Med 24:450-462
Kirschbaum, Mark H; Frankel, Paul; Synold, Timothy W et al. (2018) A phase II study of vascular endothelial growth factor trap (Aflibercept, NSC 724770) in patients with myelodysplastic syndrome: a California Cancer Consortium Study. Br J Haematol 180:445-448
Liu, Liang; Yang, Lin; Yan, Wei et al. (2018) Chemotherapy Induces Breast Cancer Stemness in Association with Dysregulated Monocytosis. Clin Cancer Res 24:2370-2382

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