Cancer Center Support Grant Site Review Date Cancer Center Support Grant Site Review Date Genomics High Throughput Facility Shared Resource Leader: Suzanne Sandmeyer, Ph.D External Scientific Advisory Board Review GHTF and IGB Personnel Genomics High-Throughput Facility Director, Suzanne Sandmeyer, Ph.D. Manager, Robert Chadwick, Ph.D. SRAIII Seung-Ah Chung SRAII Valentina Cianbanu SRAII Shiqin Xu (new appt) Institute for Genomics and Bioinformatics Analysis Pipeline Director, Pierre Baldi, Ph.D. Programmer, Christophe Magnan, Ph.D. GHTF Services Affymetrix microarray analysis Sample preparation and QC Expression analysis SNP and Copy Number Variation Re-sequencing, ChIP-Chip Illumina Next-gen DNA sequencing Covaris DNA shearing and library preparation De novo & Re-Sequencing of genomic DNA RNA-seq ChIP-seq Library preparation Nucleic acid evaluation Agilent Bioanalyzer RNA and DNA analysis NanoDrop RNA & DNA quantification qPCR of Illumina libraries Affymetrix GeneChip Analysis Hybridization Oven 640 Fluidics Station 450 (3 each) GeneArray Scanner 7G ArrayPlex/Beckman FX BioRobot Agilent Mx3005P Titration by qPCR using Sequencing primers (KAPA) Covaris S2 DNA shearing Qubit 2.0 fluorometer quantification HiSeq 2000 DNA-,RNA-, ChIP-seq Next-Gen DNA seq Seq library preparation cBot Cluster Station Genomics High- Throughput Facility HiSeq 2000 Institute for Genomics and Bioinformatics Computation Resources Storage Capacity Public Web Servers ~ 800 processors Sun Grid Engine ~ 100TB (secured) Fast drives 30TB for HTS HTTP, FTP Dedicated hosts User accounts HTS: 700GB/day Bandwidth: 10Gb/s USER Sample Analysis Requests (via web interface) Analysis Results (FTP server) Magnan and Baldi IGIG IGB data analysis pipeline DATA analysis workflow Magnan and Baldi Data downloaded to users via IGB webserver CCSG metrics Programmatic connections IGB CFCCC Personalized Medicine CFCCC Personalized Medicine Stem Cell Center Stem Cell Center CFCCC Growth Factors And signaling CFCCC Growth Factors And signaling $364,000 toward HiSeq 2000 Client users for HTS $30,000 BIT training grant toward GHTF manager support and online course development $30,000 BIT training grant toward GHTF manager support and online course development CFCCC GHTF Collaborations with OIT, ICTS, RCE, and CCBS CFCCC BSA Client users for HTS Microarray Expression and ChIP-Seq Studies of the Grainyhead-like Epithelial Transactivator Transcription Factor Bogi Andersen MD, Ph.D ChIP-Seq analysis of Get1 transcription factor binding sites shows that Get1 binds primarily at intergenic sites and that Chip-Seq Get1 Peaks correlate with differentiation. Research supported by the GHTF Detecting Transposable Element Insertions with High-Throughput Paired-End Sequencing. Kevin R. Thornton, Ph.D. Transposable elements can be detected quickly and accurately using high-throughput paired-end sequencing data, and these elements can be detected at modest coverage levels. Most TEs at a particular genomic location exist in only one individual in a population. However, a few TEs exist at high frequencies. Comparisons between the observed and expected SOS for TEs in our data sets lead us to reject the neutral model and suggest that the majority of TE insertions may be deleterious % of TEs in the two data sets described here exist in gene regions, the majority of these TEs falling into intronic regions. Many genes experience repeated TE insertions, though in some cases the same TE insertion appears to have spread to higher frequency. Paired-end sequence reads that overlap a TE insertion breakpoint locate an insertion to a specific region of the genome. Unmapped sequences paired with uniquely mapping reads resolve the insertion breakpoint to a specific base pair. The causal role of somatic mutations in the mitochondrial genome in the development and progression of breast cancer Taosheng Huang, M.D Ph.D. Mutations in the mitochondrial genome have been found to be associated with various types of cancer. We propose a two-hit model for the role of somatic mutations in mitochondrial DNA (mtDNA) during tumorigenesis, which includes distinct functions for these mutations at different stages. In this study, we propose to use a high-throughput, parallel sequencing technology, in combination with functional assays, to evaluate the consequences of somatic mutations in mitochondrial DNA (mtDNA) in breast cancer cells. The mutations in mtDNA identified in unbiased breast cancer specimens, and the functional significance identified for these mutations as proposed in this study, will significantly contribute to our understanding of the causal role of somatic mutations in mtDNA in the development and progression of breast cancer, and may also provide valuable insight into potential therapeutic targets. Research supported by the GHTF Examples of funded future projects Bogi Andersen: ChIP seq to investigate grainyhead transcription factor regulation of cell migration and epidermal keratinocyte terminal differentiation Marian Waterman: Affy arrays and ChIP seq to study genomewide binding of TCFs and activity in human embryonic stem cells Eugene Elmore: Affy arrays to study cancer preventive drug effects in colon polyp cells Xing Dai-ChIP-seq and microarrays to study roles of beta catenin and Pygo2 in cancer and normal cells Olivier Cinquin-identification of Notch signaling targets in important for maintenance of stem cells Dan Mercola: ChIP seq on human breast cancer cell lines NIH Shared Instrument Grant $500,000 Campus cost sharing: Year 1: $400,000 (reagents, computer hardware, equipment) Year 2: $85,000 salaries (SRA;programmer) Year 3-5 $100,000 salaries plus service contract contribution Stem Cell Center Year 2: $360,000 toward HiSeq2000 Institute for Genomics and Bioinformatics ARRA supplement: $30,000 Chao Family Comprehensive Cancer Center: $35,000 GHTF campus support GHTF web redesign Future directions Promote Personalized Medicine Program (Mercola) Advertise services: Continue website development with more user upload features and better publicity throughout CFCCC Host technology seminars on campus and UCI MC Education-Campus workshops on genomics Expand services and reduce rates: Expand library options (96 plex; methyl-seq) Introduce Ion Torrent service (RCE collaboration) Expand use of Bioinformatics Shared Resource (Garner) and IGB Promote seed grant use (ICTS) Future directions PacBio Single Molecule Real-Time Sequencer (SMRT) NIH Shared Instrument Grant with twenty-five investigators (March 2011) Advantages: Single molecule No PCR Long reads Direct methyl seq Individual cell sequence CFCCC BSR Personnel Director, Chad Garner, Ph.D. Programmer, Jenny Wu, Ph.D. OIT Computer Cluster support, Harry Mangalam, Ph.D. Services Advise CFCCC members on study design Assist with grant proposals that include HT genomics/genetics components Guide users through data generation, processing and management pipelines Provide data analysis resources and service on hourly fee-for-service basis Collaborate where appropriate Provide access to analysis software (for example CLC Workbench) Garner GOALS Bioinformatics Services Development Promote and support microarray and next generation sequence applications and genetics research among CFCCC members -Sponsorship of symposia and seminars -Develop analysis tools from GHTF website Scientific collaborations with CFCCC members Develop research component with outside funding Garner Responses to five-year renewal critique Bioinformatics limited, does not offer sophisticated biomarker analysis -BSR was founded providing staff to support this analysis; Affy SNP arrays and HTS monitor biomarkers and are heavily used Difficult to assess cost effectiveness relative to other microarray facilities -Prices are competitive; facility has operated for eleven years No plan to address concerns expressed in survey, such as other types of technologies -GAIIX (Application submitted 2009) -HiSeq2000 -IonTorrent -PacBio RS (Application submitted 2011) Limited use by Cancer Center members especially population researchers -Garner, Prof in Epidemiology appointed Director BSR -Mercola to develop Personalized Medicine Program -Symposium on HTS; Mini-symposium with ICTS, workshops, seminars campus-wide announcement of updates in facility Number of grants are supported by facility, but not clear to what extent Cancer is represented -Support is highly leveraged If usage increased, not clear how processing would be prioritized -Service is generally on a first come, first served basis -Prioritization for specific jobs by Director in consultation with Advisory Board including CFCCC representative -Web site shows real time calendar for HiSeq scheduling Five-year renewal critique