1. THANK YOU CVG SPONSORS
B Round
A Round
Venture Capital Sponsors Professional Service Firms

2. Welcome
Marketing at the Speed of Light
Konstantine Drakonakis
Director, New Haven
LaunchCapital
CTNEXT: New Haven Hub
Derek Koch
Usha Pillai

3. Three Minute Pitches
Marcia Fournier
Judson Brewer
Lew Bender
John Bala SterileWave Medical Corp.

4. Navigating the FDA: Getting to Market
Marketing at the Speed of Light
Introduction
Paul Hughes
Partner
Wiggin and Dana LLP
Keynote
Edison T. Liu, M.D
President & CEO
The Jackson Laboratory

5. Navigating the FDA
or
What is on the horizon?
March 15,2013
Edison Liu, M.D.
edison.liu@jax.org

6. We discover precise genomic solutions for disease
and empower the global biomedical community in
our shared quest to improve human health.
The Jackson Laboratory
To discover precise genomic solutions for
better medicine

7. Biomarker Discovery in Cancer
Then: Single biomarker, spurred by a some
laboratory findings, years of
development before reaching clinic
One marker  many samples
Now: Interrogation of a cancer genome,
in silico validation,
identification of new therapeutic targets
Many markers  few samples
Oct 1997

8. HER2 and clinical trials Start of study CALGB 8869: 1989
Ann Thor Don Berry Publication of final paper: 1998
Soon Paik Mei He
Lynn Dressler
Craig Henderson
Hyman Muss In vitro observation:
ARAC – RAS interaction
J Natl Cancer Inst. Koo, et al. Can Res 59:6057, 1999
90(18):1346-60 (1998)
Patients with acute myeloid leukemia and RAS
mutations benefit most from postremission treatment
with high-dose cytarabine:
a Cancer and Leukemia Group B study.
Neubauer A, et al. J Clin Oncol. 26(28):4603-9, 2008.
9 years per marker, over 1,500 patients:
There has got to be a better way

9. Biomarker Discovery in Cancer
Then: Single biomarker, spurred by a some
laboratory findings, years of
development before reaching clinic
One marker  many samples
Now: Interrogation of a cancer genome,
in silico validation,
identification of new therapeutic targets
Many markers  few samples
Oct 1997

10. Sequenced Breast Cancers: focusing on
structural mutations
PET library construction PET sequences mapping Analysis of Cancer
& sequencing to reference genome Specific Mutations
1Kb 10Kb
PET mapping span
Concordant PET tag density
Automated cancer
genome assembly:
Concordant PETs 7 month analysis to
4 days
Discordant PETs
SOLiD

11. Structure variations
Deletion Unpaired inversion (Inverted orientation)
Abnormal length Different strand
Tandem Duplication Translocation
Incorrect order Different chromosome
Fusion points  predict fusion genes

12. Structural Genomic Changes
in Breast Cancer
Genome Research 21(5):665-75 (2011)

13. Cancer rearrangements are most often private and unique:
Irrelevant mutations or part of the “long tail”
Inaki K, et al. Transcriptional consequences of genomic structural aberrations in
breast cancer. Genome Res. 2011 May;21(5):676-87.

14. Gene ontology (GO) analysis of genes with break points in cancer
genomes: There is a higher organization to the collection of single
structural mutations
Breast cancer Gastric cancer
1)
Genes with break points
RefGen Expecte Obser RefGen Expecte Obser
Biological Process3) +/‐ P value +/‐ P value
e d ved e d ved
Cell adhesion‐mediated 386 20.88 51 + 2.22E‐06 Cell adhesion 592 31.61 73 + 2.62E‐09
signaling
Cell adhesion‐
Cell adhesion 592 32.02 65 + 3.47E‐06 386 20.61 49 + 9.66E‐06
mediated signaling
Neuronal activities 561 30.34 54 + 1.52E‐03 Signal transduction 3256 173.84 222 + 1.53E‐03
Biological process unclassified 5972 322.97 269 ‐ 3.04E‐03 Synaptic transmission 275 14.68 33 + 3.24E‐03
Electron transport 230 12.44 2 ‐ 1.05E‐02 Cell communication 1207 64.44 98 + 4.47E‐03
Other intracellular signaling cascade 212 11.47 27 + 1.12E‐02 Neuronal activities 561 29.95 51 + 6.94E‐03
Cell communication 1207 65.28 97 + 1.16E‐02 Biological process unclassified 5972 318.84 273 ‐ 2.36E‐02
Chemosensory perception 204 11.03 1 ‐ 2.67E‐02 Chemosensory perception 204 10.89 1 ‐ 3.04E‐02
Developmental processes 2065 111.68 144 + 2.97E‐02
Genes in recurrent high copy regions2)
2.35E‐ Chromatin packaging and 0.0024
Signal transduction 3256 151.33 100 ‐ 194 2.21 11 +
05 remodeling 9
Cell surface receptor mediated signal 2.05E‐
1576 73.25 41 ‐
transduction 03
7.74E‐
Developmental processes 2066 96.02 65 ‐
03
1.39E‐
G‐protein mediated signaling 793 36.86 16 ‐
02

15. RPS6KB1‐TMEM49 fusion gene induced by tandem
replication is found in 30% of breast cancers.
5’ TMEM RPS6K
(~100kb)
5’ TMEM RPS6K
(~100kb)
5’ TMEM RPS6K TMEM RPS6K
(~100kb) (~100kb)
5’ TMEM RP EM RPS6K
RPS6KB1-TMEM49 fusion gene

16. Historical data
Expression of RPS6KB1‐VMP1 fusion Our data
is correlated with:
‐Poor prognosis
‐Expression of neighboring oncogenes
around the tandem duplication
‐Expression of oncogenes in ~3Mb adjacent
region
‐ Associated with gene amplification of locus
 The fusion gene is always associated with amplification of this region

17. S6K‐TMEM Fusion Transcript is an indicator
of genomic instability in an “oncogenic region”
of the genome harboring at least 2 oncogenic
components
miRNA21
TMEM 49 S6Kinase

18. Indicator structural mutation:
S6K‐TMEM Fusion Transcript is an indicator
of the amplification of an “oncogenic region” of the genome
miRNA21
Oncogenic
TMEM 49 S6Kinase
bloc
miRNA21 miRNA21
Tandem
duplication S6 TMEM
TMEM 49 Kinase S6Kinase
49
Gene
Amplification

19. Genomic Organization and Cancer:
Higher order organization of mutations in
cancer genomes
Chromosome as an oncogenic organizer
Chromosomal “origami” to generate
cancer gene cassettes
Effect of the germline on cancer therapeutic
outcome
Focus on Structural Mutations in Cancer
Systems Oncogenomics

20. Chronic Myelogenous Leukemia (CML)
Optimizing treatment for CML based on genetic
makeup of the patient
KP Ng, Axel Hillmer,… Yijun Ruan. Ong Sin Tiong
Nat Med. 2012 Mar 18;18(4):521‐8.
Imatianib (Gleevec) – primary and effective treatment
Clinical Challenge: Drug resistance
• Acquired resistance – resistance after long term
treatment ‐ due to second ABL mutation
• Primary resistance – resistance at the beginning of
treatment.
• In Asia, complete cytogenetic response rates are lower ‐
50% vs. 74%. Mechanism unknown

21. Question: is there a reason why 25% of CML cases do not
respond to imatinib?
Approach: Compared the genomes of three CML
cases with primary resistance to Imatinib with two
CML cases sensitive to Imatinib therapy
Results:
3/3 resistance cases
had the same 2.9kb
deletion in the BIM
gene not seen
in sensitive cases (0/2)
Ng KP, Nat Med. 18(4):521-8
(2012)

22. BIM:
• BIM is a gene that activates cell death (pro‐apoptotic).
• Activated BCR‐ABL1, suppresses BIM function thus
allowing leukemia cells to survive. When CML cells are
treated with Imatinib, BIM expression goes up  cell
death
Death of
Bcr-ABL: CML Intact BIM Leukemia cells
Imatinib

23. How does it work?: The 2.9kb BIM deletion polymorphism results
an abnormal transcript (E3) that a produces a truncated and inactive
BIM protein
Normal
Transcripts
E3
Imatinib
Death of
Bcr-ABL: CML Intact BIM Leukemia cells
Imatinib
Deletion Polymorphism
Bcr-ABL: CML BIM Primary
E3 Drug Resistance

24. BIM deletion polymorphism:
• This deletion polymorphism is 3‐5X more common in
CML cases resistant to imatinib that sensitive cases
• This 2.9 kb 2 deletion of BIM is not a mutation, but is a
polymorphism present in normal genomes (a germline
polymorphism):
12% in Asian individuals
0% in Africans
0% in Caucasians

25. We used this genomic intelligence to overcome
this resistance:
Imatinib
Bcr-ABL: CML BIM 3 Primary
Drug
Resistance
BH3 mimetics Imatinib
Death of
Bcr-ABL: CML BIM Leukemia
cells
Ng KP, Nat Med. 18(4):521-8 (2012)

26. This genomic experiment with 5 patients explains the lower response rate
In North Asians to a life saving treatment in CML.
Personalizing medicine in Asia
Now: New
~50% cytogenetic response
CML Patient
in Asia Check for bcr-ABL YES
rearrangement
Check for 2.9kb
deletion
polymorphism in BIM
YES
NO
Imatinib ?
? &
BH3-mimetic Imatinib
>75% cytogenetic 75% cytogenetic
? response response

27. Translation Initiative
We will construct avatars of your cancer:
So that we can discover the best drugs for
your cancer
So that we can devise personalized and
private diagnostic for your cancer
So that we understand the nature of your
cancer and explore the reasons for drug
resistance
So that we may project how your cancer
might evolve

28. PDX of patient = Patient “Avatar” of Drug
Response
Drug 1
Questions
Single tumor Drug 2 Addressed:
from a patient
What drugs will
be effective for
Drug 3 my tumor?
How to combine
these drugs?
Drug 4

29. Predictive for Therapeutics
Activity of afatinib, cetuximab and erlotinib in LG703

30. Cancer Avatar: General workflow
Patient Tumor
from Hartford Hospital
JAX CT/BH JAX West
Deep Sequencing PDX Model:
Test Drugs predicted by genomics
Genome Analysis:
Extract the Source Code
Future
Treatments
Immediate Personalized
Treatment Plan Diagnostic

31. Radiologist of the Genome
Radiologist
Interprets complex data
rendered through Is the consultants
computational algorithms to doctors

32. What is the field looking for?
• Tools and processes to enhance efficiency
in the medical system
• Life style enhancement: prolonging productive life
and healthspan
preventive therapeutics
health monitoring
performance enhancement
mobility and independence
• Personalization of information and medical care

33. Navigating the FDA
March 15,2013
Edison Liu, M.D.

34. Navigating the FDA: Getting to Market
Marketing at the Speed of Light
Panelists
Pamela Bunes
CEO, President & Director
EpiEP, Inc.
Harry Penner
Co-founder, Executive Chairman
New Haven Pharmaceuticals
Dr. Frank Sciavolino
Co-founder, Board Member, Chief
Scientific Officer & President
Thetis Pharmaceuticals LLC

35. Navigating the FDA:
Getting to Market
March 2013 Crossroads Venture Group

36. Overview
 Pre-Clinical Requirements
 Shift in Approval Requirements
 Clinical Trial Sizing
 Diagnostics
 505(b)2
36

37.  Premier Chemistry – Yale - Multiple Partners
 Pfizer – Schering Plough – Merck – Am. Home
 Anxiety / Alzheimers / Sleep / Obesity / Schiz.
 FDA Pre-Clinical Requirements Increased
37

38.  Multiple Programs - Antibiotics
 Nobel Laureate Science – Tom Steitz (Yale)
 Premier Investors
 FDA Changed Approval Criteria After Phase II
38

39.  In-Licensed Programs – Purdue + Yale
 Premier Investor Base – Domain / Canaan / FMP
 Epilepsy – Core Focus
 Equivocal Trial Results – Too Small “n”
39

40. n
 Diagnostic - CSF Detection
 CI / Launch Capital / Management Financed
 Ambitious Multi-antibody Strip Test
 510k vs. PMA
40

41.  In-licensed Programs – Flamel + Yale
 CI + Ironwood + Enhanced + Kuzari + EJ Funds
 Lead Product – Anti-Platelet
 505(b)2 – Multiple FDA Interactions
 CMC + Approval Issues
41

42. Closing Points
 Stay Abreast of All FDA Related Trends
– Pre-clinical to Approval
 Maintain Strong Contact to FDA
– Except When It Might Be Judicious Not To
 March to NDA - Process is Critical
– The Longest Path to Approval Is a Short Cut
42

43. THANK YOU CVG SPONSORS
B Round
A Round
Venture Capital Sponsors Professional Service Firms

44. CVG Upcoming Events
Boardroom Series Second Thursday
7:30 AM – 9:00 AM 4:30 PM – 7:00 PM
March 20 April 11
Investment by Strategics
Electronic Health Records (EHR)
Hartford
A Look at the Industry and Its Future
March 27 Hartford
Employment and Immigration Issues
Stamford May 9
April 3 Financial Services
Stamford
M&A: Legal Implications
Stamford
June 13
April 12
BioTech/Pharma
M&A: Tax Considerations Hartford
Glastonbury

45. CVG 2013 Calendar
Offering 60 Events
Attendance to all Second Thursday
events is free for members.