- National challenges in cancer research include lowering barriers to data access and analysis, and integrating clinical and basic research data to enable improved outcomes.
- Disruptive technologies like high-throughput biology and ubiquitous computing are generating large amounts of molecular and clinical cancer data.
- The NCI is working to build infrastructure like the Genomics Data Commons and Cloud Pilots to make these data widely accessible and support data analysis.
- The goal is to develop a national "learning health system" that applies insights from real-world cancer data to research and clinical practice to continuously improve patient care and outcomes.
FDA NGS and Big Data Conference September 2014Warren Kibbe
Presentation for the FDA NGS and Big Data Conference September 2014 held on the NIH campus. NCI initiatives, including Cancer Genomics Data Commons, NCI Cloud Pilots, big data issues for cancer
FDA NGS and Big Data Conference September 2014Warren Kibbe
Presentation for the FDA NGS and Big Data Conference September 2014 held on the NIH campus. NCI initiatives, including Cancer Genomics Data Commons, NCI Cloud Pilots, big data issues for cancer
Nci clinical genomics data sharing ncra sept 2016Warren Kibbe
Gave an update on the Cancer Research Data Ecosystem, the Genomic Data Commons, Cloud Pilots, incentives for data sharing in cancer research to the NCI Council of Research Advocates (NCRA) on Monday, September 26th, 2016
NCI Cancer Genomics, Open Science and PMI: FAIR Warren Kibbe
Talk given to the NLM Fellows on July 8, 2016. Touches on Cancer Genomics, Open Science and PMI: FAIR in NCI genomics thinking and projects. Includes discussion of the Genomic Data Commons (GDC), Cancer Data Ecosystem, Data sharing, and the NCI cancer clinical trials open API.
Cancer Moonshot, Data sharing and the Genomic Data CommonsWarren Kibbe
Gave the inaugural Informatics Grand Rounds at City of Hope on September 8th. NIH Commons, Genomic Data Commons, NCI Cloud Pilots, Cancer Moonshot and rationale for changing incentives around data sharing all discussed.
Day 2 Big Data panel at the NIH BD2K All Hands 2016 meetingWarren Kibbe
Big data in oncology and implications for open data, open science, rapid innovation, data reuse, reproducibility and data sharing. Cancer Moonshot, Precisions Medicine Initiative (PMI), the Genomic Data Commons, NCI Cloud Pilots, NCI-DOE Pilots, and the Cancer Research Data Ecosystem.
National Cancer Data Ecosystem and Data SharingWarren Kibbe
Grand Rounds at the Siteman Cancer Center at Washington University. Highlighting the Genomic Data Commons and the National Cancer Data Ecosystem defined by the Cancer Moonshot Blue Ribbon Panel
NCI Cancer Imaging Program - Cancer Research Data EcosystemWarren Kibbe
Given to the NCI Cancer Imaging Program monthly telecon on January 9th, 2017. NCI Genomic Data Commons, Beau Biden Cancer Moonshot Blue Ribbon Panel, Cancer Research Data Ecosystem and the role of imaging in precision medicine
Digital Pathology: Precision Medicine, Deep Learning and Computer Aided Inter...Joel Saltz
In this presentation, I will survey the development of Digital Pathology methodology beginning with the 1997 virtual microscope prototype at Hopkins to current tools, methods and algorithms designed to display, analyze and classify whole slide imaging data. I will describe methods, tools and algorithms to extract information from Pathology images. These tools include ability to traverse whole slide images, segment nuclei, carry out deep learning region classification and characterize relationship between extracted features and morphological structures. I will also describe some of the research efforts that motivate development of these tools, the role Pathomics is playing in precision medicine research as well as the impact of Pathology Informatics on clinical practice and health care quality.
Presentation at the Department of Biomedical Informatics, University Pittsburgh Medical Center, April 27, 2018
Converged IT Summit - NCI Data SharingWarren Kibbe
Cancer Moonshot, Data Sharing, Genomic Data Commons, NCI Cloud Pilots, Cancer Research Data Ecosystem, technology advances, chemotherapy advances, MATCH, NCI Cancer Moonshot Blue Ribbon Panel Recommendations
Advancing Innovation and Convergence in Cancer Research: US Federal Cancer Mo...Jerry Lee
Special Seminar at the 8th Taiwan Biosignatures Workshop to share overall work of NCI's Center for Strategic Scientific Initiatives since 2003 as well as CSSI's influence on select projects initiated by the 2016 WH Cancer Moonshot Task Force that include Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) network, International Cancer Proteogenome Consortium, and the Blood Profiling Atlas in Cancer (BloodPAC) commons.
CI4CC Moonshot Blue Ribbon Panel Report 20161010Warren Kibbe
Presentation to the Fall CI4CC meeting in Utah. CI4CC Moonshot Blue Ribbon Panel Report. Highlights of Vice President Biden's Cancer Moonshot and the NCI Blue Ribbon Panel Recommendations.
Twenty Years of Whole Slide Imaging - the Coming Phase ChangeJoel Saltz
I surveyed the development of Digital Pathology methodology beginning with the 1997 virtual microscope prototype at Hopkins (PMC2233368) to current tools, methods and algorithms designed to display, analyze and classify whole slide imaging data. I will describe the capabilities of current methods, describe how these methods are likely to evolve and how they will be likely to impact Pathology research and practice.
Nci clinical genomics data sharing ncra sept 2016Warren Kibbe
Gave an update on the Cancer Research Data Ecosystem, the Genomic Data Commons, Cloud Pilots, incentives for data sharing in cancer research to the NCI Council of Research Advocates (NCRA) on Monday, September 26th, 2016
NCI Cancer Genomics, Open Science and PMI: FAIR Warren Kibbe
Talk given to the NLM Fellows on July 8, 2016. Touches on Cancer Genomics, Open Science and PMI: FAIR in NCI genomics thinking and projects. Includes discussion of the Genomic Data Commons (GDC), Cancer Data Ecosystem, Data sharing, and the NCI cancer clinical trials open API.
Cancer Moonshot, Data sharing and the Genomic Data CommonsWarren Kibbe
Gave the inaugural Informatics Grand Rounds at City of Hope on September 8th. NIH Commons, Genomic Data Commons, NCI Cloud Pilots, Cancer Moonshot and rationale for changing incentives around data sharing all discussed.
Day 2 Big Data panel at the NIH BD2K All Hands 2016 meetingWarren Kibbe
Big data in oncology and implications for open data, open science, rapid innovation, data reuse, reproducibility and data sharing. Cancer Moonshot, Precisions Medicine Initiative (PMI), the Genomic Data Commons, NCI Cloud Pilots, NCI-DOE Pilots, and the Cancer Research Data Ecosystem.
National Cancer Data Ecosystem and Data SharingWarren Kibbe
Grand Rounds at the Siteman Cancer Center at Washington University. Highlighting the Genomic Data Commons and the National Cancer Data Ecosystem defined by the Cancer Moonshot Blue Ribbon Panel
NCI Cancer Imaging Program - Cancer Research Data EcosystemWarren Kibbe
Given to the NCI Cancer Imaging Program monthly telecon on January 9th, 2017. NCI Genomic Data Commons, Beau Biden Cancer Moonshot Blue Ribbon Panel, Cancer Research Data Ecosystem and the role of imaging in precision medicine
Digital Pathology: Precision Medicine, Deep Learning and Computer Aided Inter...Joel Saltz
In this presentation, I will survey the development of Digital Pathology methodology beginning with the 1997 virtual microscope prototype at Hopkins to current tools, methods and algorithms designed to display, analyze and classify whole slide imaging data. I will describe methods, tools and algorithms to extract information from Pathology images. These tools include ability to traverse whole slide images, segment nuclei, carry out deep learning region classification and characterize relationship between extracted features and morphological structures. I will also describe some of the research efforts that motivate development of these tools, the role Pathomics is playing in precision medicine research as well as the impact of Pathology Informatics on clinical practice and health care quality.
Presentation at the Department of Biomedical Informatics, University Pittsburgh Medical Center, April 27, 2018
Converged IT Summit - NCI Data SharingWarren Kibbe
Cancer Moonshot, Data Sharing, Genomic Data Commons, NCI Cloud Pilots, Cancer Research Data Ecosystem, technology advances, chemotherapy advances, MATCH, NCI Cancer Moonshot Blue Ribbon Panel Recommendations
Advancing Innovation and Convergence in Cancer Research: US Federal Cancer Mo...Jerry Lee
Special Seminar at the 8th Taiwan Biosignatures Workshop to share overall work of NCI's Center for Strategic Scientific Initiatives since 2003 as well as CSSI's influence on select projects initiated by the 2016 WH Cancer Moonshot Task Force that include Applied Proteogenomics Organizational Learning and Outcomes (APOLLO) network, International Cancer Proteogenome Consortium, and the Blood Profiling Atlas in Cancer (BloodPAC) commons.
CI4CC Moonshot Blue Ribbon Panel Report 20161010Warren Kibbe
Presentation to the Fall CI4CC meeting in Utah. CI4CC Moonshot Blue Ribbon Panel Report. Highlights of Vice President Biden's Cancer Moonshot and the NCI Blue Ribbon Panel Recommendations.
Twenty Years of Whole Slide Imaging - the Coming Phase ChangeJoel Saltz
I surveyed the development of Digital Pathology methodology beginning with the 1997 virtual microscope prototype at Hopkins (PMC2233368) to current tools, methods and algorithms designed to display, analyze and classify whole slide imaging data. I will describe the capabilities of current methods, describe how these methods are likely to evolve and how they will be likely to impact Pathology research and practice.
2016 Data Commons and Data Science Workshop June 7th and June 8th 2016. Genomic Data Commons, FAIR, NCI and making data more findable, publicly accessible, interoperable (machine readable), reusable and support recognition and attribution
di Pier Giuseppe Pelicci, MD-PhD, Istituto Europeo di Oncologia IEO, Università degli Studi di Milano.
Slide per l'intervento tenuto in Fondazione Giannino Bassetti in occasione del primo incontro del ciclo "La medicina di precisione", primo progetto dalla convenzione tra Università di Pavia e Fondazione Bassetti.
12 marzo 2018
Presentation "The Impact of All Data on Healthcare"
Keith Perry
Associate VP & Deputy CIO
UT MD Anderson Cancer Center
With continuing advancement in both technology and medicine, the drive is on to make all data meaningful to drive medical discovery and create actionable outcomes. With tools and capabilities to capture more data than ever before, the challenge becomes linking existing structured and unstructured clinical data with genomic data to increase the industry’s analytical footprint.
Learning Objectives:
∙ Discuss the need to make all data meaningful in order to speed discovery of new knowledge
∙ Provide examples of an analytical direction that supports evolution in medicine
∙ Expose the challenges facing the industry with respect to ~omits
Challenges and Opportunities for Digital PCR in the CLIA Laboratory of the Mo...Kate Barlow
Anthony Magliocco, Chair of Anatomical Pathology, Moffitt Cancer Center, USA
The Moffit Cancer Center is one of the largest NCI designated comprehensive free-standing cancer centers in the USA. The center has developed one of the most advanced personalized cancer medicine treatment programs in the world. This program is supported by a comprehensive and advanced CLIA molecular diagnostics. Digital PCR assays are currently being developed for several clinical applications including TKI resistance monitoring in patients with advanced lung cancer. The challenges and opportunities in deploying digital PCR into clinical practice will be discussed.
Data sharing drivers in precision oncology, biomedical research, and healthcare. Accelerating discovery, innovation, providing credit for all stakeholders - patients, researchers, care providers, payers.
DOE-NCI Pilots presentation at the Frederick National Laboratory Advisory Com...Warren Kibbe
May 2016 FNLAC presentation of the DOE-NCI partnership around three pilots focused on existing projects in NCI and existing NSCI directives and activities in DOE.
Presentation to the Department of Biology at the University of Windsor, Windsor, Ontario. The description and update of activities related to the International Cancer Genome Consortium (ICGC)
3. Overview
• National Challenges in Cancer Data
• Disruptive Technologies
• NCI Genomics Data Commons
• NCI Cloud Pilots
• Building a national learning health system
for cancer clinical genomics
4. National Challenges in Cancer
Informatics
• Lowering barriers to data access,
analysis and modeling for cancer
research
• Integration of data and learning from
basic and clinical research with
cancer care that enable prediction
and improved outcomes
5. We need:
• Open Science (Open Access, Open Data,
Open Source) and Data Liquidity for the
cancer community
• Semantic interoperability through CDEs
and Case Report Forms mapped to
standards
• Sustainable models for informatics
infrastructure, services, data
7. Disruptive Technologies
• Printing
• Steam power
• Transportation
• Electricity
• Antibiotics
• Semiconductors &VLSI design
• http
• High throughput biology
Systems view - end of reductionism?
8. Precision Oncology
• The era of precision medicine and precision
oncology is predicated on the integration of
research, care, and molecular medicine and
the availability of data for modeling, risk
analysis, and optimal care
How do we re-engineer
translational research policies
that will enable a true learning
healthcare system?
9.
10. Disruptive Technologies
• Printing
• Steam power
• Transportation
• Electricity
• Antibiotics
• Semiconductors &VLSI design
• http
• High throughput biology
• Ubiquitous computing
Everyone is a data provider
Data immersion
World:
6.6B active mobile contracts
1.9B smart phone contracts
1.1B land lines
World population 7.1B
US:
345M active mobile contracts
287M smart phone contracts
US population 313M
11. What about social media?
• Social media may be one avenue for
modifying behaviors that result in cancer
• Properly orchestrated, social media can
have dramatic impact on quality of life
for patients and survivors
• It can reach into all segments of our
society, including underserved populations
12. Public Health
• These three modifiable factors -
infectious disease, smoking, and poor
nutrition and lack of exercise contribute
to at least 50% of our current cancer
burden. And the cost from loss of quality of
life, pain and suffering is incalculable.
13. Some NCI Big Data activities
• TCGA, TARGET and ICGC
– Cancer Genomics Data Commons
– NCI Cloud Pilots
• Molecular Clinical Trials:
– MPACT, MATCH, Exceptional Responders
15. From the Second Machine Age
From: The Second Machine Age: Work, Progress, and Prosperity in a Time of Brilliant
Technologies by Erik Brynjolfsson & Andrew McAfee
16. Molecular data is Big Data
• Brief trip down memory lane
• Sequencing and the Human Genome
Project
21. HGP outcomes
• $5.6B investment in 2010 dollars
• $800B economic development
• Enabled many basic discoveries, clinical
therapies and diagnostics, and applied
technologies
22. TCGA history
• About three years post-HGP
• Initiated in 2005
• Collaboration of NHGRI and NCI to
examine GBM, Lung and Ovarian cancer
using genomic techniques in 2006.
• Expanded to 20+ tumor types.
23. TCGA drivers
• Providing high quality reference sets for
20+ tissue types
• Providing a platform for systems biology
and hypothesis generation
• Providing a test bed for understanding the
real world implications of consent and data
access policies on genomic and clinical
data.
28. The Mutational Burden of Human Cancer
Mike Lawrence and Gaddy Getz
Increasing genomic
complexity
Childhood
cancers
Carcinogens
29. TCGA Nature 497:67 (2013)
Molecular Subgroups Refine Histological Diagnosis
Of Endometrial Carcinoma
POLE
(ultra-
mutated)
MSI
(hypermutated)
Copy-number low
(endometriod)
Copy-number high
(serous-like)
Histology
Mutations
Per Mb
PolE
MSI / MSH2
Copy #
PTEN
p53
Serous
misdiagnosed
as endometrioid?
Endometrioid
Serous
Histology
30. TCGA Nature 497:67 (2013)
Molecular Diagnosis of Endometrial Cancer May
Influence Choice of Therapy
POLE
(ultra-
mutated)
MSI
(hypermutated)
Copy-number low
(endometriod)
Copy-number high
(serous-like)
Histology
Mutations
Per Mb
PolE
MSI / MSH2
Copy #
PTEN
p53
Adjuvant
chemotherapy?
Adjuvant
radiotherapy?
Surgery only?
31. GDC
NCI Cancer Genomics Data Commons
NCI Genomics
Data Commons
Genomic +
clinical data
. . .
32. GDC
NCI Cancer Genomics Data Commons
NCI Genomics
Data Commons
Genomic +
clinical data
. . .
Cancer
information
donor
34. Driver for the Cloud Pilots
• An inflection point for TCGA is looming
0
500,000
1,000,000
1,500,000
2,000,000
2,500,000
7/1/09
1/1/10
7/1/10
1/1/11
7/1/11
1/1/12
7/1/12
1/1/13
7/1/13
1/1/14
7/1/14
Gigabytes(GB)
35. NCI Cloud Pilots
• Funding for up to 3 cloud pilots - 24
month pilots that are meant to inform the
Cancer Genomics Data Commons
– Explore models for cancer genomics APIs
– Explore cloud models for data+analysis
• Announced this week: The Institute for
Systems Biology, The Broad Institute, and
Seven Bridges will be the initial consortium
36. NCI Cloud Pilots
• A way to move computation to the data
• Sustainable models for providing access
to data
• Reproducible pipelines for QA, variant
calling, knowledge sharing
• Define genomics/phenomics APIs for
discovering new variants contributing to
cancer, enhancing response, modulating
risk
37. GDC
Relationship of the Cancer Genomics
Data Commons and NCI Cloud Pilots
NCI Cloud
Computational Centers
Periodic
Data Freezes
Search /
retrieve
Analysis
NCI Genomics
Data Commons
39. Institute of Medicine Report
Sept 10, 2013
Delivering High-Quality Cancer Care: Charting
a New Course for System in Crisis
Understanding the outcomes of individual cancer patients as
well as groups of similar patients
1
Capturing data from real-world settings that researchers
can then analyze to generate new knowledge
2
A “Learning” healthcare IT system that learns routinely and
iteratively by analyzing captured data, generating evidence,
and implementing new insights into subsequent care.
3
40. “Learning IT System”
IOM Report on Cancer Care
Search Prior Knowledge: Enable clinicians to use
previous patients’ experiences to guide future care.
1
Care Team Collaboration: Facilitate a
coordinated cancer care workforce & mechanisms for
easily sharing information with each other.
2
Cancer Research: Improve the evidence base for quality
cancer care by utilizing all of the data captured during real-
world clinical encounters and integrating it with data captured
from other sources.
3
43. Netflix’s Cinematch software analyzes each customer’s film-viewing habits and
recommends other movies.
Can we make a Cinematch
for cancer patients?
44. Patients like me
• Patients with diagnoses,
symptoms and labs like yours are
eligible for these trials…
• Patient-centered resources…
45. If we can forecast
the weather, can
we forecast
cancer?
46. Where is the weather moving?
Doppler & Map Fusion
51. Modeling Tumor Growth
Mathematical model: proliferation
of cells with the potential for
invasion and metastasis
Swanson et al., British Journal of Cancer, 2007: 1-7.
56. Precision Oncology
• The era of precision medicine and precision
oncology is predicated on the integration of
research, care, and molecular medicine and
the availability of data for modeling, risk
analysis, and optimal care
How do we re-engineer
translational research policies
that will enable a true learning
healthcare system?
57. The future
• Elastic computing ‘clouds’
• Social networks
• Big Data analytics
• Precision medicine
• Measuring health
• Practicing protective medicine
Semantic and
synoptic data
Intervening
before health is
compromised
Learning systems that enable learning
from every cancer patient