Mayu Takagi
1602-111 St. Clair Ave W
Toronto, ONM4V 1N5

Deep Genomics
About the Company• Headquarter in Toronto: MaRS Centre, 661 University Avenue Suite 480• What they do: develop genetic medicines using biologically accurate artificial
intelligence technology
o Focusing on the preclinical development of oligonucleotide therapies• They have the world’s first drug design system built around a molecular biology AI• Over 30 employees with expertise in fields including automation, AI, machine learning,
software engineering, genomics, molecular and cell biology, human genetics, moleculardiagnostics, organic chemistry, and business• Founder and CEO: Brendan Freyo PhD, FRSC
o Led the launch of Deep Genomics in 2015o Is a professor of Engineering and Medicine at the University of Torontoo Co-Founder of the Vector Institute for Artificial Intelligenceo Senior Fellow of the Canadian Institute for Advanced Research• Twitter account: https://www.theglobeandmail.com/report-on-business/robmagazine/canadas-ai-explosion-visit-three-labs-where-machines-are-being-taught-tothink-likepeople/article38336675/•The Platform• Genetic Medicineso Their platform allows them to find drug candidates with desirable properties
efficientlyo Their medicines target the genetic determinants of disease at the level of RNAand DNA• The platformo On-target and genome-wide off target effect data is produced for every compound
identified using the platformo The platform is getting better at identifying targets and compounds at anincreasingly faster speedo It incorporates the most advanced biological knowledge and is driven by the mostpowerful automation technologies
o Built using proprietary and public datasetso Discoveries published by other scientists and engineers are evaluated and ifappropriate, are incorporated into the platform• The work of the company has appeared in journals such a Science, Nature, NatureGenetics, Nature Medicine, Nature Methods, Proceedings of the IEEE, NIPS,Bioinformatics, RECOMB, and ISMB
Project Saturn•••

Their AI platform allows for smart drug design that predicts outcomes
Aim of Project Saturn: use the platform to evaluate over 69 million molecules against 1
million targets, in silico, to generate a library of 1000 compounds that are experimentally
verified to manipulate cell biology as intendedThe hope is that this will become a toolkit for controlling cell biology, helping to unlock
therapies with greater potential

Saturn Tech Specs• Anticipates the universe of molecular effects achievable by antisense
oligonucleotide compounds (ASOs) in reference human cells.
• Automatically identifies all ASOs that achieve a particular change,
tailored to individual genotype and leveraging up to six biologicalmechanisms, and counting.
• Analyses over 100,000 standard RNA isoforms for altered expression,plus thousands of novel and anticipated isoforms.
• Evaluates over 69 billion ASOs against 1 million target sites in silico.
• AI components continuously improve in a closed loop, learning fromboth successes and failures.
• Back-of-envelope calculation of entire ASO design space: 10^50compounds, or, mathematically, sqrt(googol)
https://www.deepgenomics.com/updates/discovering-therapies-for-neuromuscular-disorders/
Wave Life Sciences and Deep Genomics Form Collaboration to Discover Novel
Therapies for Genetic Neuromuscular Disorders (April 10, 2018).
• Wave Life Sciences Ltd. (a biotechnology company that focuses on deliveringtransformational therapies for patients with serious, genetically-defined diseases_ andDeep Genomics announced that they will collaborating to develop novel therapies for thetreatment of genetic neuromuscular disorderso https://www.wavelifesciences.com• The companies will use Deep Genomics’ machine learning platform to identify cause andeffect relationships that are specific to neuromuscular-related targets that involve splicing
regulation• They will then analyze and test oligonucleotides against therapeutic targets within
multiple genes that are associated in neuromuscular disorders• Wave’s propriety chemistry platform will then be used to validate targets and makeapparent the implications of target intervention across different phenotypes
https://www.deepgenomics.com/updates/taking-on-metabolic-neurodegenerativedisorders/
Deep Genomics Takes on Metabolic & Neurodegenerative Disorders (March 26,2018)

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In March 2018, Deep Genomics announced they are investing $10 million toexpand their preclinical platform and develop therapies for metabolic anddegenerative disorders
In the next 3 years, their goal is to use its platform to unlock new anti -sense
oligonucleotide therapies and advance them for clinical evaluation
Dr. Arthur A. Levin – a leader in the field of oligonucleotide therapeutics and EVPof Research and Development at Avidity Biosciences joined the Scientific
Advisory Board of Deep Genomics
The company’s belief is that oligonucleotide therapeutics will make it possible todesign targeted medicines based on genomic information

https://www.utoronto.ca/news/u-t-s-deep-genomics-raises-us13-million-fund-expansion
Deep Genomics Raises $13M to Develop Genetic Medicines (Sep. 25, 2017)• Received a $13 millions USD investment led by Khosla Ventures (one of the topSilicon Valley venture capital firms)• The money will be used to hire a range of scientific experts• Deep Genomics previously raised $3.7 million in a seed round in 2015
https://www.forbes.com/sites/bernardmarr/2018/11/16/the-amazing-ways-artificialintelligence-is-transforming-genomics-and-gene-editing/#37469cae42c1• By 2021, it is estimated that AI systems will generate 6.7 billion in revenue fromhealthcare globally• AI systems make DNA sequencing and analysis faster, cheaper, and more accurateo Gives perspective on the particular genetic blueprint of an organism• Genetic sequencing and analysis could also be ground-breaking for agriculture andanimal husbandryo It can give insight into what kinds of mutations and diseases that anorganism may be susceptible to in the future → this helps them think about
how they can prepare for the future• Sequencing the genome is a critical first step to understanding the human genomeo High-throughput sequencing (HTS), the latest technology, allows thesequencing of DNA to occur in 1 dayo This used to take a decade to do• Machine learning is decreased the cost and making personalized medicine morepossible• Google’s tool, Deep Variant uses the latest AI techniques to turn high-throughput
sequencing (HTS) into a more accurate picture of a full genome
o They are able to distinguish small mutations from random errors
o Deep Learning played a big role in effectively training DeepVariant• Deep Genomics uses its AI platform to decode the meaning of the genome todetermine the best drug therapies for certain individuals based on their DNA• Sophia Genetics is a company that hopes to use artificial intelligence to identify
genetic mutations, and help doctors prescribe the best drug treatment for patients.
o https://www.sophiagenetics.com/home.html

https://tech.economictimes.indiatimes.com/news/technology/from-agriculture-to-art-theai-wave-sweeps-in/66315315• Typically, it takes several years and billion of dollars for pharmaceuticalcompanies to bring a new drug to market• AI holds the promise of reducing this cost and time
• It also reduces aero by decreasing the amount of guesswork• Deep Genomics is still in its early stages• It first compounds will be tested in clinical trials beginning in 2020
https://www.marketwatch.com/press-release/healthcare-artificial-intelligence-ai-marketrapidly-moving-to-reach-usd-12000-mn-by-2023-2018-11-13• Deep Genomics is listed as one of the top key players in the global Healthcare AI
Markethttps://www.marsdd.com/magazine/robots-and-researchers-are-teaming-up-to-designbetter-drugs/?utm_medium=social&utm_source=Twitter&utm_campaign=content_promotion&utm_c
ontent=Drugs• Deep Genomics is planning to apply their AI platform to rare Mendelian disorders(a class of inherited diseases that result from a single genetic mutation)• They’re hope is to make better medicines available to more people, more quickly• The Ontario Institute for Cancer Research is using machine learning to develop
genomic tools for early cancer detection and to categorize tumorso This will help doctors develop more effective treatments• AI can also speed up the assessment of new compounds for their ef fectiveness,
toxicity, and ability to be metabolizedo They use pre-existing data to predict potentially new interactionso This helps them screen our molecules with undesired effects and prioritize
effective oneso This takes second or minutes with AI processes, compared to months andyears of experimentation• The downside however of AI is that its ability to predict outcomes is based on theavailability of high-quality data which can be difficult to come by• Without enough data, the predictive power of AI falls• The FEO of Deep Genomics also believes that AI can also help scientists andpatients to share data more effectively
Podcast about Reprogramming the Human Genome with AI features Brendan Frey, theCEO of Deep Genomics
https://soundcloud.com/twiml/talk-012-brendan-frey-interview-reprogramming-humangenome-ai