Integrative Genomics and Bioinformatics Core

Beckman Research Institute/City Of Hope, Duarte CA

Investigators

Linked publications, trials & patents

Abstract

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.