Cancer Center Support Grant Site Review Date Cancer Center Support Grant Site Review Date Genomics High-Throughput Facility (GHTF) and Bioinformatics Core Suzanne Sandmeyer, Ph.D. Robert Chadwick, Ph.D. Chad Garner, Ph.D.

Outline Update on personnel and services Revisions of recharge rates and approvals Responses to previous critique Capacity Prioritization Bioinformatics Services and coordination with Biomedical Statistics Developments Services Equipment Web redesign Bioinformatics core-Chad Garner

Director, Suzanne Sandmeyer, Ph.D. Manager, Robert Chadwick, Ph.D. Staff SRAs Seung Ah Chung, SRAIII Valentina Ciobanu, SRAII Sharmila Mallya, SRAII Co-Director for Bioinformatics, Pierre Baldi, Ph.D. Staff postdoctoral fellow/programmer Chrisophe Magnan, Ph.D. GHTF Personnel

Affymetrix microarrays Gene expression Re-sequencing SNP analysis High throughput DNA sequencing DNA-seq (36, 54, 72 bp, SE or PE, single or multiplex lanes) Sample quality control Qubit/Nanodrop quantification Agilent RNA/DNA size and integrity assessment qPCR DNA library titration Services

Recharge rate approval process Removed custom array services Revised description of microarray services Added DNA sequencing services Failed to get waiver of %15 surcharge on outside billing Approved preliminarily by budget office 08/10 Total recharges for / :$586,426/$698,085 Net (after service contracts and salaries): / :$104,721/$1,191 Campus sharing: instrument purchases, first year, $415,000; second year, $85K salaries for first five years of Illumina instrument;partial service contract for last three years Recharge operations

Capacity: Removed custom arrays Microarray and sequencing running at full capacity (~one week turnaround) Sequencing booked until October Advisory Board prioritizes as necessary Responses to previous critique (1 of 2)

Responses to previous critique (2 of 2) Coordination with Biomedical Statistics Core and bioinformatics support High throughput sequencing pipeline established for sequence data alignment and assembly through IGB (Baldi and Magnan) User site for sequence assembly and RNA seq Established CFCCC Bioinformatics Core

HiSeq 2000 and Cbot cluster station acquisition Stem Cell Center contributed $464 to trade in of GAIIx and cluster station upgrade; GHTF will purchase $100K reagents at 50% rate (obligated) HiSeq2000 runs 2 flow cells simultaneously and will provide more than twice as much sequence per lane as current instrument Developments (1 of 3)

Developments (2 of 3) Services expanding: RNA-seq Chip-seq Multiplex DNA library production by staff Bioinformatics (CFCCC Bioinformatics Core)

Developments (3 of 3) Web redesign with new features Updated appearance Descriptions of new services and equipment Protocols On line sales and service forms Bioinformatics portal Calendar of service status News of seminars and workshops

Cancer Center Support Grant Site Review Date Cancer Center Support Grant Site Review Date Update on the Bioinformatics Core Chad Garner Director

What the Bioinformatics Core Offers  Advising CFCCC members on optimal study design for high-throughput studies.  Assisting with grant proposals that include HT genomics/genetics components.  Helping to facilitate experimental aspects of study.  Guidance through data generation, processing and management pipelines.  Providing data analysis resources and service.  Offering collaborative opportunities. Bioinformatics Core

The Realm of the Bioinformatics Core  Planning and development of HT Genomic/Genetic Studies.  Management through the data processing pipeline.  Data analysis infrastructure, software, consulting and services. Scientific collaboration with CC members on HT genomic/genetic studies. Bioinformatics Core

Data Pipeline  Core relies on genomic data pipeline developed by Pierre Baldi and the IGB.  IGB has infrastructure and expertise for management of massive HT datasets.  Genetic data is processed directly by Core.  Processed data is downloadable from IGB by CC member and/or Core for data analysis. Bioinformatics Core

Data Analysis  Personnel  Chad Garner  Jenny Wu (GHTF/Bioinformatics Core)  Harry Mangalam (NACS/RCS)  Computer Software  Many programs installed on the Broadcom Distributed Unified Cluster (BDUC)  CLC Genomics Workbench  Computer Hardware  BDUC and dedicated CLC GW server Bioinformatics Core

Bioinformatics Core Development  Goal of Core: promote and support high- throughput genomics and genetics research among CC members.  Outreach to CC Members  Retreats  New HTGF Website  Close relationship with GHTF  Scientific collaboration with CC members  Research component and outside funding opportunities Bioinformatics Core