GENOMICS IN PRECISION ONCOLOGY XCHANGE
EAST COAST
Boston
April 5, 2023

Welcome to hubXchange’s East Coast Genomics in Precision Oncology 2023, bringing together executives from pharma and biotech to address and find solutions to the key issues faced in genomics-led oncology precision medicine strategies.

Discussion topics will cover Cancer Genomics, Translational Bioinformatics, Data Quality & Access and Genomics Informed Clinical Decisions.

Take advantage of this unique highly interactive meeting format designed for maximum engagement, collaboration and networking with your peers.

Venue Details: Hilton Boston Woburn Hotel, 2 Forbes Road, Woburn MA 01801

SNAPSHOTS OF DISCUSSION TOPICS

Track 1: Cancer Genomics

How to design drug combinations with Immuno-oncology treatment
The state of progress of precision medicine in immuno-oncology
ctDNA for cancer monitoring and MRD

Track 2: Translational Bioinformatics

The path from raw data to enabling biomarkers in translational research: challenges and opportunities
Translating genomics into decisions

Track 3: Data Quality & Access

Data quality & access to single cell data: How can we do better? A pharmaceutical perspective and siscussion
Opportunities and challenges in leveraging real-world data to support patient care inprecision oncology
Utilizing local genomic testing for precision trial enrollment

Track 4: Genomics Informed Clinical Decisions

Clinical trial design & its use in silico modelling for combination therapies and analyzing clinical trial designs
How can new multiomics technologies be incorporated into the clinic?
Functional integration of genomic markers in clinical research

Full Xchange Agenda

Click on each track for detailed agenda

Cancer Genomics

Time

Titles and Bullets

Facilitator

08:00 – 08:30

Registration

08:30 – 09:00

Opening Address & Keynote Presentation by Stilla

09:05 – 10:05

How to design drug combinations with Immuno-oncology treatment

How to identify resistance mechanisms to I/O therapy from a data, experimental and algorithmic perspective ?
How to potentiate existing I/O therapy ? Which experimental models can help us find a combination therapy ?
Promise of multi omics in I/O drug discovery. Why do we need multi omics and how to analyze the data ?
What are the current challenges in I/O drug discovery and what data, experiments and computational tools can help address them ?

Mi Yang

Senior Scientist, Sanofi

With a dual background in pharmaceutical sciences and cancer bioinformatics, Mi Yang uses machine learning to elucidate disease mechanisms, with the ultimate goal of new drug discovery and combination. Mi was initially trained as a pharmacist at the University of Paris-Sud. Then as a PhD student at Heidelberg University, he developed computational methods for drug synergy prediction and mechanistic exploration from large scale cancer drug screening datasets. At Stanford, he built a computational framework for drug discovery in immuno-oncology. At PrognomIQ, he worked on multi-omics cancer early detection from liquid biopsy. Mi is currently working as a senior scientist in oncology bioinformatics at Sanofi.

10:10 – 10:40

1-2-1 Meetings/Networking Break

10:40 – 11:10

1-2-1 Meetings / Networking Break

11:10 – 11:20

Morning Refreshments

11:20 – 12:20

Boosting the IO within bIOmarker analysis and precision medicine: The NeXT generation of comprehensive molecular characterization of tissue and liquid biopsy

Rapid advances in Next Generation Sequencing (NGS) technologies have revolutionized progress in personalized cancer vaccines, precision medicine and biomarker discovery and MRD detection.
Despite many advancements there are still challenges that must be addressed for both tissue profiling and liquid biopsy approaches.
This roundtable discussion will review various prevailing issues and strategies facing the field.

Travis Yates

Field Application Scientist, Personalis

12:20 – 13:20

Networking Lunch

13:20 – 13:50

Spotlight Presentation

Aleksander Bagaev

Vice President of Product Development, BostonGene

Since joining BostonGene in 2016, Dr. Alexander Bagaev has been instrumental in the company’s growth through product and business initiatives. He joined BostonGene as a cancer immunology specialist and has provided strategic direction for the company’s vision and product development. As Vice President of Product Development at BostonGene, he manages the product roadmap and product teams while leading the Research & Development Bioinformatic teams. Dr. Bagaev has over 12 years of experience and extensive training in molecular biology, oncology and immunology. Before joining BostonGene, Dr. Bagaev worked on multiple projects associated with novel vaccine development, studying myeloid tumor microenvironment and testing novel immunomodulatory therapeutics. In addition, Dr. Bagaev was involved in projects of mathematical modeling of molecular pathways and cancer evolution. Dr. Bagaev holds PhD in immunology. Dr. Bagaev has published over 20 articles in leading peer-review journals and received more than 50 US and International patents.

13:55 – 14:25

1-2-1 Meetings / Networking Break

14:25 – 14:55

1-2-1 Meetings / Networking Break

15:35 – 16:35

The state of progress of precision medicine in immuno-oncology

With more than 70 immunotherapy drugs in the clinical pipeline, how are we balancing our understanding of the tumor specific immune landscape and the feasibility of trying to address all our questions clinically?
What are the features of the successful patient enrichment biomarkers in immune oncology and what can we learn from them?
Beyond a mouse! How do we develop better model systems to reflect the complexity of the human immune system and cancer?
What is the role of the ‘surrogate biomarker’ that we could consider adopting in immune therapy
How do we consider the ‘immune therapy combination’ and the need to establish biomarkers in drug development

Rachael Brake

Chief Scientific Officer, Corbus Pharmaceuticals

A molecular and cellular biologist by training, Rachael is a deeply experienced drug developer that has been employed by various bio/pharma organizations including Amgen, Millennium/Takeda, and most recently Corbus Pharmaceuticals, where she currently serves as the Chief Scientific Officer. There Rachael is focused on attempting to wrangle the cytokine TGFb a known immunosuppressive growth factor in many cancers. Rachael’s 20+ years of drug development experience has been focused on advancing therapeutic programs across various mechanisms of action and modalities in immunology /oncology. Rachael brings significant pharmaceutical research and development experience, having focused on translating basic research concepts into effective clinical development strategies for many years. Previously at Takeda Rachael led the US Medical Affairs organization in Oncology, and also led the late-stage clinical development portfolio for solid tumors, where she successfully led the teams responsible for the front line approval of ALUNBRIG and established development strategies for programs like mobocertinib and sapanistertib. Rachael is an Australian, but currently resides in Boston, MA. She completed her BSc at the Australian National University and her PhD at the University of Western Australia /Institute for Child Health Research in Perth, WA.

16:35 – 16:45

Afternoon Refreshments

16:45 – 17:45

ctDNA for cancer monitoring and MRD

Limited predictive markers exist for PD1/PDL1 inhibitors- can we improve measurements?
How can we define novel biomarkers for PD1/PDL1 inhibitors?
How can we identify predictive biomarkers for novel IO agents?

Carl Barret

Vice President, Translational Science, Oncology, AstraZeneca

Dr. J. Carl Barrett is Vice President & Global Head of Translational Medicine Oncology R&D at AstraZeneca. He is responsible for development and execution of biomarker strategies and translational sciences efforts to support compound development from research through early and full development in oncology.

Previously, Dr. Barrett was the founding Director of the NCI Center for Cancer Research (CCR), the NCI intramural center for translation medicine. He was also Scientific Director at the National Institute of Environmental Health Sciences where he focused on integrating new approaches to toxicogenomics, molecular toxicology, and the Environmental Genome Project.

17:45 – 18:45

Evening Drinks Reception

Translational Bioinformatics

Time

Titles and Bullets

Facilitator

08:00 – 08:30

Registration

08:30 – 09:00

Opening Address & Keynote Presentation by Stilla

TBC

09:05 – 10:05

The path from raw data to enabling biomarkers in translational research: challenges and opportunities

Lack of standardized pre-processing steps in transcriptomics and proteomics data; need for uniformity. What can be done to take full advantage of published data? E.g., recount3
Mapping single cells to a reference atlas; translatability power between bulk and single cell assays. The need for systemic global reference data?
Varying levels of resolution and scaling to higher dimensionalities. Are data quality and sparsity of data posing a challenge to data analysis?
Designing flexible statistical frameworks for discovering complex differential patterns.
Keeping us with the emerging and ever-changing tools and pipelines to elucidate potential biomarkers in translational research. When it’s too much? How do we navigate in this space?

Iulian Pruteanu

Director of Bioinformatics, Pioneering Medicines

lulian joined Flagship Pioneering, Cambridge MA early 2022 and is responsible for leading the bioinformatics efforts within the division of Pioneering Medicines, by leveraging omics data and a vast array of analysis tools that ultimately support the ecosystem of scientific innovation.

He has over 15 years of cutting-edge probabilistic modeling and computational biology experience, in oncology and immuno-oncology omics related projects.

Prior to joining Pioneering Medicines, Iulian spent 3 years at Novartis Cell and Gene Therapy Unit, where he led the bioinformatics efforts for the first two BLA filings of a CAR-T therapy in the world (pediatric Acute Lymphocytic Leukemia and Diffuse Large B-Cell Leukemia) and 3 years in the Immuno-Oncology department with project leads across a broad range of check-point inhibitor and CAR-T efforts.

Iulian received his PhD in Computer Engineering from Duke University and his B.S. in Software and Networks in Telecommunications from Politehnica University in Bucharest, Romania.

10:10 – 10:40

1-2-1 Meetings/Networking Break

10:40 – 11:10

1-2-1 Meetings / Networking Break

11:10 – 11:20

Morning Refreshments

11:20 – 12:20

Multimodal real-world data for accelerating translational research and de-risking drug development

Harmonized multimodal data sources can help researchers uncover actionable biomarkers and signatures of response or resistance to:
- identify subpopulations of unmet need;
- select the most appropriate patient populations to enroll in clinical studies;
- and validate clinical trial designs
Data-driven approach to drug development in precision oncology helps biopharma organizations bring important treatments to patients faster and at lower cost

Kathleen Burke

Director of Computational Biology, Tempus

Kathleen Burke brings nearly a decade of bioinformatics experience in translational research and precision medicine across academia and the pharmaceutical industry. Prior to joining Tempus, she supported the interpretation of clinical trial biomarker strategy and novel target identification at AstraZeneca; and led improvements in the clinical trial matching aspect of the Watson for Genomics Platform at IBM. Dr. Burke graduated from Stony Brook University with a B.Eng. in Biomedical Engineering, and received her PhD in Biomedical/ Medical Engineering from the University of Rochester.

12:20 – 13:20

Networking Lunch

13:20 – 13:50

Spotlight Presentation

Aleksander Bagaev

Vice President of Product Development, BostonGene

13:55 – 14:25

1-2-1 Meetings / Networking Break

14:25 – 14:55

1-2-1 Meetings / Networking Break

15:35 – 16:35

PEDAL: Bringing tumor heterogeneity into drug discovery for increase probability of clinical success

There is extensive variation among patients in their response to drugs and it is costly to screen drugs against 100s of patient samples
PEDAL is an AI/ML platform to drive experimental testing (coupled with tumor assay capabilities) to evaluate 100s of tumor samples against 100s of drug compounds reducing the timeframe and increasing the agility of the drug discovery process
PEDAL’s AI component iteratively selects pairs of drug-tumor samples to test in vitro and utilizes the new data to make high confidence predictions of drug response
PEDAL enables more informed selection of drug/tumor type combinations to increase the probability of clinical success by efficiently addressing tumor heterogeneity during pre-clinical stages
PEDAL provides the opportunity to repurpose drugs through new evaluation in additional tumor types

Pamela A. Bush

Chief Business Officer, Predictive Oncology

Pamela Bush has over twenty years of experience in venture creation, finance, and business development in the life sciences industry. At Predictive Oncology, she leads the strategy and business development activities across the portfolio. Prior to joining Predictive Oncology, Pamela worked at Eli Lilly & Company in various roles including Corporate Business Development, Finance and Patient Services. In addition to her Lilly work experience, Pamela has worked in economic development, academia, and business consulting supporting the creation and growth of 80+ life sciences start-ups. Pamela holds an Ph.D. in Molecular Genetics and an MBA from Carnegie Mellon University. Prior to Predictive Oncology, Bush spent over a decade working for Eli Lilly in a number of commercial and technical roles including Vice President of Corporate Business Development. Bush has a PhD in Molecular Genetics and an MBA from Carnegie Mellon University.

16:35 – 16:45

Afternoon Refreshments

16:45 – 17:45

Translating genomics into decisions

What type of data have provided most actionable data
Best approaches to decipher signal from noise
Approaches to validating findings
Future directions

Melanie Frigault

Vice President, Translational Medicine, Vincerx Pharma

Melanie Frigault, PhD is the Vice President of Translational Medicine of Vincerx. Previously, Dr. Frigault was head of Translational Medicine at AstraZeneca with a focus on precision medicine and accelerating clinical development using novel biomarker-based endpoints in hemes and solid tumors. From 2016 to 2020, Dr. Frigault established a translational science department at Acerta to support development of CALQUENCE® with clinical biomarker data. Dr. Frigault held positions of increasing responsibility at AstraZeneca from 2011 to 2016 where she inserted science into the development of the portfolio ranging from target selection to phase 3 pivotal trials including biomarker discovery and companion diagnostic development. Dr. Frigault began her career at Novartis where she developed biomarkers and drove pre-clinical collaborations to address the knowledge gap. Dr. Frigault obtained her PhD in Biochemistry from McGill University.

17:45 – 18:45

Evening Drinks Reception

Data Quality & Access

Time

Titles and Bullets

Facilitator

08:00 – 08:30

Registration

08:30 – 09:00

Opening Address & Keynote Presentation by Stilla

TBC

09:05 – 10:05

Opportunities and challenges in leveraging real-world data to support patient care in precision oncology

Key clinical questions for investigating use of real-world data to support patient care in precision oncology
Opportunities to use data collected in routine patient care to inform precision medicine efforts for the population at large
What kind of health policies are needed to define appropriate uses of real-world evidence to support patient care and to incentivize data sharing
How can real-world data be leveraged to design precision clinical trials
Barriers to achieving precision medicine interventions for the benefit of the individual
Opportunities/Barriers to enhance interoperability between clinical EHR and molecular information systems

Meena Subramanyam

Vice President & Global Program Leader Oncology, Takeda

Meena Subramanyam is Vice President and Global Program Leader in Oncology, at Takeda Pharmaceuticals, in Cambridge MA. In this capacity, Dr. Subramanyam oversees the strategic development of therapeutic assets from pre-clinical through clinical development, for regulatory approval and commercialization in multiple tumor indications. She also serves as the Portfolio Lead for the novel conditionally activated immune cell engager platform (COBRA) assets. Previously, Dr. Subramanyam was Vice President at Biogen in Cambridge, Massachusetts in the Global Biomarker Discovery and Development Division and Head of the Translational Sciences and Technology group. Dr. Subramanyam has served as President and Chair of the Board, Women in the Enterprise of Science and Technology (WEST). She has won several leadership awards, including the Luminary Award from the Healthcare Business Women’s Association (HBA) and the Global Leader Award from AAPS. Dr. Subramanyam currently serves as an observer on the Board of Portal Instruments Inc., and as a member on the advisory board of several not-for-profit organizations.

10:10 – 10:40

1-2-1 Meetings/Networking Break

10:40 – 11:10

1-2-1 Meetings / Networking Break

11:10 – 11:20

Morning Refreshments

11:20 – 12:20

Getting de-centralized testing into routine clinical oncology

The potential for de-centralized liquid biopsy early cancer detection through resistance and recurrence applications
Enabling ongoing disease molecular assessment and treatment management based upon molecular endpoints using ctDNA assays
Allowing for more treatment options for patients and expanded utility of drug therapies at earlier disease stages

Representative of Stilla

12:20 – 1:20

Networking Lunch

13:20 – 13:50

Spotlight Presentation

Aleksander Bagaev

Vice President of Product Development, BostonGene

13:55 – 14:25

1-2-1 Meetings / Networking Break

14:25 – 14:55

1-2-1 Meetings / Networking Break

16:35 – 16:45

Afternoon Refreshments

16:45 – 17:45

Utilizing local genomic testing for precision trial enrollment

How can we ensure consistency across laboratories and tests?
How do we create a central database from disparate local data?
How can we confirm/compare local results with a single central assay?
Accounting for ctDNA false-negatives in low-shedding tumor types

Ian Silverman

Associate Director, Bioinformatics, Repare Therapeutics

Ian Silverman is a computational biologist specializing in cancer genomics and a leader in clinical diagnostics for precision oncology drug development. In his current role as Associate Director, of Bioinformatics at Repare Therapeutics, he established the clinical bioinformatics group and serves as the bioinformatics lead for camonsertib (RP3500), a selective ATR inhibitor being developed in patients with biallelic loss of function alterations in DNA damage repair and homologous recombination deficient cancers. He previously worked at Incyte Corporation, where he led the genomic analysis for the pemigatinib (Pemazyre®) program, leading to worldwide regulatory approval in FGFR2 fusion or rearrangement-positive cholangiocarcinoma. Prior to Incyte, he worked at Ignyta Inc. where he developed diagnostics and analyzed translational data for entrectinib (Rozlytrek®) which has gained worldwide regulator approval as a tumor-agnostic therapy for cancer patients with NTRK fusions and ROS1 fusion-positive NSCLC. Ian earned a PhD in Cell and Molecular Biology from the University Of Pennsylvania School Of Medicine and a Bachelor of Science in Biochemistry from Binghamton University.

17:45 – 18:45

Evening Drinks Reception

Genomics Informed Clinical Decisions

Time

Titles and Bullets

Facilitator

08:00 – 08:30

Registration

08:30 – 09:00

Opening Address & Keynote Presentation by Stilla

TBC

09:05 – 10:05

Clinical trial design & its use in silico modelling for combination therapies and analyzing clinical trial designs

How can we effectively use in silico modeling to optimize dosing?
How can we identify potential drug-drug interactions?
How can we predict outcomes?
How can we design clinical trials for combination therapies that adequately assess the safety and efficacy of each individual component as well as the combination as a whole?
How can we address challenges related to patient recruitment, randomization, and blinding in clinical trials of combination therapies, particularly when in silico models as part of the preclinical research?

Peter Carr

Principal Software Architect, Lantern Pharma

Peter Carr is a principal software architect at Lantern Pharma where he focuses on developing platforms and tools to support oncology research and development. He began his career as a C/C++ programmer at NIST before developing interactive exhibits at the Boston Museum of Science. Later, he joined the Cancer Program at the Broad Institute of MIT and Harvard as a Software Engineer. At Lantern Pharma, he has built a leading edge cloud infrastructure for artificial intelligence and machine learning. With his expertise in software engineering and biomedical research, Peter is a respected voice in the field of genomics and precision oncology.

10:10 – 10:40

1-2-1 Meetings / Networking Break

10:40 – 11:10

1-2-1 Meetings / Networking Break

11:10 – 11:20

Morning Refreshments

12:20 – 13:20

Networking Lunch

13:20 – 13:50

Spotlight Presentation

Aleksander Bagaev

Vice President of Product Development, BostonGene

13:55 – 14:25

1-2-1 Meetings / Networking Break

14:25 – 14:55

1-2-1 Meetings / Networking Break

15:00 – 15:30

Poster Session
ResponderID TM: the biology-first machine learning platform for biomarker discovery

Rarely has a complex gene signature been successfully translated from conception to a predictive biomarker algorithm ready for clinical practice. Genialis’ ResponderID TM is a biomarker discovery platform that espouses a people-first framework to model underlying disease biology. The platform consists of software and data/signature assets, and has been validated through the development of the Xerna TM TME panel. The Xerna TME Panel is a novel machine learning based transcriptomic biomarker designed to predict therapeutic response to various targeted therapies across multiple cancers. ResponderID continues to support the commercialization and market acceptance of the Xerna TME Panel.

Daniel Pointing

Manager of Strategic Scientific Partnerships, Genialis

Daniel is the Manager of Strategic Scientific Partnerships at Genialis, a computational precision medicine company unraveling complex biology to find new ways to address disease. Daniel brings a decade of experience in medical device commercialization and clinical trial operations to the Genialis team. He holds a Masters in Epidemiology.

15:00 – 15:30

Poster Session
Value of tumor fraction in liquid biopsy testing & association with therapy outcomes in advanced prostate cancer

Foundation Medicine has developed a novel biomarker algorithm in liquid biopsy testing known as Tumor Fraction, which estimates the level of ctDNA in a patient’s blood sample and can increase confidence in results to help guide next steps in patient care. This research showcases a prospective-retrospective analysis completed on blood samples from IMbassador250, a prospective phase III international trial which showed no overall survival (OS) benefit for adding atezolizumab to enzalutamide for men with mCRPC who had prior progression on abiraterone. The results show that tumor fraction may be useful to anticipate patient benefit from enzalutamide switch after abiraterone progression.

David Fabrizio

Vice President of Early Clinical Development, Foundation Medicine

David Fabrizio serves as the Vice President of Early Clinical Development at Foundation Medicine in Cambridge, MA. Under his leadership, Foundation Medicine has pioneered new genomic biomarkers for immunotherapy, including tumor mutational burden (TMB), and launched the first comprehensive genomic profiling test approved by the FDA, FoundationOne CDx. David also led the development of the first blood-based assay to determine immunotherapy response, published in Nature Medicine, which was also selected as one of Nature’s most notable advances of 2018. He holds ten different patents or patent applications for therapeutic and diagnostic methods for cancer, as well as over 30 publications in peer reviewed journals including Nature, Cell, The Lancet, and the Journal of American Medical Association (JAMA), and is a member of ASCO and AACR.

15:35 – 16:35

How can new multiomics technologies be incorporated into the clinic?

What is required for greater adoption of large omics readouts in the clinic?
How can we better change from thinking about small numbers of biomarkers to entire multiomic signatures?
How can multiomic readouts best be leveraged given the cost and challenges of implementation?
What role should personalized medicine play and how can the data be leveraged for precision oncology?
What threats are there to patient privacy when so much information is collected and how can they be addressed?

Seth Garren

Senior Principal Scientist, Head of Genomics, Sanofi

Seth Garren is a Senior Principal Scientist and Head of Genomics in Precision Oncology at Sanofi. His team generates bulk, single cell, and spatial transcriptomics and proteomics data for discovery, preclinical, and reverse translational efforts. Before joining Sanofi in 2022, Seth worked at Pfizer for four years building the NGS Technology center to provide omics expertise and data generation for the Inflammation & Immunology, Rare Disease, and Internal Medicine Research Units. Seth did his postdoc at MGH studying whole exome sequencing of liquid biopsies and single cell sequencing of MC38 immune checkpoint blockade. Seth received a PhD in Biomedical Sciences in the department of Genetics and Genome Sciences from University of Connecticut Health studying whole transcriptome expression of host and viral RNA from cells infected with the oncogenic mouse polyomavirus.

16:35 – 16:45

Afternoon Refreshments

17:45 – 18:45

Evening Drinks Reception

GENOMICS IN PRECISION ONCOLOGY XCHANGEEAST COASTBoston April 5, 2023

SNAPSHOTS OF DISCUSSION TOPICS

Full Xchange Agenda

Cancer Genomics

Translational Bioinformatics

Data Quality & Access

Genomics Informed Clinical Decisions

Partners

GENOMICS IN PRECISION ONCOLOGY XCHANGE
EAST COAST
Boston
April 5, 2023