Genomics and Computational Biology

Director

Kelly A. Frazer, PhD
858-246-0208
kafrazer@ucsd.edu
igm.ucsd.edu

Co-Director

Pablo Tamayo, PhD
858-822-4665
ptamayo@ucsd.edu

Overview

The major objectives of the Genomics and Computational Biology Shared Resource are to provide Moores Cancer Center 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 Center
Campus Branch Location: Leichtag Family Foundation Biomedical Research Building, Room 172
Website: igm.ucsd.edu/core-services/

Leader: Kristen Jepsen, PhD, 858-822-2754, kjepsen@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 Center

  • Illumina Sequencing
  • PacBio Sequencing
  • 10x Genomics Single Cell RNA Sequencing
  • Library Preparation (DNA / RNA / small RNA)
  • Sample QC
  • Agilent 2100 Bioanalyzer / TapeStation
  • Genotyping Arrays
  • Methylation Arrays
  • Covaris Shearing
  • Roche 454 Sequencing
  • Fluidigm Access Array System
  • Affymetrix Microarrays / Nimblegen Arrays
  • Agilent 2100 Bioanalyzer / Nanodrop

Core Resources

  • IGM Genomics Center - Illumina HiSeq 4000, Illumina HiSeq 2500, 10x Genomics Chromium Controller, Illumina MiSeq, Pacific Biosciences RS, Illumina HiScan System, Covaris E220, Agilent Bioanalyzer, Agilent TapeStation, Roche Lightcycler 480, NanoDrop ND-1000, Qubit 2.0 Fluorometer