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

Scientific SessionAbstracts(S5) High-Throughput Genome Centers(S5-1) Overview of the Illumina Sequencing Platformat the Broad InstituteK. ConnollyProcess & Technology Development, Genome SequencingPlatform, The Broad Institute, Cambridge, MA, United StatesThe constant increase in quality and quantity of Next-Generationsequencing data necessitates a parallel growth in sample preparationand a scalable tracking system. The Broad Institute’s Illumina SequencingPlatform handles a variety of applications and comprises Illumina’s latesthardware, software and kit releases, and a high-throughput samplepreparation process. With our automated sample preparation and QCprocesses, we have been able to meet our increased capacity goals ofup to 3,840 libraries per week, and have reduced our rework rate to5% through attaining target cluster densities with high reproducibility.We continue to work closely with Illumina to develop the sequencingtechnology, using data to drive process improvements and exploringmethods to improve GC bias. Maximizing platform-wide efficiency ispossible through the implementation and continuous development oftools for process quality control and centralized communication, suchas our real-time run monitoring dashboard and JIRA tracking system.We were able to convert rapidly from GAIIxs to HiSeq2000s byestablishing and using an enterprise Knowledge Management system,with which we can efficiently accumulate and disseminate a changingknowledge base. All of these improvements are applicable to both theGA and HiSeq platforms.(S5-2) Science and Technology at a HighThroughput Genome CenterL. Fulton, R. Wilson, The Genome Center ProductionGroupThe Genome Center at Washington University School ofMedicine, St. Louis, MO, United StatesThe Genome Center (GC) at Washington University School of Medicinehas developed a state of the art genomics facility. Our scientists workon a variety of cutting edge projects with researchers from aroundthe world. These collaborative research projects lead to cutting edgeadvances in the field of genomics. The structural organization at theGC reflects these efforts and is centered around six major scientificareas: Transcriptome Sequencing, Genome Assembly, Whole GenomeSequencing, Human Microbiome, Human Genetics, and TargetedResequencing. These specific scientific areas are supported by onecentral data production pipeline. Attributes of this pipeline includedetailed sample screening protocols, sample barcoding capabilitiesthat allow for a broad range of sample cohorts, multiplatform dataproduction, and the ability to select from more than one method ofsequencing strategies. All of this is supported by one centralized LIMSgroup dedicated to maintaining and developing the data productioncapabilities. The technology development group investigates newtechniques and instrumentation prior to any changes in the main dataproduction pipeline. Only robust protocols and instrumentation areallowed into the data production pipeline. This strategy allows TheGenome Center to run a base data production pipeline while constantlyinfusing high quality advances. Sequence data for each project is sentinto an advanced analysis pipeline built to conduct a multitude ofassessments. When needed, validation (a second sequence event) canbe used to confirm variants detected by the analysis software.(S5-3) High-Throughput Next GenerationSequencing Methods and ApplicationsD. Muzny 1 , M. Wang 1 , I. Newsham 1 , Y.Q. Wu 1 , H. Dinh 1 ,C. Kovar 1 , J. Santibanez 1 , A. Sabo 1 , J. Reid 1 , M. Bainbridge 1 ,E. Boerwinkle 2 , T. Albert 3 , R. Gibbs 11Baylor College of Medicine, Human Genome SequencingCenter, Houston, TX, United States; 2 University of TexasHealth Science Center at Houston, School of Public Health,Houston, TX, United States; 3 Roche NimbleGen, Inc.,Madison, WI, United StatesSecond Generation high-throughput sequencing technologies haverevolutionized the genome sequencing applications and will ultimatelyhave great impact on personalized medicine. The increase in capacityof both the AB/Life Technologies SOLiD 4.0 and Illumina HiSeqinstrumentation and the ability of the platforms to multiplex sampleshas led to process innovations impacting many ongoing projectsat the HGSC. Applications have ranged from regional and wholeexome capture sequencing to the use of whole genome shotgun fordeep coverage and determining structural rearrangements. Internaladvancements have complemented the higher capacity instrumentationthrough the implementation of library automation, low DNA inputsamples, capture hybridization multiplexing and application of readmapping tools such as BFAST and BWA. Development of sample intakeprocedures, LIMS tracking and defined reporting metrics has enabledNexGen sequencing pipelines that can effectively deliver targetedand whole genome shotgun data for thousands of samples. Thesetechnical advancements to the pipeline have allowed us to achievea rate of ~1500 libraries/captures per month. To date the center hascompleted over 5000 exome and regional capture libraries for TheCancer Genome Atlas (TCGA), NIMH Autism, Cohorts for Heart andAging Research in Genomic Epidemiology (CHARGE-S) and 1000Genomes Project. Development of these applications and methods willbe discussed along with key data metrics, process management andpipeline organization.(S6) Strategies for Deep Mining of ComplexProtein Mixtures(S6-1) Coverage and Recovery of Upstream ProteinFractionation Methods in LC-MS/MS WorkflowsL.J. FosterCentre for High-Throughput Biology, The University of BritishColumbia, Vancouver, BC, CanadaThe proteome of any cell or even any subcellular fraction remainstoo complex for complete analysis by one dimension of liquidchromatography-tandem mass spectrometry (LC-MS/MS). Hence, toachieve greater depth of coverage for a proteome of interest, mostgroups routinely subfractionate the sample prior to LC-MS/MS sothat the material entering LC-MS/MS is less complex than the originalsample. Protein and/or peptide fractionation methods that biochemistshave used for decades, such as strong cation exchange chromatography(SCX), isoelectric focusing (IEF) and SDS-PAGE, are the most commonprefractionation methods used currently. There has, as yet, been nocomprehensive, controlled evaluation of the relative merits of thevarious methods, although some binary comparisons have been made.We will discuss the most popular methods for fractionating samples atboth the protein and peptide level, demonstrating quantitatively which40 • ABRF 2011 — Technologies to Enable Personalized Medicine