Genomics and Bioinformatics

Director

Kelly A. Frazer, PhD
Phone: (858) 246-0208
E-mail: kafrazer@ucsd.edu
Website: igm.ucsd.edu

Co-Director

Trey Ideker, PhD
Phone: (858) 822-4665
E-mail: tideker@ucsd.edu

Overview

The major objectives of the Genomics and Bioinformatics Shared Resource are to provide MCC investigators with high quality standard, cutting-edge, and custom genomics services and data analyses, as well as consultation on experimental design and training/education about genomic methods and bioinformatics.

  1. To provide expert consultation on experimental designs and analysis approaches of large-scale microarray and NGS datasets.
  2. To generate microarray and high-throughput sequence data in a cost-effective efficient manner with rapid-turn around.
  3. To perform intermediate analysis of high-throughput sequence data including, DNA variant calling, mRNA isoform calling, miRNA analysis and DNA methylation analysis using established pipelines.
  4. To analyze genomic data including tumor profiling for DNA somatic mutations, differential expression analysis, as well as network and systems analysis.

Facilities

Institute for Genomic Medicine (IGM) Genomics Facility
Campus Branch Location: Leichtag Family Foundation Biomedical Research Building, Room 172
Moores Cancer Center (MCC) Branch Location: Moores Cancer Center Room 4347
Website: igm.ucsd.edu/core-services/

Leader: Kristen Jepsen, PhD, 858-822-2754, kjepsen@ucsd.edu
Lab Manager: Rebecca Orlando, 858-822-4231, rorlando@ucsd.edu

VA / VMRF Microarray & NGS Core
Location: Stein Clinical Research Building, Room B066
Website: http://www.vmrf.org/researchcenters/microarray-ngs/microarray-ngs.html

Leader: Nick Webster, PhD, nwebster@ucsd.edu
Lab Manager: Jorge Valencia, 858-552-8585, Ext. 7202 or 7100, genechip@vapop.ucsd.edu

Core Services

  • Consultation for experimental design and assistance with project preparation
  • Training and education (contact any of the resource leaders to be placed on mailing list for announcements)

IGM Genomics Facility

  • Illumina Sequencing
  • PacBio Sequencing
  • Exome Sequencing
  • Library Preparation (DNA / RNA / small RNA)
  • Sample QC
  • Agilent 2100 Bioanalyzer / TapeStation
  • Genotyping Arrays
  • Methylation Arrays
  • Expression Arrays
  • Covaris Shearing

VA / VMRF Microarray & NGS Core

  • Roche 454 Sequencing
  • Fluidigm Access Array System
  • Affymetrix Microarrays / Nimblegen Arrays
  • Agilent 2100 Bioanalyzer / Nanodrop

Core Resources

  • IGM Genomics Facility - Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina MiSeq, Pacific Biosciences RS, Illumina HiScan System, Covaris E220, Agilent Bioanalyzer, Agilent TapeStation, Roche Lightcycler 480, NanoDrop ND-1000, Qubit 2.0 Fluorometer
  • VA GeneChip Core - Genome Sequencer FLX; Affymetric GeneChip ® System; Biomicro Maui hybridization station; Fluidigm Access Array System; Molecular Dynamics/Axon GenePix 4000B scanner; Agilent 2100 Bioanalyzer; NanoDrop spectrophotometer