Part B: Genome Editing for Functional Genomics Screens Conference - Part 2 header

About This Conference:

Cambridge Healthtech Institute’s eleventh annual conference on Genome Editing for Functional Genomics Screens will bring together experts to try to figure out how and where genome editing can be best applied in functional screening. What are the different tools and reagents that can be used, and based on those choices what are the downstream challenges encountered with assay design and data analysis? What are the strengths and limitations of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) -based screens, when compared to siRNA and shRNA screens? Can some of the lessons learned from the early days of RNAi screening, help with setting up these newer screens? Screening experts will share their experiences leveraging the utility of gene editing for creating cell lines and models for a wide range of applications and screening platforms.

Thursday, October 9

11:30 am Registration

1:00 pm Plenary Keynote Program 

Chas BountraChas Bountra, Ph.D., Professor of Translational Medicine & Head, Structural Genomics Consortium, University of Oxford

Martin TolarMartin Tolar, M.D., Ph.D., Founder, President & CEO, Alzheon, Inc.

Andrew L. Hopkins, Andrew L. Hopkins, D.Phil, FRSC, FSB, Chair of Medicinal Informatics and SULSA Research Professor of Translational Biology, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee

2:45 Refreshment Break in the Exhibit Hall with Poster Viewing


3:45 Chairperson’s Opening Remarks

Christophe Echeverri, Ph.D., CEO & CSO, Cenix BioScience USA, Inc.

3:55 Functional Dissection of Coding and Long Non-coding Transcripts in Pluripotent Cells

Frank Buchholz, Ph.D., Professor, Medical Systems Biology, UCC, University Hospital and Medical Faculty Carl Gustav Carus, Technische Uuniversitat Dresden

Pluripotent cells can be isolated and cultured from pre- and post implantation embryos. We present data from genome-wide RNAi screens for protein coding and long non-coding transcripts coupled with genetic interaction, protein localization and protein level dependency studies to delineate connectivity between the factors that control the pluripotent program in ES and EpiSCs. The data reveals a systematic view on these two closely related stem cells.

4:25 First Screens Using a LncRNA siRNA Library: Shedding Some Light on the Dark Matter of the Transcriptome

Eugen Buehler, Ph.D., Group Leader, Informatics, National Center for Advancing Translational Sciences National Institutes of Health

Recently, commercial RNAi libraries have become available to target long non-coding RNAs. Using screening results of one of these libraries in several assays that we have previously interrogated using a conventional library, we can begin to compare frequencies of detection for coding versus non-coding siRNA libraries. We will discuss the implications of these results for the functional activity of lncRNAs and the cost/benefit of screening for functional members of this of genes.

4:55 Sensor-Based shRNA-mir Reagents for More Effective RNAi Screens

Gwen D. Fewell, Ph.D., Co-Founder & Chief Commercial Officer, transOMIC
New shERWOOD algorithm, based on a high throughput sensor assay, provides potent shRNA designs for single copy gene-knockdown. When combined with an improved microRNA scaffold, this algorithm provides consistently effective shRNAs, making hit analysis in multiplexed RNAi screens more straightforward. Here we present the advantages of employing next generation shRNA libraries, designed using these strategies, in gene knockdown assays including multiplexed RNAi screens.  

5:10 Sponsored Presentation (Opportunity Available)

5:25 Coffee Break in the Foyer

5:40 Using ncRNAs to Identify Cancer Cell Vulnerabilities

Alexander Pertsemlidis, Ph.D., Associate Professor, Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio

In an unbiased and comprehensive approach, we have combined a high-throughput screening platform with a library of inhibitors of short and long non-coding RNAs. We use this platform to identify ncRNAs that reduce cell viability and specifically sensitize cells to microtubule-targeting agents. Regulatory targets of candidate ncRNAs are identified and the response of cancer cells to perturbations in ncRNA levels are assessed through a combination of in vitro, in silico and in vivo approaches.

6:10 TECHNOLOGY PANEL: Tools for Next-Generation Functional Genomics Screens

Moderator: Christophe Echeverri, Ph.D., CEO & CSO, Cenix BioScience USA, Inc.


Paul Diehl, Ph.D., Director, Business Development, Cellecta, Inc.

Gwen D. Fewell, Ph.D., Chief Commercial Officer, TransOMIC Technologies, Inc.

Alex Amiet, Senior Product Manager, Dharmacon, part of GE Healthcare


This panel will bring together 4-5 technical experts from leading technology and service companies to discuss screening trends and improvements in assay platforms and reagents that users can expect to see in the near future.

(Opportunities Available for Sponsoring Panelists)

Topics to be covered:

-For what types of applications will emerging CRISPR-Cas9 capabilities replace RNAi, as opposed to complementing it?

-What efforts are being made to update RNAi reagents to help users tackle off-target effects?

-To what degree are vendors making efforts to address the risk of off-target effects with CRISPR-Cas9 reagents?

-Are there plans to build and offer genome-scale CRISPR-Cas9 libraries only for pooled, selection-based screening or also for arrayed screening?

6:40 Close of Day

7:00 Dinner Short Course: Setting Up Effective Functional Screens Using 3D Cultures (SC10)*

*Separate registration required

Friday, October 10

7:30 am Registration

8:00 Interactive Breakfast Breakout Discussion Groups

This interactive session provides conference delegates and speakers an opportunity to choose a specific roundtable discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion.

RNAi and Gene Editing in Pluripotent Stem Cells

Ralph J. Garippa, Ph.D., Director, RNAi Core Facility, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center

Danwei Huangfu, Ph.D., Assistant Professor, Developmental Biology, Memorial Sloan-Kettering Cancer Center

  • Design and use of stem cell-based screens
  • Selecting appropriate cell models for high throughput screening 
  • Selecting the right technology and protocol for gene editing

Phenotypic Screens for Drug Discovery

Jing Li, Ph.D., Director of Genomics and Phenotypic Screening, Merck Research Laboratories

  • People’s view on phenotypic drug discovery 
  • What are some of compelling phenotypes suitable for phenotypic drug discovery 
  • Robust assays to identify compounds that modulate the phenotype (both in vitro and in vivo) 
  • Hit finding enabled by flexible, high-throughput screening systems and appropriate chemical libraries 
  • Target identification approaches for understanding underlying mechanism of action 

Putting shRNA and CRISPR Screens to The Best Use

Michael Bassik, Ph.D., Assistant Professor, Department of Genetics, Stanford University
Roderick Beijersbergen, Ph.D., Group Leader, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute

  • The feasibility of large scale genome wide screening 
  • Selecting the most suitable technology for your screening model 
  • Cross-platform validation strategies 

9:00 Chairperson’s Remarks

Ralph J. Garippa, Ph.D., Director, RNAi Core Facility, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center

9:10 Creating a State-of-the-Art Pipeline for RNAi and Gene Editing in an Academic Setting

Ralph J. Garippa, Ph.D., Director, RNAi Core Facility, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center

As a multi-faceted core lab, we have instituted a broad genomics platform to address biological questions using the tools of RNAi interference and gene editing via the CRISPR-Cas9 system. Screening is offered in both pooled and arrayed formats, with subsequent readouts via HCS, HTS, FACS or NGS deconvolution. Here we present a series of case studies highlighting the flexible utility of this platform, and innovative methodologies to improve and enhance interpretation of RNAi screening results.

9:40 Exploring the Secretory Pathway Using ER-Trafficking Toxins, High-Complexity shRNA Libraries, and Genetic Interaction Maps

Michael Bassik, Ph.D., Assistant Professor, Department of Genetics, Stanford University

We have developed high-complexity shRNA libraries (25 shRNAs/gene) that greatly reduce false negatives/false positives for RNAi screens, and have adapted these libraries to knock down gene pairs to perform systematic genetic interaction maps in mammalian cells. We are using this strategy for functional genomics efforts and identification of novel drug targets, and are continuing to develop our screening platform using the CRISPR/Cas9 system.

10:10 Coffee Break in the Exhibit Hall with Poster Viewing


10:55 FEATURED PRESENTATION: Analyses of Signaling Networks in Drosophila

NorbertPerrimonNorbert Perrimon, Ph.D., Professor, Department of Genetics, Harvard Medical School and Investigator, Howard Hughes Medical Institute

I will describe how our laboratory is applying the tools of CRISPR genome engineering to analyze the structure and spatio-temporal regulation of signaling pathways both in tissue culture cells and in vivo.

11:25 FEATURED PRESENTATION: Developments in Mammalian Functional Genomics Tools and Applications

DavidRootDavid Root, Ph.D., Director, RNAi Platform and Project Leader, The RNAi Consortium, The Broad Institute of MIT and Harvard

11:55 EXPERT PANEL: How to Best Utilize Gene Editing for Functional Genomics Screens

Moderator: Christophe Echeverri, Ph.D., CEO & CSO, Cenix BioScience USA, Inc.

Panelist: Session Speakers

12:25 pm Driving Integrated Solutions for Functional Genomics – CRISPRs, TALENs and RNAi
Nitin Puri, Ph.D., Associate Director, Product Management, Gene Silencing & Gene Editing, Life Technologies, Brand of Thermo Fisher
CRISPR technology has revolutionized functional genomics and how the field is approaching discovery to validation of novel drug targets. In this highlight, we will share efforts for a holistic approach in adoption of this technology along with TALENs and RNAi. 

12:40 Rewriting the Genome: Gene Construction and Genome Modification with gBlocks® Gene Fragments

Adam Clore, Ph.D., Manager, Synthetic Biology Design, Integrated DNA Technologies
The development of the CRISPR/CAS9 system in conjunction with rapid and inexpensive DNA synthesis and Fragment construction has created opportunities in genome design and manipulation on an unprecedented scale. This talk will describe proven methods to create gene deletions, insertions, and modulation of gene regulation using gBlocks® Gene Fragments with CRISPR/CAS9 systems. 

12:55 Session Break

1:05 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:45 Session Break


1:55 Chairperson’s Remarks

2:00 Genome-Scale CRISPR Knock-Out Screen in Human Cancer and Stem Cells

Neville Sanjana, Ph.D., Simons Postdoctoral Fellow, Laboratory of Dr. Feng Zhang, Broad Institute and the Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology

The simplicity of programming the CRISPR/ Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on a genome-wide scale. We show that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 human genes enables both negative and positive selection. When compared to shRNA knock-down, CRISPR reagents are more consistent in their ability to knock-out (not knock-down) genes, resulting in a greater number of validated hits.

2:30 Functional Genomics, Genomics and Clinical Need: The Successful Output of Large Genetic Screens for Novel Treatment Combinations

Roderick Beijersbergen, Ph.D., Group Leader, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute

Several screening technologies exist that allow for large scale perturbation of gene expression in mammalian cells including siRNA, shRNA, gene traps and CRISPR based gene editing. In particular, pooled screening approaches have been applied widely to identify genes that are lethal under specific circumstances, e.g. in combination with a drug treatment or only in the context of disease specific genetic alterations. We will discuss the challenges associated with these efforts, their performance and their power in the identification of novel treatment combinations.

3:00 Refreshment Break in the Exhibit Hall with Poster Viewing

3:30 Functional Human Genetics through Genome Editing in Human Embryonic Stem Cells

Danwei Huangfu, Ph.D., Assistant Professor, Developmental Biology, Memorial Sloan-Kettering Cancer Center

Through applying TALENs and CRISPRs to human embryonic stem cells (hESCs), we have generated knockout hESCs for 8 of the 10 neonatal diabetes-associate transcription factors identified to date. Mutations in these genes may also contribute to juvenile and adult onset diabetes. Through directed differentiation of these mutant hESCs, our studies are beginning to shed light on both conserved and human-specific mechanisms of pancreatic development and neonatal diabetes.

4:00 A Computational Algorithm to Predict shRNA Potency

Simon Knott, Ph.D., Postdoctoral Fellow, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory

To date, no established method has emerged to identify effective shRNAs. Using a multiplexed assay we have generated over ~250,000 shRNA efficacy data points. Using these data, we developed shERWOOD, an algorithm capable of predicting, for any shRNA, the likelihood that it will elicit potent target knockdown. Combined with additional shRNA design strategies, shERWOOD allows the ab initio identification of potent shRNAs that target, the majority of each gene’s multiple transcripts.

4:30 Phenotypic Screening: Opportunities and Challenges

Jing Li, Ph.D., Director, Genomics and Phenotypic Screening, Merck Research Laboratories

In the first-in-class drug category, phenotypic screens have yielded more approved drugs than target-centric approach during 1999-2008. The lack of chemistry support and the immaturity of technologiess for protein target identification have contributed to the low success rate for phenotypic screens. Recent advances in affinity capture, quantitative mass spectrometry, and chemoinformatics greatly improve the identification of underlying protein targets. With the lessons learnt, the possibility of successfully applying phenotypic screens in drug discovery can improve significantly.

5:00 Close of Conference

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2014 Discovery on Target Brochure  

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The exhibit hall was sold out in 2013, so please contact us early to reserve your place. To customize your sponsorship or exhibit package for 2014, contact:

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2014 Discovery On Target CAG 



October 8 – 9

Targeting Epigenetic Readers and
Chromatin Remodelers

Targeting the Ubiquitin Proteasome System  

Big Data Analytics and Solutions  

GPCR-Based Drug Discovery  

RNAi for Functional Genomics Screening
– Part 1

Protein-Protein Interactions as Drug Targets  

Antibodies Against Membrane Protein Targets
– Part 1

October 9 – 10

Targeting Histone Methyltransferases and Demethylases  

Screening Drug Transporter Proteins  

Maximizing Efficiency in Discovery  

GPCR-Targeted Therapeutics  

Genome Editing for Functional Genomics
Screens – Part 2

Cancer Metabolism  

Antibodies Against Membrane Protein Targets
– Part 2


October 7

Next Generation Histone Deacetylase Inhibitors  


October 7

SC1: Designing Scalable Software Systems for Big Data Analytics  

SC2: Approaches for Biologically-Relevant Chemical Diversity  

SC3: Setting Up Effective RNAi Screens: From Design to Data to Validation  

SC4: Targeting Protein-Protein Interactions  

SC5: GPCR Structure-Based Drug Discovery  

SC6: Advances in Metagenomic Drug Discovery for New Anti-Infective Agents  

SC7: Targeting of GPCRs with Monoclonal Antibodies  

SC8: A Primer to Gene Editing: Tools and Applications  

SC9: Introduction to Targeted Covalent Inhibitors  

October 9

SC10: Setting Up Effective Functional Screens Using 3D Cell Cultures  

SC11: Integration of BDDCS and Extended Clearance Principles  

SC12: Introduction to Allosteric Modulators and Biased Ligands of GPCRs  

SC13: Introduction to Drug Metabolism