POSTER SESSION ABSTRACTS
`
`ABRF 2011
`
`resources. ABRF Affiliates
`facilities and biomolecular
`are special interest organizations that are autonomous from
`the ABRF, have common and complementary interests with
`the ABRF, and have the goal of developing a collaborative
`relationship with the ABRF. Please join us for the ABRF
`Affiliates and Chapters Open Mic Session from 6:00 pm to
`6:45 pm on Sunday.
`
`115
`The Midwest Association of Core Directors
`W. Hendrickson1, P. Hockberger2
`1University of Illinois, Chicago, IL, United States;
`2Northwestern University, Evanston, IL, United States
`The Midwest Association of Core Directors (MWACD)
`was organized in 2010 by a group of scientists at 6 different
`institutions to foster closer interactions among directors and
`managers of core facilities throughout the Central Plains.
`The organization shares the same goals as ABRF, and it has
`applied to become a chapter of ABRF. The MWACD differs
`from ABRF only in that its focus is on regional matters
`rather than on issues of national concern. Towards this goal,
`the first annual meeting of the MWACD took place on
`October 21–23, 2010, at the Crowne Plaza Hotel in Chi-
`cago. The goal of the meeting was to provide an opportunity
`for networking among core directors and managers, to en-
`able interactions with colleagues, sharing of technical advice,
`and discussions of continuing challenges associated with the
`operation of shared research resources and technologies.
`Keynote presentations were delivered by leaders of NIH-
`NCRR and FASEB, and there were panel discussions on
`networking, bioinformatics, and information management
`systems. There was a poster session, vendor exhibits, and
`breakout sessions on 8 different core-related topics. The
`meeting was attended by 120 researchers and supported by
`17 corporate and not-for-profit organizations.
`
`116
`Automated Isolation of Genomic DNA from Large
`Volumes of Whole Blood
`E. Vincent1, S. Krueger1, J. Kennedy2,
`S. Lee2, C. Helt1, A. Bonk2, C. Cowan1
`1Promega Corporation, Madison, WI, United States;
`2Hamilton Robotics, Reno, NV, United States
`A key source for genomic DNA(gDNA) is blood drawn
`into a standard 10mL Vacutainer® tube. The Promega Reli-
`aPrep™ Large Volume HT gDNA Isolation Syste inte-
`grated on the Hamilton MICROLAB® STARplus liquid
`handling workstation provides a unique and dependable
`system for isolating genomic DNA from large volumes
`(3 mL–10 mL) of blood. The novel chemistry and instru-
`mentation resolve many challenges encountered when pro-
`cessing large-volume samples in a high-throughput format
`such as: loss of sample pellets during decanting of fluids,
`transport of full 50 mL tubes to various locations on a liquid
`handling robot, and manual re-suspension of final DNA
`pellets. Liquid handler resource constraints were removed by
`creation of a new accessory, the ReliaPrep HSM 32 LV
`instrument, which provides heating, shaking and magneti-
`zation of samples at one deck position. The combination of
`
`this device, the MICROLAB STARplus workstation and
`the ReliaPrep Large Volume HT gDNA Isolation System
`allows automated recovery of pure gDNA from up to 96 ten
`milliliter blood samples within 8 hours. We present verifi-
`cation studies demonstrating automated system perfor-
`mance. Comparisons between the ReliaPrep™ Large Vol-
`ume HT gDNA Isolation System and a
`standard
`precipitation-based method were made for duplicate blood
`samples from multiple donors. Yield, purity, and integrity of
`extracted gDNAwere assessed using UV absorbance spec-
`troscopy and gel electrophoresis. Genomic DNA yields from
`normal 10 mL whole blood samples were 200 400 ␮g
`(depending on white blood cell count) in an eluted volume
`of 1mL. Recovered DNA exhibited good purity with A260/
`A280 ratios greater than 1.7 and A260/A230 ratios between
`1.8 and 2.2. Isolated DNA was suitable for storage and was
`used in many downstream analysis applications. Results of
`genomic DNA purification from frozen (hemolysed) blood
`samples and blood collected using common anticoagulants
`(EDTA, heparin, citrate)are also compared to demonstrate
`the efficacy of the new system.
`
`117
`Overview of the Agilent Technologies SureSelectTM
`Target Enrichment System
`J. Ong1, A. Giuffre1, S. Joshi1, H. Ravi1,
`C. Pabon-Pena2, B. Novak2, M. Visitacion2,
`M. Hamady2, F. Useche2, B. Arezi3, B. Buehler3, E. Lin2,
`S. Hunt2, D. Roberts2, S. Happe1, E. Leproust2
`1Agilent Technologies, Cedar Creek, TX, United States;
`2Agilent Technologies, Santa Clara, CA, United States;
`3Agilent Technologies, La Jolla, CA, United States
`Next-generation DNA sequencing has revolutionized the
`discovery of rare polymorphisms, structural variants, and novel
`transcripts. To meet the demand for fast, cost-effective, and
`accurate genome analysis methods from small scale studies to
`large sample cohorts, Agilent Technologies has developed the
`SureSelect™ Target Enrichment System. Available for the
`Illumina, SOLiD, and 454 NGS sequencing platforms, Sure-
`Select is a highly robust, customizable, and scalable system that
`focuses analyses on specific genomic loci by in-solution hybrid
`capture. In addition, Agilent has introduced SureSelect XT for
`Illumina and SOLiD, which combines gDNA prep, library
`prep, and SureSelect Target Enrichment reagents in one com-
`plete kit. Both SureSelect and SureSelect XT demonstrate high
`performance, as measured by capture efficiency, uniformity,
`reproducibility, and SNP detection. We highlight the utility of
`the SureSelect system across a wide range of target sizes and
`genome complexity using pre-designed catalog libraries target-
`ing cancer gene sets, sequences encoding the kinome, and both
`human and mouse All Exon content. In addition, user-defined
`custom content can be easily developed using the Agilent
`eArray software with candidate variant coordinates as input.
`User-defined content can be manufactured on-demand as a
`custom SureSelect kit, or combined with pre-defined Agilent
`catalog content using the Plus option. We propose a novel
`approach for variant discovery - using SureSelect catalog de-
`signs to uncover candidate variants, followed by the design of
`smaller focused custom libraries for SNP validation and region
`profiling. By pooling many samples together per lane or slide,
`SureSelect multiplexing kits for Illumina and SOLiD enable
`
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`ABRF 2011
`
`POSTER SESSION ABSTRACTS
`
`validation across large sample cohorts with substantial cost
`savings. Accurate post target enrichment pooling is facilitated
`by the Agilent Bioanalyzer and QPCR NGS Library Quantifi-
`cation kits which ensure equal representation across samples.
`Further efficiencies are realized using the Bravo Automated
`Liquid Handling Platform to meet the need for parallel prepa-
`ration of multiplexed libraries.
`
`118
`Gene Synthesis: A Cost-Effective Alternative to
`Traditional Molecular Cloning
`A. Liao, M. Schwartz, H. Lo, J. Zhou, P. Yang
`GENEWIZ, Inc., South Plainfield, NJ, United States
`Gene synthesis is the process of synthesizing a gene in
`vitro without the need for initial template. Contrary to what
`many researchers’ beliefs, commercial gene synthesis service
`is quickly evolving to become a cost effective alternative to
`traditional cloning and other molecular biology procedures.
`The main reasons include: 1) Time savings: Traditional
`cloning involves a multi-step process that includes cloning
`strategy design, primer synthesis, PCR, gel extraction, bac-
`teria transformation, and other complex steps. This process
`requires considerable amount of time and human resource
`that gene synthesis does not. 2) Cost savings: In most cases,
`it costs less to order a synthetic gene than it does to order
`oligos, cloning kits, and DNA sequencing services. 3) En-
`hanced DNA performance: Gene synthesis allows for codon
`optimization which has been proven to increase the effi-
`ciency of protein expression. 4) Convenience: Without the
`need for a physical template and without design restrictions
`associated with the traditional cloning process, a researcher
`can get a gene of his/her choice by simply supplying the
`nucleotide sequence or amino acid sequence. GENEWIZ is
`a global CRO that provides a wide range of DNA services,
`including gene synthesis. GENEWIZ’s gene synthesis ser-
`vice features a 2-3 week turnaround and expert technical and
`project management support. This informational poster will
`present case studies of how GENEWIZ’s gene synthesis
`service benefited researchers who had previously relied on
`traditional molecular cloning for plasmid construction.
`
`119
`Nucleotide-Level Variant Analysis of Next-Generation
`Sequencing Data Using a Cloud-Based Data Analysis
`Pipeline
`B. Ganter, G. Asimenos, A. Sundquist
`DNAnexus, Palo Alto, CA, United States
`To demonstrate the flexibility of a cloud-based solution for
`analyzing disparate sets of next-generation sequencing data, we
`looked at carefully chosen samples across different populations
`from the 1,000 Genomes Project
`(www.1000genomes.
`org) and conducted an extensive analysis on two Chinese
`populations, the “Chinese in Beijing” (CHB) and the “Chi-
`nese in metropolitan Denver” (CHD), each consisting of 28
`exomes. Each dataset was uploaded into the system using
`raw data files acquired from the 1,000 Genomes Project.
`Using these data and a cloud-based data analysis pipeline, we
`performed a nucleotide-level variant analysis combined with
`a population allele frequency analysis across all samples for
`
`the two populations. To identify alleles that are significantly
`different across the two populations, a Pearson’s chi-square
`test was applied, which resulted in a total of 1.5 Mio SNPs,
`of which 84 were non-synonymous with a p-value of less
`than 0.01. Interestingly, the genes associated with non-
`synonymous variants of the Chinese in metropolitan Denver
`population were enriched for biological annotations such as
`endocrine system disorder, metabolic disease, cardiac fibro-
`sis, and inflammation (includes ZNF264, RPS6KA2,
`ROBO2, CRK, MUSK, CBL, CRK, and others). Further-
`more, genes usually associated with liver injury were also
`identified for this population, suggesting the liver is exposed
`to toxic agents more so in this population compared to the
`CHB population. The observed genomic differences in
`these two different Chinese populations living in different
`parts of the world hint towards a potential link between
`nutrition and different diseases (e.g. heart disease or meta-
`bolic diseases). Using this analysis as a case study, we will
`demonstrate how a scalable computational infrastructure
`can provide researchers and sequencing service providers
`alike, a cost effective and secure cloud-based computing
`platform as a powerful and collaborative technology solution
`for large scale sequence data analysis and management.
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`120
`Genome Technology Center at the NYU Langone
`Medical Center: New Support for Clinical and
`Translational Science
`J. Zavadil, S. Mische
`New York University Langone Medical Center, New York,
`NY, United States
`To significantly enhance support for clinical and transla-
`tional research within the framework of its CTSI, the NYU
`Langone Medical Center consolidated the Microarray and
`DNA Sequencing Cores into a new Genome Technology
`Center, a shared resource overseen by the Office for Collab-
`orative Science. The GTC’s team of 4 technical personnel
`and one faculty level director assists ⬎120 NYULMC labo-
`ratories in their basic, clinical and translational research. The
`Sequencing Unit operates 2 Illumina GAIIs, and a HiSeq
`sequencer will be added in Q1 2011. The GAII capacity is
`applied to research applications (ChIP-seq, small-RNA-seq
`and RIP-seq) and to identification of disease-related ge-
`nome-level structure changes and correlates (e.g. RNA-seq
`of cancer transcriptomes). GTC also has a Roche GS FLX
`System (454) used for de novo sequencing of microbial
`species and for amplicon sequencing in clinical genetics,
`patient microbiome diversity, etc. The Microarray Unit
`operates Affymetrix GeneChip system and high-capacity
`QPCR (ABI 7900HT) with automated plate setup and
`loading for gene and microRNA profiling and for SNP
`genotyping in clinical genetics. The GTC cooperates closely
`with the newly established Center for Health Informatics
`and Bioinformatics (CHIBI) supported by the NIH/NCRR
`CTSA Award. CHIBI provides an HPC facility for sequenc-
`ing and microarray data storage and offers a full range of
`informatics services. The GTC is committed to regional and
`nationwide collaborations with other Cores. GTC partici-
`pates in the activities of the Genomic Analysis and Technol-
`ogy Excellence (GATE) Working Group of the Academy for
`Medical Development and Collaboration (AMDeC), par-
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