Welcome to The Conference

View Final Agenda

Download Conference Documents (request your password, if you haven’t received it already).

The conference addressed applications of genome editing in a variety of biological systems, featuring:

• A high-impact, packed day of talks, discussions and  several hours of networking
• Oral presentations on latest developments in the field of genome editing by an international faculty of leading researchers from academia and industry
• Update on CRISPR patent wars
• Ethical debate
• Posters
• Trade exhibition
• Excellent networking opportunities, and a relaxed and friendly environment

Speakers  and Agenda (PDF)

(subject to change)

Monday 9th April 2018 | The Jarvis Doctorow Hall | St Edmund Hall | Oxford, UK

0830: Registration, networking and welcome coffee

Session 1: Chair  Marie-Christine Birling

0930: Dr Mark Behlke, Chief Scientist, Integrated DNA Technologies, USA

A novel multiplexed amplicon-based NGS method to assess CRISPR off-target editing

1000: Dr Cornelia Hampe, Scientific Support Specialist, Takara Bio Europe, Paris, France

CRISPR/Cas9 knockins – Get better specificity with single-stranded DNA

1030: Dr Gurpreet Balrey, Global Technical Applications Manager, Merck/Sigma Life Science, UK

New strategies & insights into CRISPR driven genome editing

1100: Refreshments, posters, exhibition and networking

Session 2: Chair Mark Behlke

1130: Dr Ryan Cawood, Founder and CEO, Oxford Genetics, Oxford, UK

Optimising CRISPR-Cas9 High-throughput Library Construction and Cell Line Engineering Strategies

1200: Professor Steven Pollard, The University of Edinburgh, Edinburgh, UK

An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein

1230: Dr Marie-Christine Birling, Head Associate of the Genetic Engineering and Model Validation Department, Group Leader Genetic Engineering, Institut Clinique de la Souris, ILLKIRCH Cedex, France

Generation of genomic structural variants and chromosomal manipulation by CRISPR/Cas9 genome editing in rodents

1300: Lunch, posters, exhibition and networking

Session 3: Chair Andrew Bassett

1350: Dr Andy Greenfield, Programme Leader, MRC Harwell Institute, Oxfordshire, UK

Editing mammalian genomes: ethical considerations

1420: Dr Philip Webber, UK and European Patent Attorney, Dehn Patent and Trade Mark Attorneys, Oxford, UK

CRISPR Patent Wars Update:  EPO rules that Broad’s first European patent is invalid

1440: Dr Annaleen Vermeulen, Senior Scientist II, Dharmacon, a Horizon Discovery Group Company, Lafayette, CO, USA

Using synthetic guide RNAs in CRISPR-mediated transcriptional activation to understand gene function

1510: Professor Douglas Higgs, FRS, University of Oxford, Oxford, UK

Editing a Globin Gene Enhancer as a General Approach to Ameliorating the Clinical Phenotype of β-Thalassaemia

1540: Refreshments, posters, exhibition and networking

Session 4: Chair Annaleen Vermeulen

1620: Dr Andrew Bassett, The Wellcome Trust Sanger Institute, Cambridge, UK

GenERA – using CRISPR to understand miRNA target site regulation

1650: Dr Lydia Teboul, MRC Harwell Institute, Oxfordshire, UK

TBA

1720: Dr Robin Ketteler, University College London, London, UK

The use of CRISPR to study Autophagy – Lessons learned

1750: Discussion and close

Posters

Knock-in and Correction of ALS-associated Mutations in Induced Pluripotent Stem Cells Using Footprint-Free Drug Selection

Jenny S Greig, Graham Cocks, Erin C Hedges, Chris E Shaw

Maurice Wohl Clinical Neuroscience Institute, King’s College London, Institute of Psychiatry, Psychology and Neuroscience. London, UK

In order to investigate the effects of specific ALS-associated mutations on disease-specific cell types, mutations in ARPP21 have been introduced into induced pluripotent stem cells (iPSCs) from a control line, and mutations in TARDBP have been corrected from patients with the disease. The genome editing was performed using CRISPR Cas9, introducing a drug selection cassette within a piggyBac transposon which is seamlessly removed after puromycin selection of edited clones. The edited lines can then be differentiated into various cell types such as motor neurons to model disease.

A fast and reliable method for detecting single base editing in clonal cell lines

Cornelia Hampe¹, Montse Morell², Tatiana Garachtchenko², Patrick Martin², Baz Smith², Michael Haugwitz², and Andrew Farmer²

¹ Takara Bio Europe SAS, 78100 Saint-Germain-en-Laye, France

² Takara Bio USA, Inc., Mountain View, CA 94043, USA

One of the most powerful applications of genome editing is the introduction of base changes in specific genomic sites that mimic single nucleotide polymorphisms (SNPs) related to human diseases or the introduction of stop codons to generate gene knockouts. However, screening a large number of clones to identify those containing the engineered base of interest is still a bottleneck, especially in the absence of a phenotypic readout. To address this need, we developed a SNP-detection method that allows quick screening of clones from a 96-well plate. The method is based on PCR amplification of the genomic target site, followed by an enzymatic assay with fluorescence readout. The overall workflow takes approximately four hours and any positive fluorescent signal is highly correlated with the successful introduction of the desired SNP. SNP detection using this method is independent of the engineered nucleotide substitution and the surrounding targeted genomic loci.

The in(del)s and outs of automated CRISPR-Cas9 genome editing: A robust CRISPR-Cas9 pipeline for high throughput mammalian genome editing

Jennifer A Harbottle, Daniel A Mestre, Kethan S Suvarna, Tom Payne, Ryan Cawood, Lee Spraggon

Oxford Genetics Ltd., The Oxford Science Park, Medawar 1, Oxford OX4 4GA, UK

CRISPR-Cas9 technology has revolutionised the field of genome editing and has enabled high efficiency mammalian cell engineering for a variety of downstream applications. The Gene Editing Technologies group at Oxford Genetics Ltd has developed an automated, streamlined pipeline for the generation of knock-out cell lines starting from the selection of efficient sgRNA through to NGS validation of edited clonal cell lines. Each step of the CRISPR-Cas9 workflow has been optimised and quality-assured for high throughput, large-scale demands, but is also flexible and adaptable to more specialised, small-scale projects. Characteristics of the host cell line are first established by qPCR to determine copy number of the target gene of interest, and Hamilton robotics-driven CellMetric® imaging software to ascertain growth kinetics. TIDE analysis of indel formation is performed to precisely determine the cleavage efficiency of the Cas9-sgRNA complex at the gene target site of interest. Once validated, the Cas9-sgRNA complex is delivered to the host cell line via an optimised delivery method that is suited to the cell type; this includes plasmid-based transfection, lentiviral transduction, and delivery of the nuclease as an active ribonucleoprotein complex. FACS enrichment of fluorescent protein-expressing cells from a transfected cell pool is used to maximise the frequency of targeted cells thereby decreasing the number of clones required for successful editing. Clone expansion and assurance of single cell clonality are monitored by the automated and systematic use of CellMetric® imaging software. Finally, clone screening for correctly targeted gene knock-out is performed by NGS genotyping and subsequent phenotype validation by Wes™ protein analysis. The Gene Editing Technologies platform at Oxford Genetics Ltd thus offers expertise and state-of-the-art resources and facilities for rapid high throughput and efficacious generation of CRISPR-Cas9 gene-edited clonal cell lines.

Targeted gene knockout of dUTPase using CRISPR/Cas9 genome editing technology leads to early embryonic lethality in mice

Hajnalka Laura Pálinkás^1,2, Gergely Rácz^1,3, Zoltán Gál⁴, Gergely Tihanyi^1,3, Elen Gócza⁴, László Hiripi⁴, Beáta G. Vértessy^1,2,3

¹ Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary

² Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary

³ Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary

⁴ Agricultural Biotechnology Institute, Department of Animal Biotechnology, Gödöllő, Hungary

Multiple knock-out mouse models can provide key novel insights into dynamics of genome integrity. The object of our studies, dUTPase, is a key enzyme in genome maintenance. It catalyzes the hydrolysis of dUTP into pyrophosphate and dUMP, supporting low cellular dUTP/dTTP ratio thus prevents genomic uracil accumulation. The molecular mechanism of thymine-less cell death, induced by the lack of dUTPase, is poorly understood although several routinely applied chemotherapeutic drugs in the clinic (fluoropyrimidines, methotrexate and its derivatives); interfere with the de novo thymidylate biosynthetic pathway. Previous reports showed that overexpression of dUTPase causes partial resistance against fluoropyrimidines, while its deficiency sensitizes tumor cells. Therefore a better knowledge of dUTPase role and function is particularly important in medicine. To investigate the physiological role of dUTPase in vivo, we established mice lacking dUTPase using CRISPR/Cas9-mediated genome engineering. So far two transgenic mouse models (dut +/-) were gained with 6 or 47 base pairs deletion in the coding gene of dUTPase. After crossing heterozygous mutants no viable homozygous pups were born indicating a lethal mutation. dUTPase homozygous mutant embryos were identified among blastocysts, which exhibited a normal appearance, but homozygous embryos were never found by E8.5, suggesting that mutant embryos die immediately after implantation. Single blastocysts are being undertook real-time PCR analysis to investigate potential maternal contribution of dUTPase transcripts at pre-implantation stages. We also performed Western blot studies on tissues derived from wild type and dut +/- heterozygote tissues in order to quantify dUTPase protein expression level and immunohistochemical staining on mouse sections to investigate cellular localization pattern. Our results establish for the first time that dUTPase is indispensable for proper post-implantation embryogenesis in mouse.

Comparison of three methods to measure successful knock down of EGFP in HEK293-EGFP cells using CRISPR/Cas9

Caroline F Peddle ¹, Michelle E McClements ¹, Robert E MacLaren ^1,2

¹ Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford

² Oxford Eye Hospital, Oxford, United Kingdom

HEK293-EGFP cells were transfected with plasmids expressing Staphylococcus aureus Cas9 and a gRNA construct, and harvested 48 hours post-transfection. 6 x EGFP-targeting gRNAs and 2 x non-targeting control gRNAs were screened. The reduction in EGFP expression following CRISPR/Cas9-mediated gene disruption was measured via three methods: mean grey value of fluorescence microscopy images, fluorescence spectroscopy, and qPCR. The greatest detected reduction of EGFP varied between these methods of measurement, at 20.1 %, 35.2 %, and 50.0 % when using mean grey value, fluorescence spectroscopy, and qPCR, respectively (One-way ANOVA, n = 5). qPCR detected, on average, 25.3 % and 11.5 % greater knock down than mean grey value and fluorescence spectroscopy, using the same gRNAs. However, qPCR demonstrated the most variation between biological replicates. Only 4 of the 6 x EGFP-targeting gRNAs produced a significant reduction in EGFP expression compared to the untransfected control when using qPCR assessment, whereas mean grey value and fluorescence spectroscopy measurements of EGFP were significantly reduced with all 6 x EGFP-targeting gRNAs.

Genome Editing 2018 Sponsors

Gold Sponsor and Exhibitor

Merck is the preeminent life science company, supplying Sigma-Aldrich brand gene editing products and services. With over 300,000 products, including CRISPR reagents, whole genome screening libraries (including Sanger arrayed and GeCKO pooled libraries), validation services and technical expertise, Merck has committed to solving the toughest problems in life science.

Website: www.sigma-aldrich.com.

Gold Sponsor and Exhibitor

Oxford Genetics mission is the creation of transformative systems and services to aid in the discovery and development of biologics, cell and gene therapies. Since 2015 the business has been developing systems for the high-throughput development of CRISPR libraries and CRISPR based cell line engineering through robotic automation. A unifying theme across the Oxford Genetics portfolio is the rational design of DNA systems using a LEGO-like approach for improving the productivity of viral and protein production systems. Founded in 2011, the company was founded by two University of Oxford academics and is headquartered at the Oxford Science Park.

Gold Sponsor and Exhibitor

Integrated DNA Technologies (IDT) is a leader in the manufacture and development of products for the research and diagnostic life science market. The largest supplier of custom nucleic acids in the world, IDT serves academic research, biotechnology, and pharmaceutical development communities.

IDT products support a wide variety of applications, including next generation sequencing (NGS), DNA amplification, SNP detection, microarray analysis, expression profiling, gene quantification, and synthetic biology. Platform-independent NGS products and services are available in addition to DNA and RNA oligonucleotides, qPCR assays, siRNA duplexes, and custom gene synthesis. Individually-synthesized xGen™ Lockdown™ Probes enable improved target capture. IDT also manufactures custom adaptors, fusion primers, Molecular Identifier tags (MIDs), and other workflow oligonucleotides for NGS. A TruGrade™ processing service is also available to reduce oligonucleotide crosstalk during multiplex NGS.

Serving over 80,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotide manufacture due to its unique capabilities. IDT pioneered the use of high throughput quality control (QC) methods and is the only oligonucleotide manufacturer to offer purity guarantees and 100% QC. Every oligonucleotide is analyzed by mass spectrometry and purified oligonucleotides receive further analysis by CE and HPLC. The company maintains an engineering division dedicated to advancing synthesis, processing technology, and automation. An in-house machine shop provides rapid prototyping and custom part design/control. Additionally, IDT offers unrivalled customer support, receiving approximately 100,000 calls annually with an average wait time of only 8 seconds.

A dedicated GMP manufacturing facility for molecular diagnostics provides oligonucleotides for In Vitro Diagnostic Devices (IVDs) or Analyte Specific Reagents (ASRs) for Laboratory-Developed Tests (LDTs). This manufacturing process is customer-defined and controlled, and facilitates progression from research to commercialization.

Bronze Sponsor and Exhibitor

Lonza provides the pharma market with the tools that life-science researchers use to develop and test therapeutics, beginning with basic research stages on to the final product release. Lonza’s bioscience products and services range from cell culture and discovery technologies for research to quality control tests and software that ensures product quality. Lonza Bioscience Solutions serves research customers worldwide in pharmaceutical, biopharmaceutical, biotechnology and personal care companies. The company delivers physiologically relevant cell biology solutions and complete solutions for rapid microbiology.

Lonza Cologne GmbH, Nattermannallee 1, Koeln, 50829, Germany
Phone: +49-221-99199-0, Fax: +49-221-99199-111
e-mail: scientific.support.eu@lonza.com