This document discusses challenges with accessing and using biomarker information from various dispersed sources. It introduces BiomarkerBase as a solution that aggregates biomarker data from public sources into a centralized knowledge base to facilitate analysis and biomarker planning. BiomarkerBase allows users to organize information, generate reports, and collaborate to overcome issues of information overload and siloed data.

1. H O W TO ACC E L E R AT E
O U TCO M E S
O F B I O M A R K E R
I N F O R M AT I O N A N A L Y S I S
A DA M C A R R O L L , P H D
C S O , A M P L I O N I N C .
A DA M @ A M P L I O N . CO M
F E B R UA R Y 1 7 , 2 0 1 5

2. Information overload is a persistent problem for
professionals interested in molecular biomarkers
and is exacerbated by ‘single-use information
culture’ within organizations.
Do you want to discover how your organization
can solve these challenges?
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

3. At Amplion, we see biomarkers as the key to delivering on the
promise of personalized medicine. From drug research and discovery
and companion diagnostic development to patient care, we
understand that biomarkers will drive personalized care.
Researchers can now have an unprecedented view of the clinical
biomarker landscape with every biomarker in an FDA-approved test
or drug label, thousands of biomarkers in clinical trials.
And with the recent inclusion of Laboratory Developed Tests (LDTs,)
30% more of the newest and most innovative clinical biomarkers are
now normalized and readily accessible through the intuitive interface
of BiomarkerBase™.
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

4. How Do You Stay Up To Date
With Biomarker Trends?
Subscribe to the Biomarker Trends Blog to keep up
with the issues related to developing and
commercializing biomarker-based IVD tests.
Click here and
subscribe.

5. W H AT DO YO U W R I T E O N A N E P I T U B E ?
http://www.flickr.com/photos/jepoirrier/349580669/
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

6. W H AT N A M E DO YO U G I V E A F I L E ?
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

7. U S E R E X P E R I E N C E
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

8. T W O K E Y C H A L L E N G E S :
1. PRESERVING
INFORMATION
-Institutional Knowledge
-“Single-Use” Information
Culture
2. FINDING
INFORMATION
-High volume & velocity
-Information, not data
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

9. N OV E L B I O M A R K E R
P U B L I C AT I O N S
Publications
0
1000
2000
3000
4000
Publication Year
2003200420052006200720082009 2010 2011 2012 2013 2014
Researchers
announce new
candidate biomarkers
daily.
Many of these will not
prove to be useful in a
clinical setting.
Biomarkers already in
the clinic provide
essential, actionable
opportunities for use
in test and drug
development.
Clinical
Biomarkers
Are Essential
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

10. F I N D I N G C L I N I C A L
B I O M A R K E R S I S H A R D
Information exists in
numerous, unconnected
databases.
Each of these databases is
challenging to search in a
comprehensive way.
Result?
There is significant
potential for missed
opportunities.
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

11. Use Case 1:
Search Term Studies Returned
Ca 125 251
Ca-125 251
Mucin-16 187
Mucin 16 187
Muc16 3
Which trials measure CA-125?
Synonyms are not
normalized
Results must be
parsed
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

12. Biomarkers can be described in:
• Conditions
• Interventions
• Arms
• Outcome Measures
• Measure
• Description
• Brief Description
• Detailed Description
• Eligibility > Criteria
Use Case 2:
Find ALL clinical trials that measure levels of
epidermal growth factor receptor.
Search interface
limits which fields
are searched
Only way to search
completely is to parse
XML documents
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

13. Test Names:
• OVA1™ Test
• ROMA™
• VIDAS® CA 125 II Assay™
• Others...
Can’t search
test databases
by Intended
Use.
Can’t search
more than one
Product Code.
OVA1 & ROMA:
same Product
Code, different
FDA Databases.
Can’t search by
the molecular
target
measured.
Use Case 3:
Find tests available for supporting
diagnosis of ovarian cancer.
Product Code:
• [ ONX]
• [ ONX]
• [ LTK]
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

14. Create a comprehensive
summary using tests, drugs,
clinical trials, and publications.
Use Case 4:
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

15. T H E S O L U T I O N I S
B I O M A R K E R B A S E
http://www.biomarkerbase.com
A manually curated
knowledge base that
aggregates and organizes
clinical biomarker information
from publicly available
sources.
A solution to the challenges of
accessing and using those
sources.
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

16. Begin
Commercialization
H OW D O W E B U I L D O U R
B I O M A R K E R P L A N ?
Gather Biomarker
Information
Organize
Information
Analyze
Information
Act
FDA Test
Databases
Drugs@FDA
ClinicalTrials.gov
Manual
AnalysisPowerPoint
Access
Excel
PubMed
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

17. Begin
Commercialization
Gather Biomarker
Information
Organize
Information
Analyze
Information
Act
K N OW L E D G E B A S E
Manual
AnalysisPowerPoint
Access
Excel
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

18. K N O W L E D G E M A N AG E M E N T
Gather Biomarker
Information
Organize
Information
Analyze
Information
Begin
Commercialization
Act
Manual
Analysis
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

19. Gather Biomarker
Information
Organize
Information
Analyze
Information
Begin
Commercialization
Act
K N O W L E D G E M A N AG E M E N T
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

20. S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E

21. About Amplion
Remember the last scene from Raiders of the Lost Ark where the Ark of the
Covenant becomes lost in a sea of identical wooden crates inside a
gigantic warehouse?
At Amplion, we liken the Ark of the Covenant to how hugely valuable — but
largely inaccessible — biomarker data is currently housed. Sure, it’s there —
but good luck finding it.
We want to change that, which is why we created Amplion’s flagship
product, BiomarkerBase™ that’s already reinventing translational research
for a number of the largest drug and diagnostics companies worldwide.
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E
Based in Bend, Oregon, Amplion is
accelerating personalized medicine by
making it easier for drug and
diagnostic development professionals
to both access and analyze
information about clinical biomarkers.

22. Want To Stay Up To Date
with Biomarker Trends?
Subscribe to the Biomarker Trends Blog to keep
up with the issues related to developing and
commercializing biomarker-based IVD tests.
Click here and
subscribe.

23. Ready to Escape the Single-Use
Information Culture?
Turbo Charge Your Biomarker Planning
with BiomarkerBase™
Schedule your
demo here.
Manage, analyze and share both public and proprietary information that drives your
biomarker planning
Stop losing organizational biomarker knowledge when someone walks out the door
Assess the risks and benefits of applying a particular biomarker to your project
Collaborate with colleagues on appropriate biomarker planning for all clinical
applications
Automatically generate your biomarker plans and other reports

24. T H A N K Y O U
A DA M C A R R O L L , P H D
C S O , A M P L I O N I N C .
A DA M @ A M P L I O N . CO M
F E B R UA R Y 1 7 , 2 0 1 5
S TAY U P TO DAT E W I T H B I O M A R K E R T R E N D S H E R E