Why There Needs to be Open Data for Ultra-Rare and Rare Disease
Drug Discovery
Sean Ekins1, Alex M. Clark2, Jill Wood3,4, ...
• Very few researchers chasing
>7000 diseases
• NIH $3.5bn in rare diseases -
orphan drugs $749M 11.4%
budget in 2011 numb...
Examples of Rare Diseases
This is Jonah
• Parents founded
• He needs a cure for Sanfilippo
syndrome (MPS IIIC)
• Collaborates with global groups
• R...
This is Hannah
• Parents founded
• She needs a cure for Giant Axonal
Neuropathy
• Searching for small molecule
therapy (fu...
The Rare Disease Parent
Odyssey
• Diagnosis of child
• Try to find out about disease – papers behind paywall
• Try to conn...
Let me repeat….A Parent/ Patient
Advocate with no Ph.D. can do all this
• Start a foundation
• Raise funds
• Become an exp...
Abigail Alliance for Better Access to Developmental Drugs
Addi & Cassi Fund
American Behcet's Disease Association
Amschwan...
Crowdfunding Science
Huffington Post The O’Neills raised > $1M through
crowdfunding to date
http://www.curesff.org/
www.SavingEliza.com
Funding...
Disruption needed
• #1: NIH and other international scientific
funding bodies should mandate …open
accessibility for all d...
Rare disease foundations
publishing their ideas and
recommendations
• New ways to do research
• Sharing data openly
Examples of Open Science and Tools to
Share Openly
Linked Open
data cloud
2011 (Wikipedia)
Insert disease of choice here
Learning from OSDD TB and Malaria efforts
Open Source Drug Discovery (OSDD) is the concept o...
Openness..can be confusing
• Open Access versus Free Access
• Open Data versus free to download
• Open Source and all of i...
Barriers
• Priority
• Ownership of data
• IP, patenting, How people make money
• Ethical
• Personal privacy
• Publishing, ...
Benefits
• Other families and scientists can find your data
• Minimize repetition
• Lower costs of research, increase effi...
A Mobile App for Open Drug Discovery
A flipboard for science
#ODDT
iOS only
Embraced by rare disease
advocates
Getting peo...
Uses of ODDT for Sanfilippo syndrome http://goo.gl/Zlpmyc
What is needed?
• “Helpers” to take the weight off the parent/patient
• How to manage the complex data?
• How to make sens...
Support human Champions with
software and systems
• Parents need expert advice
• Drug Discovery advice
• Preclinical advic...
A mashup of..
• Crowdfunding
• Crowdsourcing
• Open Innovation
• Open Source
• Open Science
• Precompetitive Initiative
• ...
Start a company
Enables you to apply for
SBIR /STTR grants
Fund research – help
academics and
commercialize their work
The...
Getting the word out there – publish in open journals
Study using patient fibroblasts and
plasma showed TGF-B1 elevated
Published in closed journal
Knowns drugs that down regul...
Finding Promiscuous Old Drugs for New Uses
everolimus
5-fluorouracil
ceftriaxone
Could In silico / in vitro repositioning ...
One family found another family with a child
with the disease by reading a blog
Increasing awareness – rare diseases go ma...
..So lets make rare disease data open
PAPER ID: 22104 “Collaborative sharing of molecules and data in the mobile age” (final paper number: 43)
DIVISION: COMP; D...
We gratefully acknowledge all the scientists who have worked on the rare
diseases described and shared their data
Lisa M. ...
 Email: ekinssean@yahoo.com
 Slideshare: http://www.slideshare.net/ekinssean
 Twitter: collabchem
 Blog: http://www.co...
Why there needs to be open data for ultra-rare and rare disease drug discovery
Why there needs to be open data for ultra-rare and rare disease drug discovery
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Why there needs to be open data for ultra-rare and rare disease drug discovery

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ACS presentation 11th Aug San Francisco on the need for open data in ultra rare and rare diseases. Describes efforts of parent/ patient advocates to fund drug discovery research. Also it describes software for open collaboration and what needs to be done to create software champions for rare diseases. Mentions diseases like Sanfilippo Syndrome, giant axonal neuropathy and Charcot Marie Tooth. Apps like ODDT are also mentioned as a means to share data.

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  • Imagine a future
    Where we help cure rare diseases
    Where we help tailor medicines to overcome variability and side effects
    Where most academics use CDD
    Where all scientists collaborate securely
  • Why there needs to be open data for ultra-rare and rare disease drug discovery

    1. 1. Why There Needs to be Open Data for Ultra-Rare and Rare Disease Drug Discovery Sean Ekins1, Alex M. Clark2, Jill Wood3,4, Lori Sames5,6 and Allison Moore7 1Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay Varina, NC27526, USA. 2Molecular Materials Informatics, 1900 St. Jacques #302, Montreal, Quebec, Canada H3J 2S1 3Jonah's Just Begun, P.O. Box 150057, Brooklyn, NY 11215, USA. 4Phoenix Nest, P.O. BOX 150057, Brooklyn NY 11215, USA. 5Hannah's Hope Fund, P.O. Box 130, Rexford, NY 12148, USA. 6BioGAN Therapeutics, P.O. Box 130, Rexford, NY 12148, USA. 7Hereditary Neuropathy Foundation, 432 Park Avenue South – 4th floor,New York, NY 10016, USA.
    2. 2. • Very few researchers chasing >7000 diseases • NIH $3.5bn in rare diseases - orphan drugs $749M 11.4% budget in 2011 numbers • Relatively easy to treat. At the forefront of gene therapy resurgence • Only miniscule clinical trials possible Rare disease biology not well known Affects 10s- 1000s per disease Treatments need to be expensive $1M/yr pp The Problem/ Opportunity
    3. 3. Examples of Rare Diseases
    4. 4. This is Jonah • Parents founded • He needs a cure for Sanfilippo syndrome (MPS IIIC) • Collaborates with global groups • Researchers just developed a KO mouse funded by Sanfilippo foundations globally • Searching for small molecule therapy, study animal models (Dr. Alexey Pshezhetsky, University of Montreal) • Working on gene therapy (Dr. Brian Bigger, University of Manchester) • Natural History Study (Dr. Paul Levy, Montefiore) • Started registry
    5. 5. This is Hannah • Parents founded • She needs a cure for Giant Axonal Neuropathy • Searching for small molecule therapy (funded postdoc with Dr. Jim Inglese, NIH) • Funded gene therapy - entering clinical trial (Dr. Steven Gray, UNC) • Funded - Natural history study (Dr. Douglas Sproule, Columbia) • Started Registry - GRIN
    6. 6. The Rare Disease Parent Odyssey • Diagnosis of child • Try to find out about disease – papers behind paywall • Try to connect with scientists • Form not-for-profit • Raise funds • Fund Scientific research on disease • Advocate for support from NIH, FDA etc • Start a company • Try to find a cure before its too late Wood J et al., Drug Disc Today, 18: 1043–1051, 2013
    7. 7. Let me repeat….A Parent/ Patient Advocate with no Ph.D. can do all this • Start a foundation • Raise funds • Become an expert on their/childs disease • Set up a scientific advisory board • Fund scientific projects • Submit NIH grants • Start a company • Leverage social media, traditional media
    8. 8. Abigail Alliance for Better Access to Developmental Drugs Addi & Cassi Fund American Behcet's Disease Association Amschwand Sarcoma Cancer Foundation BDSRA (Batten Disease Support and Research Association) Beyond Batten Disease Foundation Blake’s Purpose Foundation Breakthrough Cancer Coalition Canadian PKU & Allied Disorders Center for Orphan Disease Research and Therapy, University of Pennsylvania Children’s Cardiomyopathy Foundation Cooley's Anemia Foundation Dani’s Foundation Drew’s Hope Research Foundation EveryLife Foundation for Rare Diseases GIST Cancer Awareness Foundation Hannah's Hope Fund Hope4Bridget Foundation Hypertrophic Cardiomyopathy Association - HCMA I Have IIH ISRMD (International Society for Mannosidosis and Related Diseases) Jacob’s Cure Jain Foundation Jonah's Just Begun-Foundation to Cure Sanfilippo Inc. Kids V Cancer Kurt+Peter Foundation LGMD2I Research Fund Lymphangiomatosis & Gorham's Disease Alliance MAGIC Foundation Manton Center for Orphan Disease Research MarbleRoad Mary Payton's Miracle Foundation Midwest Asian Health Association (MAHA) MPD Support National Gaucher Foundation National MPS Society National Organization Against Rare Cancers National PKU Alliance National Tay-Sachs & Allied Diseases Association New Hope Research Foundation NextGEN Policy Noah's Hope - Batten disease research fund Our Promise to Nicholas Foundation Oxalosis and Hyperoxaluria Foundation Partnership for Cures Periodic Paralysis Association RARE Project Ryan Foundation for MPS Children Sanfilippo Foundation for Children Sarcoma Foundation of America Solving Kids' Cancer Taylor's Tale: Fighting Batten Disease Team Sanfilippo Foundation The Alliance Against Alveolar Soft Part Sarcoma The Life Raft Group The NOMID Alliance The Transverse Myelitis Association The XLH Network, Inc. United Pompe Foundation Many of these groups are doing R&D on a shoestring how can we help? How do they fund it? Just some of the many rare disease groups
    9. 9. Crowdfunding Science
    10. 10. Huffington Post The O’Neills raised > $1M through crowdfunding to date http://www.curesff.org/ www.SavingEliza.com Funding gene therapy for Sanfilippo A Jonny Lee Miller raised >$177,526 for Sanfilippo C on Crowdrise Crowdfunding Rare Disease Science
    11. 11. Disruption needed • #1: NIH and other international scientific funding bodies should mandate …open accessibility for all data generated by publicly funded research. • #2: Reboot the pharmaceutical industry by extending the notion of ‘‘precompetitive’’ collaboration to encompass later stages of research to allow PPPs to flourish. • #3: FDA takes a proactive role in making relevant clinical data available that will help all drug developers (as well as NCATS) to bridge the valley of death and remove a bottleneck. • #4: Companies listen to the patients as they generate data on social media, mine it for indications and off target effects. Companies and funding bodies will find the innovators to exploit this information and use collaborative tools to share data
    12. 12. Rare disease foundations publishing their ideas and recommendations
    13. 13. • New ways to do research • Sharing data openly
    14. 14. Examples of Open Science and Tools to Share Openly Linked Open data cloud 2011 (Wikipedia)
    15. 15. Insert disease of choice here Learning from OSDD TB and Malaria efforts Open Source Drug Discovery (OSDD) is the concept of drug discovery where all data and ideas are shared in real time, and anyone may participate at any level. This prior disclosure means that there will be no patents and that any technology is both academically and commercially exploitable by whoever wishes to do so.
    16. 16. Openness..can be confusing • Open Access versus Free Access • Open Data versus free to download • Open Source and all of its “licenses”
    17. 17. Barriers • Priority • Ownership of data • IP, patenting, How people make money • Ethical • Personal privacy • Publishing, rewards and promotions – kudos • Publishing open access has cost involved..
    18. 18. Benefits • Other families and scientists can find your data • Minimize repetition • Lower costs of research, increase efficiency • Analogy to Linux – open source can be commercial success • Some open scientists are notable
    19. 19. A Mobile App for Open Drug Discovery A flipboard for science #ODDT iOS only Embraced by rare disease advocates Getting people to share data openly is a challenge NIH SBIR reviewers want closed systems to preserve IP Developed with Alex Clark Open Drug Discovery Teams – brings data from Twitter and the internet together Ekins et al., Mol Informatics, 31: 585-597, 2012 http://goo.gl/r9NP7p
    20. 20. Uses of ODDT for Sanfilippo syndrome http://goo.gl/Zlpmyc
    21. 21. What is needed? • “Helpers” to take the weight off the parent/patient • How to manage the complex data? • How to make sense of the literature? • How to foster collaboration? • How to leverage what is learnt from other diseases? • How scientists find funding or projects to work on? • How parents find scientists to solve their problems? • How to accelerate the process of discovery? • Find patients for registries and clinical studies
    22. 22. Support human Champions with software and systems • Parents need expert advice • Drug Discovery advice • Preclinical advice • Awareness of research outside of their disease This could be you here
    23. 23. A mashup of.. • Crowdfunding • Crowdsourcing • Open Innovation • Open Source • Open Science • Precompetitive Initiative • Open Collaboration
    24. 24. Start a company Enables you to apply for SBIR /STTR grants Fund research – help academics and commercialize their work Then use NIH TRND and NCATS programs
    25. 25. Getting the word out there – publish in open journals
    26. 26. Study using patient fibroblasts and plasma showed TGF-B1 elevated Published in closed journal Knowns drugs that down regulate it not tested Losartan, statins, puromycin, rimonabant, Aliskiren http://goo.gl/Y2iBBF Helping the researchers to help the patients
    27. 27. Finding Promiscuous Old Drugs for New Uses everolimus 5-fluorouracil ceftriaxone Could In silico / in vitro repositioning find leads-drugs quicker?
    28. 28. One family found another family with a child with the disease by reading a blog Increasing awareness – rare diseases go mainstream
    29. 29. ..So lets make rare disease data open
    30. 30. PAPER ID: 22104 “Collaborative sharing of molecules and data in the mobile age” (final paper number: 43) DIVISION: COMP; DAY & TIME OF PRESENTATION: August 10, 2014 from 4:45 pm to 5:15 pm LOCATION: Moscone Center, West Bldg., Room: 2005 PAPER ID: 22094 “Expanding the metabolite mimic approach to identify hits for Mycobacterium tuberculosis ” (final paper number: 78) DIVISION: COMP: DAY & TIME OF PRESENTATION: August 11, 2014 from 9:00 am to 9:30 am LOCATION: Moscone Center, West Bldg., Room: 2005 PAPER ID: 22120 “Why there needs to be open data for ultrarare and rare disease drug discovery” (final paper number: 48) DIVISION: CINF:SESSION DAY & TIME OF PRESENTATION: August 11, 2014 from 10:50 am to 11:20 am LOCATION: Palace Hotel, Room: Marina PAPER ID: 22183 “Progress in computational toxicology” (final paper number: 125) DIVISION: TOXI: DAY & TIME OF PRESENTATION: August 12, 2014 from 6:30 pm to 10:30 pm LOCATION: Moscone Center, North Bldg. , Room: 134 PAPER ID: 22091 “Examples of how to inspire the next generation to pursue computational chemistry/cheminformatics” (final paper number: 100) DIVISION: CINF: Division of Chemical Information DAY & TIME OF PRESENTATION: August 13, 2014 from 8:25 am to 8:50 am LOCATION: Palace Hotel, Room: Presidio PAPER ID: 22176 “Applying computational models for transporters to predict toxicity” (final paper number: 132) DIVISION: TOXI: DAY & TIME OF PRESENTATION: August 13, 2014 from 9:45 am to 10:05 am LOCATION: InterContinental San Francisco, Room: Grand Ballroom A PAPER ID: 22186 “New target prediction and visualization tools incorporating open source molecular fingerprints for TB mobile version 2” (final paper number: 123) DIVISION: CINF: DAY & TIME OF PRESENTATION: August 13, 2014 from 1:35 pm to 2:05 pm LOCATION: Palace Hotel, Room: California Parlor You can find me @...
    31. 31. We gratefully acknowledge all the scientists who have worked on the rare diseases described and shared their data Lisa M. Jarvis for covering rare diseases at C&E News Antony J. Williams for inspiring open research
    32. 32.  Email: ekinssean@yahoo.com  Slideshare: http://www.slideshare.net/ekinssean  Twitter: collabchem  Blog: http://www.collabchem.com/  Website: http://www.collaborations.com/CHEMISTRY.HTM
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