Contents GRCF Divisions...Abstract: Hallmarks of cancer initiation and progression are the...

The Genetic Resources Core Facility (GRCF) is a JHU service center including the Core Store and five Research Services: Cell Center and BioRepository; DNA Analysis Facility; Fragment Analysis Facility; High Throughput Sequencing Center and the SNP Center. Collectively, these divisions produce a number of products and services to assist researchers performing studies in molecular biology and genetics. For more information go to our website at http://grcf.jhmi.edu.

Contents

GRCF Divisions

Each of the GRCF’s six Divisions will have an exhibit table with representatives to answer questions.

Scientific Exhibitors

Nineteen of the GRCF’s Corporate Partners will have exhibit tables. Please visit their exhibits to learn about their products and services.

Seminar Directory

Twelve exciting seminars will be presented at this year’s event.

Seminar Schedule

The back cover has a complete schedule of the seminar offering.

GRCF Mission Statement To bring high quality, cost effective, research services and products to Investigators throughout the Johns Hopkins

Scientific Community

GRCF DivisionsGRCF Divisions

Core Store

The Core Store is a non-profit resource that offers appreciable savings and fast delivery of a wide variety of research products. The Core Store provides one-stop shopping, saving researchers both time and money. In addition to its product offering the store charges no shipping and handling fees and has free delivery to East Baltimore, Bayview & Homewood. There is also convenient 24/7 access to several hundred products via the Core Store 24/7 at these locations; Blalock 1026, CRB I B02A, Asthma & Allergy Building 1st floor.

SYMPOSIUM – March 13, 2012, Turner Concourse

Seminars Start at 9:00 a.m. and End at 2:15 p.m.

Exhibit Floor – 10:00 a.m. – 2:00 p.m.

Win an iPad2!

See details on

page 9

Keynote Address

Elliot H. Margulies, Ph.D, Director of Sequencing Applications, Illumina, Inc., will be featured.

Attend a Seminar

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Visit our website at http://grcf.jhmi.edu March 13, 2012, 9:00 a.m. – 2:15 p.m. p.m. p.m.

GRCF DivisionsGRCF Divisions

Center and BioRepository

The Cell Center and BioRepository specializes in blood processing procedures such as Buffy Coats, Plasma, and Serum separation. We are a leader in Epstein-‐Barr virus lymphocyte transformation and mammalian cell culture. These services expand into our large secure BioRepository facility. Other services available include Dry Ice and Biological shipping for our BioRepository clients.

The GRCF BioRepository is a dedicated facility to meet all of your long-‐term cryostorage needs. Located at Johns Hopkins, we offer a range of frozen storage conditions for sera, plasma, and viable cells. Convenient deposit and retrieval of cryopreserved specimens is possible twice daily from our Blalock 1017 laboratory. This facility is environmentally monitored 24-‐7 using the Rees monitoring system. Samples are tracked utilizing Barcode labeling and Freezerworks relational database.

DNA Analysis Facility (DAF)

• Sanger Sequencing with 24 hour urn around time • Pyrosequencing • Access to two 7900 Real Time PCR machines • Discounted pricing and fee shipping on oligos and assays from: Applied Biosystems, Bioneer, IDT, QIAGEN and

Sigma

Fragment Analysis Facility (FAF)

The Fragment Analysis Facility offers services for custom projects such as TaqMan SNP analysis, SNP discovery, sequencing (Sanger and Pyrosequencing), STR sizing, and whole genome amplification. The FAF also offers genomic DNA isolation, cell line authentication, mycoplasma testing, and plating and storage of DNA samples.

High Throughput Sequencing Center (HTS)

At the GRCF HTS Center, in conjunction with the Center for Inherited Disease Research, our goal is to provide the research community at Johns Hopkins University access to high throughput sequencing platforms. We currently feature Illumina HiSeq2000 sequencers.

We currently support:

• Sequencing of indexed libraries, which allows multiplexing of multiple samples per lane, at no extra charge • Genomic, RNAseq, ChIPseq, methylation, de novo, and DGE sequencing • Free consultation and analysis • Simple, per lane pricing • End-‐to-‐end service for targeted resequencing using Agilent's SureSelect All Exon Kit or custom targeted kits

ranging from 500kb to 6.8Mb and greater

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Scienti f ic ExhibitorsScienti f ic Exhibitors

Agilent Technologies

Bio-Rad Laboratories

Cell Signaling Technology

Complete Genomics, Inc.

Corning Mediatech

GE Healthcare Life Sciences

Integrated DNA Technologies

Illumina, Inc.

Knome, Inc.

Life Technologies, Inc.

New England Biolabs, Inc.

PerkinElmer, Inc.

Promega Corporation

QIAGEN, Inc.

Quality Biological, Inc.

Roche Applied Science

Sigma-Aldrich

Thermo Fisher, Hyclone

Thermo Scientific, Fermentas

Keynote AddressKeynote Address –– 12 p.m. 12 p.m.

Title: “Increased accuracy and utility of whole-genome sequencing analyses for biomedical interpretations”

Room: Tilghman Auditorium Time: 12 p.m Sponsor: Illumina, Inc.

Presented by: Elliott H. Margulies, Ph.D., Director of Sequencing Applications, Illumina, Inc.

Abstract: Producing the most accurate and comprehensive representation of an individual’s genome is critical for the future of personalized healthcare and genomic medicine. As the data generation component of whole-genome sequencing becomes more rapid and routine, attention to upstream and downstream processes is becoming increasingly important for diagnostic and prognostic use. For example, the ability to quickly capture whole genome information from very small quantities of DNA expands the utility of DNA sequencing to investigate a broader scope of diseases and applications Additionally, improving on variant calling accuracy and annotating genomes with actionable information in coding and non-coding parts of the genome further enables physicians and scientists to re-focus on the biology rather than the technology. Highlighted examples of our progress in these areas and the implications for personalized medicine will be discussed.

SNP Center

High throughput Genotyping on the Illumina platform. A variety of arrays available ranging from custom SNP assays to Genome Wide Association chips.

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Seminar DirectorySeminar Directory –– 9:00 a.m. 9:00 a.m.

Title: “Targeted Genome Editing in Eukaryotic Systems using CompoZr Zinc Finger Nucleases”

Room: Tilghman Auditorium Time: 9:00 a.m. Sponsor: Sigma Aldrich

Presented by: Joe Frangipane, Ph.D., Field Applications Specialist

Abstract: Targeted genome engineering in cells and animals is of enormous potential across basic research, drug-discovery and genomic medicine. To this end, Sigma-Aldrich has commercialized a novel technology that enables high-frequency genome editing using engineered zinc finger nucleases (ZFNs). Within these chimeric proteins, the DNA-binding specificity of the zinc finger protein determines the site of nuclease action. These ZFNs can recognize and bind to a specified locus and cause a double-strand break in the target DNA with high efficiency and base-pair precision. The cell then employs one of two natural DNA repair processes to heal the targeted break, resulting in genomic editing at that locus.

ZFNs allow researchers to achieve gene deletion, gene correction or targeted gene addition within the genome of cell lines, stem cells and one-celled embryos. The speed and efficiency of this process has enabled the creation of transgenic knockout rats and mice from ZFN-edited embryos in as little as 10 weeks, without the use of traditional ES cell-based methods. We will present several examples of gene knockout and targeted integration using cell lines and stem cells, as well as the creation of transgenic animals expressing novel genes or gene knockouts using ZFN technology.

Title: “Digital PCR and the QuantStudio 12K Flex | Taking real-time PCR quantification of DNA and RNA to the next level”

Room: BRB-G03 Time: 9:00 a.m. Sponsor: Life Technologies, Inc.

Presented by: Marcia Slater, Sr. Gene Expression/Gene Variation Specialist

Abstract: The use of Digital PCR was first reported 20 years ago, but was limited in its utility due to the large reaction volumes used by PCR at the time. Digital PCR uses limiting dilutions and high replicate numbers to provide extreme precision for absolute quantification of nucleic acids targets.

The new QuantStudio 12k Flex Real-time PCR system as offers researchers the ability to swap blocks between standard volumes of 96-wells, 384-wells, TaqMan array cards. It also has the ability to run high density QS-OpenArray plates - an ideal solution for digital PCR.

When running QS-OpenArray plates, the QuantStudio 12k Flex Real-time PCR system can test over 12,000 wells per run. With their 33nl reaction volumes and higher numbers of wells, the OpenArray plates are making digital PCR a practical and cost-effective choice for PCR applications requiring the highest levels of precision.

Theory and applications of digital PCR will be reviewed. Considerations for selecting between traditional qPCR and digital PCR for gene expression studies, absolute quantification, miRNA profiling will be discussed.

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Title: ““Clonal evolution in blood cancers: the use of quantitative assessment in the investigation of pathologic cancer alleles”

Room: West Room Time: 9:00 a.m. Sponsor: DNA Analysis Facility

Presented by: Alison Moliterno, MD, Associate Professor JHU

Abstract: Hallmarks of cancer initiation and progression are the development of acquired somatic mutation in pivotal genes which control growth or differentiation, in a sequential, stepwise fashion. Dr. Moliterno will discuss the application of pyrosequencing assays designed to track cancer alleles and their association with disease evolution in the chronic myeloproliferative neoplasms.

Title: “Applications for Large Scale Whole Genome Sequencing”

Room: Tilghman Auditiorium Time: 10:00 a.m. Sponsor: Complete Genomics

Presented by: Steve Lincoln, VP, Scientific Applications, Complete Genomics, Mountain View, California, USA

Abstract: Complete Genomics has developed a novel, highly accurate (99.9997%), high-throughput, low-cost, human genome sequencing technology based on submicron patterned arrays and unchained base reads (Science 327, 78, 2010). These advances reduce reagent consumption and imaging time and thus enable low-cost, large-scale human genome sequencing with very high coverage depth. Scientific studies using this technology include discovery of somatic variation in tumor and matched normal specimens (for ex. Lee, Nature 465, 473, 2010) and studies of affected individuals with simple or complex traits (for ex. Roach, Science 328, 636, 2010). Recently analysis methods have been developed which improve false positive and false negative rates in detecting SNPs and indels, and which also allow for detection of larger variations including copy number and structural variants. With well over 4,000 human genomes deeply sequenced using these methods we will discuss examples of the application of whole human genome sequencing in various study designs for medical research.

Title: “Cost Effective Research Tools and Solutions”

Room: Miles Room Time: 10:00 a.m. Sponsor: Roche Applied Science

Presented by: Dwayne W. Dexter, PhD

Abstract: Challenges in research funding continue to impact both academic and pharmaceutical research programs, while there is greater pressure to reduce delivery timelines of publications or new therapeutics. Roche Applied Sciences continues to build on more than a half century of expertise in delivering cost-effective research products and services to help advance discovery. Our extensive portfolio includes advanced systems and reagents for genomics, molecular biology, and cellular analysis. Whether you need an integrated instrument and reagent solution, novel kits or assays, or expert technical support, you can continue to count on quality products for results you can trust.

Seminar DirectorySeminar Directory –– 9 a.m. & 10 a.m. 9 a.m. & 10 a.m.

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Title: “The Many Applications of the MiSeq Personal Sequencing System”

Room: BRB-G03 Time: 10:00 a.m. Sponsor: Illumina, Inc.

Presented by: Omaya Al-Alwar, PhD

Abstract: The MiSeq system is a fully integrated sequencing ecosystem, in a compact and economical instrument. For results in hours, MiSeq uses TruSeq, Illumina's reversible terminator-based sequencing by synthesis chemistry to deliver the fastest time to answer. Perform the widest breadth of sequencing applications, including highly multiplexed PCR amplicon sequencing, small genome resequencing and de novo sequencing, small RNA sequencing, library quality control, and 16S metagenomics, with automated, on-instrument or cloud-based data analysis workflows to take your research further.

Title: “ New V3 Western Workflow for Protein Analysis – Visualize / Validate / Verify”

Room: West Room Time: 10:00 a.m. Sponsor: Bio-Rad Laboratories

Presented by: Steve Freeby, Bio-Rad Laboratories Product Manager

Abstract: Improving the Speed and Reliability of Western Blotting —New Stain-Free Technology Ensures Quality and Offers an Alternative Protein Normalization Method for Western Blot Analysis. Achieving sample quality assurance with unsurpassed speed and reproducibility with new gels, a new blotter, and unique imaging options– Bringing best-in-class performance to traditional methods. Over the last year, Bio-Rad Laboratories has launched several new products that provide researchers with unprecedented speed, performance and reliability to address the quality of the protein sample and transfer before proceeding to the detection steps in Western blotting. This seminar will establish how long shelf-life TGX™ Stain-Free™ gels, the award-winning Gel Doc™ EZ, the new ChemiDoc™ MP, and the Trans-Blot® Turbo™ Transfer System work as a product suite to provide protein separation, transfer and verification in 30 minutes with built in quality control steps. This portfolio provides the researcher with quality assurance to complete Western blots with confidence. Learn how Stain-Free technology can be used as an alternative method to performing total protein normalization for western blot analysis.

Seminar DirectorySeminar Directory -‐-‐10 a.m.10 a.m.

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SeminarSeminar Directory Directory –– 11:00 a.m. 11:00 a.m.

Title: “The whole genome interpretation company: Finding the genetic basis of human disease and drug response”

Room: Tilghman Auditorium Time: 11 a.m. Sponsor: Knome, Inc.

Presented by: Nathaniel Pearson, PhD/Director of Research Knome, Inc.

Abstract: Knome interprets whole genomes and exomes to find the genetic basis of human disease and drug response. Since our launch in 2007 as the first commercial organization to offer human whole genome interpretation services, our sole focus has been on interpreting genomes. Due to this focus, we believe we have more real-world experience than any other organization in managing through the massive technical and operational challenges associated with interpreting whole genomes. Our main offering is knomeDISCOVERY, an end-to-end solution that includes next generation sequencing and in-depth interpretation. Solution areas include rare disease, common disease, cancer, and drug response. knomeDISCOVERY is an end-to-end solution that includes both whole genome sequencing and in-depth interpretation. Enabling our service is kGAP, a genome interpretation engine that automates the identification of the genetic variants that govern disease or drug response. Built to annotate, compare, and distill many genomes at once, kGAP completes in a day what would otherwise require months of effort and a team of specialists.

Title: “Analysis of Post-Translational Modifications in Cellular Signaling”

Room: Miles Room Time: 11 a.m. Sponsor: Cell Signaling Technolgy

Presented by: Jeff Silva, PhD

Abstract: Cellular signaling is predominantly mediated by changes in the post-translational modification (PTM) status of cellular proteins. However, the relatively low level of PTMs in the cellular protein pool limits the global analysis of PTMs at the proteomic level. To overcome this limitation Cell Signaling Technology, Inc. has developed the PTMScan® method, an antibody-based peptide enrichment strategy combined with tandem mass spectrometry, allowing the quantitative profiling of PTMs, including phosphorylation, ubiquitination and acetylation, from cell and tissue lysates. New innovations, applications, and advancements in PTMScan® method will be discussed.

Title: “A genome-wide gene-environment interaction study in autism”

Room: BRB-G03 Time: 11 a.m. Sponsor: SNP Center

Presented by: Christine Ladd-Acosta, Ph.D.,Postdoctoral Fellow, Department of Epidemiology, Johns Hopkins School of Public Health

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Abstract: Autism is a common neurodevelopmental disorder characterized clinically by three key features: incomplete language development; inability to respond appropriately to social stimuli; and limited or restricted interests, with considerable heterogeneity among children. Despite high heritability estimates for autism, genetic variants identified to date account for a small portion of total heritable risk and none have been definitively confirmed. One plausible explanation for the heterogeneity and genetic complexity in autism is that environmental factors also contribute to risk. In fact, several recent studies suggest environmental factors, especially in utero exposures, play a larger role in autism risk than previously thought. Thus, to fully understand the contribution of environmental and genetic factors to autism risk, genome-wide studies integrating genetic and environmental factors are needed. Both technical and practical limitations have hindered this type of integrated study in the past. However, the recent development of two new analytic methods coupled with the recent availability of environmental exposure, genetic, and phenotypic information from the Study to Explore Early Development (SEED) now make a gene-environment interaction (GxE) study in autism possible. Here, we sought to identify genetic and environmental factors that together influence risk for autism by performing the first genome-wide gene-environment interaction study (GEWIS) in autism. More specifically, we aim to identify SNPs whose effects on autism risk vary across levels of selected prenatal environmental exposures, including maternal use of tobacco, alcohol, β-2 adrenergic receptor agonist or antidepressant medications, and maternal infection. To achieve these goals we sent DNA samples from 968 SEED children to the Johns Hopkins University SNP Center for processing on the Illumina HumanOmni1-Quad BeadChip, measuring genotypes at over 1 million loci per individual. Several data quality control measures were implemented and potential genotyping errors at both the sample and SNP level were removed, leaving 878 samples (356 cases and 522 controls) and over 800,000 SNPs for GxE analysis. Results from our GEWIS analysis, currently underway, will be presented at the symposium.

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Title: “3rd Generation Real-‐Time PCR: Digital PCR enables absolute quantitation of nucleic acids”

Room: West Room Time: 11 a.m. Sponsor: Bio-‐Rad Laboratories

Presented by: John Chuckalovcak, Bio-‐Rad Laboratories Field Application Scientist

Abstract: Introducing a High-‐Throughput Droplet Digital™ PCR System for Copy Number Variation (CNV), detection of Rare Sequences, Single Cell Analysis, Next Generation Sequencing and Gene Expression. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. This talk will provide a technical overview of a commercially available droplet digital PCR (ddPCR™) system that enables processing of 2 million PCR reactions using conventional TaqMan assays with a 96-‐well plate workflow. Data from key applications will be presented to demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-‐time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100,000-‐fold excess of wildtype background. Third, we demonstrate the power of absolute quantitation for applications including sequencing library quantitation and measuring miRNAs in plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.

Seminar Directory Seminar Directory –– 11:00 a.m. 11:00 a.m.

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Seminar Directory - 1:15 p.m. Title: “PGM for Genes. Proton for Genomes. Sequencing for everyone”

Room: Tilghman Auditorium Time: 1:15 p.m. Sponsor: Life Technologies

Presented by: Jeremy Stuart

Abstract: Last year, Ion Torrent introduced the world's first post-‐light sequencing platform by which biological processes are translated directly into digital information using semiconductors. During the course of 2011, Ion's Personal Genome Machine achieved a 100-‐fold increase in throughput and an expanding portfolio of applications, including RNA-‐seq and multiplexed amplicon sequencing. Ion Torrent is now pleased to introduce the Proton system, which will deliver exome and whole genome sequencing within a single day at a price of $500 and $1000 respectively. Technology and applications of both the PGM and Proton systems will be discussed, along with application-‐specific and performance data. It's Watson meets Moore, which could greatly impact the field of translational and molecular medicine.

Genetic Resources Core Symposium Promotions

Seminar Attendance Promotion: Win a chance to get an iPad2 or a GRCF 20 oz tumbler! Here’s how you can participate. To qualify to enter you:

1.Must attend from start to end one of the 13 Seminars on the Core Symposium’s schedule

2.Complete an entry card and at the end of the seminar turn it into the Core representative staffing the seminar.

3.Only one entry per person/per seminar from 10 a.m. – 2:15 p.m.

4.Two entries will be permitted per person/per seminar for ALL 9:00 a.m. seminars.

Entry cards may be obtained prior to the start of each seminar or prior to the Symposium at any of the six GRCF Divisions.

Door Prizes: To be eligible to participate in the Door Prize contest please sign in at the Symposium Registration Desk.

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CORE SYMPOSIUM SEMINAR SCHEDULE CORE SYMPOSIUM SEMINAR SCHEDULE

Turner Concourse, March 13, 2012 Turner Concourse, March 13, 2012

West Room

DNA Analysis Facility "Clonal evolution in blood

cancers: the use of quantitative assessment in

the investigation of pathologic cancer alleles"

Bio-Rad New V3 Western

Workflow for Protein Analysis – Visualize /

Validate / Verify

Bio-Rad 3rd Generation Real-Time PCR: Digital PCR enables absolute quantitation of

nucleic acids

DARK

DARK

BRB-G03

Life Technologies Digital PCR and the

QuantStudio 12K Flex | Taking real-time PCR

quantification of DNA and RNA to the next level

Illumina The Many Applications of

the MiSeq Personal Sequencing System

SNP Center "A genome-wide gene-environment interaction

study in autism."

DARK

DARK

Miles Room

DARK

Roche Cost Effective Research

Tools and Solutions

Cell Signaling “Analysis of Post-

Translational Modifications in Cellular Signaling”

DARK

DARK

Tilghman Auditorium

Sigma Aldrich Targeted Genome Editing

in Eukaryotic Systems using CompoZr Zinc

Finger Nucleases

Complete Genomics Applications for Large Scale Whole Genome

Sequencing

Knome The whole genome

interpretation company: Finding the genetic basis

of human disease and drug response

Illumina Increased accuracy and utility of whole-genome sequencing analyses for

biomedical interpretations

Life Technologies PGM for Genes. Proton

for Genomes. Sequencing for everyone

10.-10:50. a.m.

11-11:50 a.m.

9-9:50 a.m.

12 -1:00 p.m. KEYNOTE ADDRESS

1:15 p.m. Bonus Session

Contents GRCF Divisions...Abstract: Hallmarks of cancer initiation and progression are the...

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