Healthcare analytics, AI solutions for biological big data, providing an AI platform for the biotech, life sciences, medical and pharmaceutical industries, as well as for related technological approaches, i.e., curation and text analysis with machine learning and other activities related to AI applications to these industries.
Role of Informatics in Precision Medicine: Notes from Boston Healthcare Webinar: Can It Drive the Next Cost Efficiencies in Oncology Care? Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)
Role of Informatics in Precision Medicine: Notes from Boston Healthcare Webinar: Can It Drive the Next Cost Efficiencies in Oncology Care?
Reporter: Stephen J. Williams, Ph.D.
Boston Healthcare sponsored a Webinar recently entitled ” Role of Informatics in Precision Medicine: Implications for Innovators”. The webinar focused on the different informatic needs along the Oncology Care value chain from drug discovery through clinicians, C-suite executives and payers. The presentation, by Joseph Ferrara and Mark Girardi, discussed the specific informatics needs and deficiencies experienced by all players in oncology care and how innovators in this space could create value. The final part of the webinar discussed artificial intelligence and the role in cancer informatics.
Below is the mp4 video and audio for this webinar. Notes on each of the slides with a few representative slides are also given below:
Please click below for the mp4 of the webinar:
worldwide oncology related care to increase by 40% in 2020
big movement to participatory care: moving decision making to the patient. Need for information
cost components focused on clinical action
use informatics before clinical stage might add value to cost chain
Key unmet needs from perspectives of different players in oncology care where informatics may help in decision making
Needs of Clinicians
– informatic needs for clinical enrollment
– informatic needs for obtaining drug access/newer therapies
2. Needs of C-suite/health system executives
– informatic needs to help focus of quality of care
– informatic needs to determine health outcomes/metrics
3. Needs of Payers
– informatic needs to determine quality metrics and managing costs
– informatics needs to form guidelines
– informatics needs to determine if biomarkers are used consistently and properly
– population level data analytics
What are the kind of value innovations that tech entrepreneurs need to create in this space? Two areas/problems need to be solved.
innovations in data depth and breadth
need to aggregate information to inform intervention
Different players in value chains have different data needs
Data Depth: Cumulative Understanding of disease
Data Depth: Cumulative number of oncology transactions
technology innovators rely on LEGACY businesses (those that already have technology) and these LEGACY businesses either have data breath or data depth BUT NOT BOTH; (IS THIS WHERE THE GREATEST VALUE CAN BE INNOVATED?)
NEED to provide ACTIONABLE as well as PHENOTYPIC/GENOTYPIC DATA
data depth more important in clinical setting as it drives solutions and cost effective interventions. For example Foundation Medicine, who supplies genotypic/phenotypic data for patient samples supplies high data depth
technologies are moving to data support
evidence will need to be tied to umbrella value propositions
Informatic solutions will have to prove outcome benefit
How will Machine Learning be involved in the healthcare value chain?
increased emphasis on real time datasets – CONSTANT UPDATES NEED TO OCCUR. THIS IS NOT HAPPENING BUT VALUED BY MANY PLAYERS IN THIS SPACE
Interoperability of DATABASES Important! Many Players in this space don’t understand the complexities integrating these datasets
Other Articles on this topic of healthcare informatics, value based oncology, and healthcare IT on this OPEN ACCESS JOURNAL include:
The Future of Precision Cancer Medicine, Inaugural Symposium, MIT Center for Precision Cancer Medicine, December 13, 2018, 8AM-6PM, 50 Memorial Drive, Cambridge, MA
Reporter: Aviva Lev-Ari, PhD, RN
#CPCM2018 @AVIVA1950 @pharma_BI
Aviva Lev-Ari, PhD, RN, Editor-in-Chief, will attend and cover this event in REAL TIME for
Over the past decade, there have been major advancements in the field of precision medicine, leading to exciting new treatments for some cancer patients. Much attention has been focused on genomic profiling of tumors to identify genomic alterations that might guide selection of specific therapies for individual patients. Beyond genomics, however, there is a variety of other precision approaches that can identify and exploit cancer-specific biological mechanisms including proteomics, metabolomics, and computational modeling, resulting in the more effective use of existing cancer medicines. On Thursday, December 13, 2018, the MIT Center for Precision Cancer Medicine will hold its inaugural annual symposium in the Samberg Conference Center at MIT. This full-day event will feature leading researchers and clinicians, who will highlight recent advances in precision cancer medicine and share perspectives on the future. An industry panel will also discuss the barriers to instituting precision medicine into current and future clinical trials.
Keynote Address
Charles Sawyers, MD
Chair, Human Oncology and Pathogenesis Program
Memorial Sloan Kettering Cancer Center
Speakers
Andrea Califano, PhD
Clyde and Helen Wu Professor of Chemical Systems Biology, Columbia University
Chair, Department of Systems Biology, Columbia University
Director, JP Sulzberger Columbia Genome Center
Associate Director, Herbert Irving Comprehensive Cancer Center
J. Christopher Love, PhD
Professor of Chemical Engineering, MIT
Associate Member, Ragon Institute of MGH, MIT and Harvard
Member, Koch Institute, MIT
Richard Marais, PhD
Professor of Molecular Oncology
Director, CRUK Manchester Institute
The University of Manchester
Kenna Mills Shaw, PhD
Executive Director
Sheikh Khalifa Bin Zayed al Nahyan Institute for Personalized Cancer Therapy
MD Anderson Cancer Center
Alice Shaw, MD, PhD
Professor, Harvard Medical School
Director, Thoracic Cancer Program, Massachusetts General Hospital
Matthew Vander Heiden, MD, PhD
Associate Professor of Biology, MIT
Associate Director, Koch Institute
Member, MIT Center for Precision Cancer Medicine
Michael B. Yaffe, MD, PhD
David H. Koch Professor of Science, MIT
Professor of Biology and Biological Engineering, MIT
Director, MIT Center for Precision Cancer Medicine
Director, Koch Institute Clinical Investigator Program
Jean Zhao, PhD
Professor of Biological Chemistry and Molecular Pharmacology
Harvard Medical School and Dana-Farber Cancer Institute
Panelists: Barriers to Instituting Precision Medicine in Clinical Trials
Peter Hammerman, MD, PhD
Global Head, Translational Research
Oncology Disease Area
Novartis Institutes for BioMedical Research
Steffan N. Ho, MD, PhD
Vice President, Head of Translational Oncology
Pfizer Global Product Development
Shiva Malek, PhD
Director and Principal Scientist
Department of Discovery Oncology
Genentech Inc
Kevin Marks, PhD
VP of Biology
Agios Pharmaceuticals
S. Michael Rothenberg, MD, PhD
Vice-President, Research and Development
Loxo Oncology, Inc.
Moderator:
Angela Koehler, PhD
Goldblith Career Development Professor in Applied Biology, MIT
Member, Koch Institute for Integrative Cancer Research
Member, MIT Center for Precision Cancer Medicine
8:45 am Opening remarks by Michael Yaffe (MIT’s Koch Institute)
Season of great expectation, tumor genetics is just the beginning, beyond: science, engineering, medicine: beyond genomics: immunology, cell biology, early detection, new drug development for the undrugable, system biology, RNAi
Jack Tyler was the initiator to find a donor for CPCM
9:00 am Keynote Address by Charles L. Sawyers (Memorial Sloan Kettering Cancer Center)
developed a drug for prostate cancer
Clinical trained oncologist/genomics
Lineage Plasticity:
luminal cells in histology of origin and basal cells and require androgen receptor AR) function
Article ID #155: Geneticist George Church: A Future Without Limits. Published on 10/24/2014
WordCloud Image Produced by Adam Tubman
UPDATED 12/05/2020
In the future, George Church believes, almost everything will be better because of genetics. If you have a medical problem, your doctor will be able to customize a treatment based on your specific DNA pattern. When you fill up your car, you won’t be draining the world’s dwindling supply of crude oil, because the fuel will come from microbes that have been genetically altered to produce biofuel. When you visit the zoo, you’ll be able to take your children to the woolly mammoth or passenger pigeon exhibits, because these animals will no longer be extinct. You’ll be able to do these things, that is, if the future turns out the way Church envisions it—and he’s doing everything he can to see that it does.
UPDATED 12/05/2020
George Church backs a startup solution to the massive gene therapy manufacturing bottleneck
Source: https://endpts.com/george-church-backs-a-startup-solution-to-the-massive-gene-therapy-manufacturing-bottleneck/ Jason Mast: Associate Editor George Church and his graduate students have spent the last decade seeding startups on the razor’s edge between biology and science fiction: gene therapy to prevent aging, CRISPRed pigs that can be used to harvest organs for transplant, and home kits to test your poop for healthy or unhealthy bacteria. (OK, maybe they’re not all on that razor’s edge.)
But now a new spinout from the Department of Genetics’ second floor is tackling a far humbler problem — one that major company after major company has stumbled over as they tried to get cures for rare diseases and other gene therapies into the clinic and past regulators: How the hell do you build these?
CEO Lex Vovner of 64x Bio
“There’s a lot happening for new therapies but not enough attention around this problem,” Lex Rovner, who was a post-doc at Church’s lab from 2015 to 2018, told Endpoints News. “And if we don’t figure out how to fix this, many of these therapies won’t even reach patients.”
This week, with Church and a couple other prominent scientists as co-founders, Rovner launched 64x Bio to tackle one key part of the manufacturing bottleneck. They won’t be looking to retrofit plants or build gene therapy factories, as Big Pharma and big biotech are now spending billions to do. Instead, with $4.5 million in seed cash, they will try to engineer the individual cells that churn out a critical component of the therapies.
George Church The goal is to build cells that are fine-tuned to do nothing but spit out the viral vectors that researchers and drug developers use to shuttle gene therapies into the body. Different vectors have different demands; 64x Bio will look to make efficient cellular factories for each.
“While a few general ways to increase vector production may exist, each unique vector serotype and payload poses a specific challenge,” Church said in an emailed statement. “Our platform enables us to fine tune custom solutions for these distinct combinations that are particularly hard to overcome.”
Before joining Church’s lab, Rovner did her graduate work at Yale, where she studied how to engineer bacteria to produce new kinds of protein for drugs or other purposes. And after leaving Church’s lab in 2018, she initially set out to build a manufacturing startup with a broad focus.
Yet as she spoke with hundreds of biotech executives on LinkedIn and in coffee shops around Cambridge, the same issue kept popping up: They liked their gene therapy technology in the lab but they didn’t know how to scale it up.
“Everyone kept saying the same thing,” Rovner said. “We basically realized there’s this huge problem.”
The issue would soon make headlines in industry publications: bluebird delaying the launch of Zynteglo, Novartis delaying the launch of Zolgensma in the EU, Axovant delaying the start of their Parkinson’s trial.
Part of the problem, Rovner said, is that gene therapies are delivered on viral vectors. You can build these vectors in mammalian cell lines by feeding them a small circular strand of DNA called a plasmid. The problem is that mammalian cells have, over billions of years, evolved tools and defenses precisely to avoid making viruses. (Lest the mammal they live in die of infection).
There are genetic mutations that can turn off some of the internal defenses and unleash a cell’s ability to produce virus, but they’re rare and hard to find. Other platforms, Rovner said, try to find these mutations by using CRISPR to knock out genes in different cells and then screening each of them individually, a process that can require hundreds of thousands of different 100-well plates, with each well containing a different group of mutant cells.
“It’s just not practical, and so these platforms never find the cells,” Rovner said.
64x Bio will try to find them by building a library of millions of mutant mammalian cells and then using a molecular “barcoding” technique to screen those cells in a single pool. The technique, Rovner said, lets them trace how much vector any given cell produces, allowing researchers to quickly identify super-producing cells and their mutations.
The technology was developed partially in-house but draws from IP at Harvard and the Wyss Institute. Harvard’s Pam Silver and Wyss’s Jeffrey Way are co-founders.
The company is now based in SoMa in San Francisco. With the seed cash from Fifty Years, Refactor and First Round Capital, Rovner is recruiting and looking to raise a Series A soon. They’re in talks with pharma and biotech partners, while they try to validate the first preclinical and clinical applications.
Gene therapy is one focus, but Rovner said the platform works for anything that involves viral vector, including vaccines and oncolytic viruses. You just have to find the right mutation.
“It’s the rare cell you’re looking for,” she said.
AUTHOR Jason Mast Associate Editor jason@endpointsnews.com @JasonMMast Jason Mas
In 2005 he launched the Personal Genome Project, with the goal of sequencing and sharing the DNA of 100,000 volunteers. With an open-source database of that size, he believes, researchers everywhere will be able to meaningfully pursue the critical task of correlating genetic patterns with physical traits, illnesses, and exposure to environmental factors to find new cures for diseases and to gain basic insights into what makes each of us the way we are. Church, tagged as subject hu43860C, was first in line for testing. Since then, more than 13,000 people in the U.S., Canada, and the U.K. have volunteered to join him, helping to establish what he playfully calls the Facebook of DNA.
Church has made a career of defying the impossible. Propelled by the dizzying speed of technological advancement since then, the Personal Genome Project is just one of Church’s many attempts to overcome obstacles standing between him and the future.
“It’s not for everyone,” he says. “But I see a trend here. Openness has changed since many of us were young. People didn’t use to talk about sexuality or cancer in polite society. This is the Facebook generation.” If individuals were told which diseases or medical conditions they were genetically predisposed to, they could adjust their behavior accordingly, he reasoned. Although universal testing still isn’t practical today, the cost of sequencing an individual genome has dropped dramatically in recent years, from about $7 million in 2007 to as little as $1,000 today.
“It’s all too easy to dismiss the future,” he says. “People confuse what’s impossible today with what’s impossible tomorrow.”, especially through the emerging discipline of “synthetic” biology. The basic idea behind synthetic biology, he explained, was that natural organisms could be reprogrammed to do things they wouldn’t normally do, things that might be useful to people. In pursuit of this, researchers had learned not only how to read the genetic code of organisms but also how to write new code and insert it into organisms. Besides making plastic, microbes altered in this way had produced carpet fibers, treated wastewater, generated electricity, manufactured jet fuel, created hemoglobin, and fabricated new drugs. But this was only the tip of the iceberg, Church wrote. The same technique could also be used on people.
“Every cell in our body, whether it’s a bacterial cell or a human cell, has a genome,” he says. “You can extract that genome—it’s kind of like a linear tape—and you can read it by a variety of methods. Similarly, like a string of letters that you can read, you can also change it. You can write, you can edit it, and then you can put it back in the cell.”
This April, the Broad Institute, where Church holds a faculty appointment, was awarded a patent for a new method of genome editing called CRISPR (clustered regularly interspersed short palindromic repeats), which Church says is one of the most effective tools ever developed for synthetic biology. By studying the way that certain bacteria defend themselves against viruses, researchers figured out how to precisely cut DNA at any location on the genome and insert new material there to alter its function. Last month, researchers at MIT announced they had used CRISPR to cure mice of a rare liver disease that also afflicts humans. At the same time, researchers at Virginia Tech said they were experimenting on plants with CRISPR to control salt tolerance, improve crop yield, and create resistance to pathogens.
The possibilities for CRISPR technology seem almost limitless, Church says. If researchers have stored a genetic sequence in a computer, they can order a robot to produce a piece of DNA from the data. That piece can then be put into a cell to change the genome. Church believes that CRISPR is so promising that last year he co-founded a genome-editing company, Editas, to develop drugs for currently incurable diseases.
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