Conference Program - ABRF 2011 - Association of Biomolecular ...

Workshop SessionAbstractsresolution hybrid instruments having API sources. These competitiveapproaches deliver exciting results on selection of the predictors’ paneland potential metabolic biomarkers discovery. We here report onefficiency of Metabolic Biomarkers Discovery Project as a platform forcases study: Kidney diseases (RCC and PKD); Pancreatic Cancer (PDAC);Human Embryonic Stem Cells functional characterization. However,Metabolic Networks simulation and Metabolic Pathway Analysis,which could be essential tools for Metabolic Biomarkers validation andconnections with underlying biochemical processes are still difficultand approached not systematically, but rather case wise. Challengesand developments in this field will be further presented and discussed.(W11) The Business of Running a Core FacilityN.P. Ambulos, Jr. 1 , S.A. Bobin 21University of Maryland School of Medicine, Baltimore, MD,United States; 2 Dartmouth School of Medicine, Hanover, NH,United StatesThe success and sustainability of a Core Facility has been dependenton factors which include (1) the ability to maintain state-of-thearttechnology, (2) recruiting and retaining talented technical staff,(3) a strong financial management plan, and (4) strong Institutionalsupport from both end users and the Administration. Historically,most core facilities enjoyed generous subsidies from their InstitutionalAdministration, which have helped defray costs for end users, purchasenew instrumentation, or to hire new staff. In light of the current economy,it is likely that many core facilities are now seeing these subsidiesdrastically cut, or even eliminated. In essence, core facilities are facedwith operating as a self-supporting ‘business’, and at the same time,ensure compliance with federal guidelines. This workshop will presentideas, both conventional and creative, that might provide core directorswith the tools necessary to continue to sustain a successful core facility.This will set the stage for an open discussion with the audience toencourage a free-flow of additional ideas that could benefit the futuresuccess of our cores.(W12) Microarrays: The Reports of My DeathHave Been Greatly Exaggerated(W12-1) Chip or Seq: Helping Clients ChooseD. BaldwinUniversity of Pennsylvania, Penn Molecular Profiling Facility,Philadelphia, PA, United StatesThe Penn Molecular Profiling Facility provides services using microarrayand deep sequencing platforms for a variety of applications. Drawingfrom experiences helping prospective clients to choose one approachor the other, and sometimes both, this portion of the workshop willaddress some of the factors to consider when thinking about a newproject. The budgeting process will be discussed, with particular focuson the use of interactive cost calculators.(W12-2) Microarray Analysis of FluorescenceActivated Cell Sorter-Derived Cells: CreatingHarmony Between TechnologiesS. TigheUniversity of Vermont, Advanced Genome Technology Core,Burlington, VT, United StatesAlthough microarray technology is well-established in both theresearch and clinical fields, it continues to evolve into new areas thatrequire new methods for the successful isolations of nucleic acid fromnon-traditional sources. Because RNA specifically is a labile molecule,special procedures and considerations must be implemented to avoiddegradation from methods such as fluorescence activated cell sorting(FACS) and laser capture microdissection (LCM) to name a few. Thispresentation will discuss specific methodologies to maximize the successof nucleic acid recovery from these approaches including instrumentpreparation, extraction methods, and the use of special reagents todeal with problematic samples.(W12-3) Microarray Futures: Don’t DecommissionYour Scanners Just YetS.D. CrosbyDepartment of Genetics, Washington University School ofMedicine, St. Louis, MO, United StatesThe first attempt to wind down the Washington University MicroarrayFacility was made by Genome Sequencing Center in 2008. It wasclear to most of us involved in the attempt that, with the advent ofNGS, microarrays were headed the way of differential display PCR(remember that!?). The attempt failed, and 2010 was the busiest yearyet for our microarray facility. Sequence remains a bit too expensiveand complex for many to make the leap. In addition, because of therarity of variants and the modest number of bases required to identifya locus, most sequence data is superfluous. Beyond that, as the actualcost of sequence continues to fall, so do the price of arrays, while thedensity of elements of the latter rises. It seems that until the advent ofreagentless sequencing, it is unlikely that the actual cost of sequencingwill be less than the cost of an array that covers the same loci. Whilesequencing technology will remain an important tool for discovery,over time most exons and biologically relevant variants will be capturedin toto on low cost arrays. Hospital or contract labs will (indeed arealready) use small, cheap arrays that capture disease relevant genes andvariants.50 • ABRF 2011 — Technologies to Enable Personalized Medicine