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 #
2P30CA033572-35
Application #
9491627
Study Section
Subcommittee I - Transistion to Independence (NCI)
Project Start
Project End
Budget Start
2018-04-20
Budget End
2018-11-30
Support Year
35
Fiscal Year
2018
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
Wang, Sophia S; Carrington, Mary; Berndt, Sonja I et al. (2018) HLA Class I and II Diversity Contributes to the Etiologic Heterogeneity of Non-Hodgkin Lymphoma Subtypes. Cancer Res 78:4086-4096
Wu, Chenkai; Ashing, Kimlin Tam; Jones, Veronica C et al. (2018) The association of neighborhood context with health outcomes among ethnic minority breast cancer survivors. J Behav Med 41:52-61
Wussow, Felix; Chiuppesi, Flavia; Meng, Zhuo et al. (2018) Exploiting 2A peptides to elicit potent neutralizing antibodies by a multi-subunit herpesvirus glycoprotein complex. J Virol Methods 251:30-37
Kingsmore, Kathryn M; Vaccari, Andrea; Abler, Daniel et al. (2018) MRI analysis to map interstitial flow in the brain tumor microenvironment. APL Bioeng 2:
Paz, Helicia; Joo, Eun Ji; Chou, Chih-Hsing et al. (2018) Treatment of B-cell precursor acute lymphoblastic leukemia with the Galectin-1 inhibitor PTX008. J Exp Clin Cancer Res 37:67
Slavin, Thomas P; Neuhausen, Susan L; Nehoray, Bita et al. (2018) The spectrum of genetic variants in hereditary pancreatic cancer includes Fanconi anemia genes. Fam Cancer 17:235-245
Wildes, Tanya M; Maggiore, Ronald J; Tew, William P et al. (2018) Factors associated with falls in older adults with cancer: a validated model from the Cancer and Aging Research Group. Support Care Cancer 26:3563-3570
Yoon, Sorah; Wu, Xiwei; Armstrong, Brian et al. (2018) An RNA Aptamer Targeting the Receptor Tyrosine Kinase PDGFR? Induces Anti-tumor Effects through STAT3 and p53 in Glioblastoma. Mol Ther Nucleic Acids 14:131-141
Gast, Charles E; Silk, Alain D; Zarour, Luai et al. (2018) Cell fusion potentiates tumor heterogeneity and reveals circulating hybrid cells that correlate with stage and survival. Sci Adv 4:eaat7828
Salgia, Ravi; Kulkarni, Prakash (2018) The Genetic/Non-genetic Duality of Drug 'Resistance' in Cancer. Trends Cancer 4:110-118

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