VERMONT IMMUNOBIOL/INFECTIOUS DIS CTR: MICROARRAY & BIOINFORMATIC ANALYSIS CORE

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. OVERVIEW ***Please note the Tables and Figures mentioned below would not reproduce in this format. Please see attachments sent with the paper copy.*** Core B activities during the reporting period included both +Support for 12 COBRE investigators quantifying genome-wide expression +Participation in development of a plan to bring massively parallel (next generation) sequencing technology to COBRE investigators. SUPPORT FOR GENOME-WIDE EXPRESSION EXPERIMENTS Utilization Services involving experiment design, genome-wide transcription measurements, or bioinformatics analysis were associated with 9 investigators (13 experiments, 189 microarrays). Services involving preliminary discussions or systems biology software supported an additional three investigators (Table 2). Productivity One publication resulted from earlier support (Rincon and coworkers, "The induction of antibody production by IL-6 is indirectly mediated by IL-21 produced by CD4+ T cells." J Exp Med. 2009 206:69-78), one manuscript is being revised for resubmission (Matrajt and coworkers, "Genome-wide expression reveals Toxoplamsa gondii bradyzoite differentiation mutants are also impaired with respect to switching into a novel extracellular tachyzoite stage.", PLoS One), and three manuscripts are at the stage of manuscript preparation (2 from the Teuscher laboratory and one from the Budd laboratory). EMERGING TECHNOLOGIES: Massively parallel sequencing Tim Hunter of Core B continues to play a central role in efforts to bring next generation sequencing to UVM. He participated in development of an application entitled "Next Generation DNA Sequencing Technology for Vermont " (Nicholas Heintz, PI) for earmark funding that was submitted to Senator Leahy's office from the Dean's Office in the UVM College of Medicine. Tim Hunter and Jeff Bond worked to integrate proposed Core B services related to massively parallel sequencing with services supported by the Dean's Office of the College of Medicine and the Vermont Genetics Network. Briefly (Figure 1), the earmark application proposes support for 1FTE involving library construction and sequencing, to be supervised by Tim Hunter, as well as a bioinformatics faculty member and 1 FTE for bioinformatics analysis. The Vermont Genetics Network will provide services related to data storage and preprocessing (Jim Vincent and 1 FTE TBN) as well as 1 FTE for downstream analysis. Figure 1. Development of a plan for bringing massively parallel sequencing to the VCII. Three organizational units, the VCII (Tim Hunter and Jeff Bond), the College of Medicine (COM), and the Vermont Genetics Network (VGN), are working together to provide laboratory services, informatics, and statistical services supporting experiments based on massively parallel sequencing ***Please see attachment for tables and figures: would not reproduce here.***