Geneious Biologics. Jannick Bendtsen, PhD. Vice President Technology Services Biomatters 13 December 2017

Transcription

1 Geneious Biologics Jannick Bendtsen, PhD. Vice President Technology Services Biomatters 13 December 2017

2 // About Biomatters Founded in 2003 in Auckland, New Zealand Flagship Geneious software first released in 2005 Used by over 3,000 commercial and academic research institutes in more than 100 countries Geneious used by top 20 universities globally and 16 of top 20 pharma Software developed in New Zealand Sales offices in the United States, Europe and Asia 2

3 // Today s talk The demand for antibody therapeutics is greatly increasing. OPPORTUNITIES This creates challenges and opportunities and demands new methodologies for data generation, analysis, visualization and management NGS provides ability to effectively cover diverse antibody libraries and accelerate candidate discovery and exploration of full antibody repertoires CHALLENGES NGS necessitates advanced software to process large volumes of sequence data 3

4 // NGS headache Antibody NGS data is known to create big headaches for researchers There is a demand for tools to Analyze Visualize Discover With a number of select Early Access Partners Biomatters looked at challenges and solutions for a novel scalable platform for biologics. 4

5 // Challenge Create a secure platform which support analysis and storage of NGS, Sanger and assay data Create a solution which can easily be configured to support different scaffolds and workflows. Remove data silos and remove risk of copy/paste errors in Excel and other softwares Remove need to run and maintain scripts and command line tools Make it easy to use and visually appealing 5

6 // Solution A fully managed and secure data platform using cloud infrastructure Collaboration and access management Highly configurable and extendable framework which support different customer needs Powerful bioinformatics workflows Advanced data visualization Modern intuitive, user-friendly, web interface REST API for 3rd party integrations 6

7 // Results Bicycle Therapeutics and Isogenica are successfully using Geneious Biologics to achieve deep understanding of their antibody data and improve operations. 7

8 3 antibody libraries massive diversity infinite possibilities Alexandria Fully synthetic human Fab 8 VH x 8 VK germlines All CDRs randomized Randomizations to match germline 18 CDR3 lengths across all VH Alexandria CL Common Light Chain Fab 8 VH x single fixed VK Fixed VK selected for low immunogenicity, VH pairing For bispecifics or VK based maturation llamda camelid single domain VHH Single camelid or human framework All CDRs randomized 18 CDR3 lengths across all VH Human IgG Single domain VHH The computational power and intuitive interface of Biomatters Geneious desktop and Geneious Biologics solutions have significantly simplified our analyses of these vast datasets. We have been very pleased with the quality of the software, as well as with the interaction with Biomatters staff who have proven to be very responsive to technical questions and suggestions for further development. 8 Dr. Guy Hermans, CSO Isogenica Ltd, UK

9 // Support for different scaffolds In vitro nanobody discovery for integral membrane protein targets. Doshi, R. et al., Sci Rep, 2014 Challenges and opportunities for non-antibody scaffold drugs Vazquez-Lombardi, R. et al. Drug discovery today,

10 10 // Easy to use web based interface

11 // Pre-processing and analysis pipelines QC/trim, assemble, merge paired end data Inspect and prepare data for analysis Very flexible system which can be configured for individual organizations 11

12 12 // Results view (Sanger)

13 13 // NGS results - annotation overview

14 14 // NGS results - cluster overview

15 15 // NGS results - aa composition

16 16 // NGS results - codon usage

17 // Integration with other systems REST API CLI Geneious 17

18 // Performance and accuracy No gold standard dataset is available Annotating approx 1500 seq/sec Table 1. Preliminary comparison of Geneious Biologics annotation algorithm with other well known annotation algorithms Ye J., Ma N., Madden TL, et al. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res 2013; 41: Bolotin DA., Poslavsky S., Mitrophanov I, et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat Methods 2015; 12:380 1

19 19 // Acknowledgements

20 20 // Come to booth #111 to get a demo

21 21 Thank you for your attention!

22 22 // And the winner is.

23 23 // Collaboration and data sharing

24 24 // NGS results - detailed view

25 25 // NGS results - compare datasets

26 // Search Search across all experiments Sequence name Sequence Assay data And a lot more 26

27 27 // Geneious