Better Cancer Monitoring with Cell-Free DNA October 2014

Forward-Looking Statements Statements in this presentation about the Company's expectations, applications of its technology, markets, launch of tests and other statements that are not historical facts are "forward-looking statements" within the meaning of Section 27A of the Securities Act of 1933 and Section 21E of the Securities Exchange Act of 1934 and are based on management's current beliefs, assumptions, estimates and projections.  Actual results may differ materially from those projected in the forward-looking statements for various reasons, including risks associated with product and test development, test transfer to contracting labs, government regulation, market acceptance, limited commercial experience, dependence on key personnel, obtaining financing and other factors discussed in the Company's periodic reports filed with the Securities and Exchange Commission.  Copyright©2014 Trovagene, Inc.  2

Our Goal   To Improve Treatment Outcomes with  Copyright©2014 Trovagene, Inc.   3 Noninvasive Cancer Diagnostics Trovagene’s technology noninvasively detects and quantitates circulating tumor DNA in urine and plasma for improved disease management 

Company Overview Copyright©2014 Trovagene, Inc.  4 Numerous clinical collaborations with leading cancer centers  30+ clinical studies Expanding clinical evidence to support broad market adoption Generating health economic data necessary for appropriate reimbursement CLIA certified, CAP accredited, high complexity lab to offer diagnostic services Precision cancer monitoring technology addresses a high unmet clinical need Enables frequent, non-invasive monitoring of oncogene mutation status, disease progression, and recurrence Significant patent portfolio around cell-free DNA Proprietary methods of extracting, purifying, detecting and quantifying oncogene mutations in cell-free DNA

Experienced Leadership Team Copyright©2014 Trovagene, Inc.  5 Vlada Melnikova MD, PhD VP, Research & Development Transgenomic, ApoCell, MD Anderson Cancer Center MD | PhD Biological Engineering Mark Erlander PhD  Chief Science Officer  BioTheranostics, AviaraDx, Arcturus, J&J, Scripps Research Institute BS, MS Biochem | PhD Neuroscience  Keith McCormick VP, Sales/Mktg BioTheranostics, AviaraDx, Biogen Idec, Schering Plough, Dianon Systems BBA Marketing | MBA Int’l Business Antonius Schuh PhD  Chief Executive Officer  Sorrento Therapeutics, AviaraDx,  Arcturus, Sequenom PhD Pharm. Chem Oanh Dang PhD VP, Business Development Sequenom, Gen-Probe, Illumina, Sirius Genomics, Zymeworks PhD Biomedical Sciences Stephen Zaniboni Chief Financial Officer Awarepoint, XIFIN, Sorrento Therapeutics, AviaraDx, Arcturus, Sequenom  CPA  | BS Accounting | MBA Alberto Bardelli, PhD Paul Billings, MD, PhD Charles Cantor, PhD Carlo M. Croce, MD Riccardo Dalla-Favera, MD Brunangelo Falini, MD K. Peter Hirth, PhD  Scientific Advisors Thomas Adams, PhD (Chair) Paul Billings, MD, PhD John P. Brancaccio, CPA Gary S. Jacob, PhD Rodney Markin, MD, PhD Antonius Schuh, PhD Stanley Tennant, MD     Board of Directors David Moskowitz VP, Investor Relations UBS, FBR, Caris&Co, Roth Capital BS Pharmacy | MBA Finance

Targeted Therapies for  Cancer Therapies are expensive and have side effects Specific for particular biomarkers Response monitoring required Resistance develops Clinical Problem Copyright©2014 Trovagene, Inc.  6 Need for Genomic Monitoring Driven by  Oncogene mutations and alterations Heterogeneous:  Inter-tumor  (Distal) New Understanding of Cancer Intra-tumor

Limitations of Current Technology for Cancer Monitoring Copyright©2014 Trovagene, Inc.  7 Imaging Tissue biopsy Circulating  tumor cells Rough indication  of tumor size No molecular information Radiation concerns for younger patients Invasive procedures, often not possible Potential for serious complications Serial biopsies increasingly not feasible Not representative of tumor heterogeneity Not representative of tumor heterogeneity Not informative of tumor dynamics  Low clinical sensitivity Technically challenging Traditional  blood markers Not representative of tumor heterogeneity Non-specific for cancer Low clinical sensitivity

Significant Market Opportunity Copyright©2014 Trovagene, Inc.  8    $12B In 2010    Insufficient Imaging Tools in Oncology  Still Yield Huge Market Prime Opportunity for Trovagene  525K Metastatic cancer patients per year    8-10 Imaging procedures received by cancer patient during first year of treatment    $5B Potential market Cancer already in advanced state No molecular data delivered Source: BCC Research

Circulating Tumor DNA (ctDNA) Copyright©2014 Trovagene, Inc.  9 Tumor cells Main Advantages  of ctDNA Captures intratumor heterogeneity Systemic overview of  cancer Frequent sampling options for monitoring applications Different analyte options depending on clinical context

Why Urine? Copyright©2014 Trovagene, Inc.  10 Unlimited Volume Urine ctDNA  Plasma ctDNA 3,000 –  15,000 genome equivalent 15,000 –  150,000 genome equivalent Frequency of Testing Completely Non-invasive Convenient

“The statistically significant correlation between mutational status and treatment response suggests oncogene mutation monitoring using urinary cell-free DNA can help clinicians rapidly determine responders from  non-responders, [to] improve patient outcomes”.    Dr. Frances Collins, National Institutes of Health (NIH) Director, ‘Politics on The Frontier of Science’, Wall Street Journal, November 8, 2013    Filip Janku M.D., Ph.D et al., 2014 ASCO Annual Meeting Proceedings,  a Journal of Clinical Oncology    Sarah-Jane Dawson et. al., Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer, NEJM, Vol. 368, No. 12, March 2013    ctDNA Emerging as Preferred Analyte to Monitor Cancer Copyright©2014 Trovagene, Inc.  11 “Circulating tumor DNA levels showed a greater dynamic range, and greater correlation with changes in tumor burden, than did CA 15-3 or circulating tumor cells.” “Cancer is a disease of DNA defining cancer by what tissue it arose in is going to go by the boards pretty soon.”      Sci Transl Med. 2014 Feb 19;6(224):224ra24. N Engl J Med 2013; 368:1199-1209 Sci. Transl. Med. 4, 136ra68 (2012).

Trovagene Precision Cancer Monitoring (PCM) Platform Copyright©2014 Trovagene, Inc.  12 Ultra-Sensitive Detection and Quantitative Monitoring 100-1000 fold  enrichment ~0.5µg  ctDNA/  100 mL of urine Integration with Commercially  Available Platforms Single Molecule Detection  Proprietary error rate detection and normalization. ctDNA 4.9 ng/ul gDNA 0.04 ng/ul ctDNA 2.0 ng/ul gDNA 1.4 ng/ul Extraction and Isolation  of ctDNA Mutant Allele Enrichment Platform Agnostic Detection and  Quantification 59% 92%

Patent Portfolio Copyright©2014 Trovagene, Inc.  13 51-110 bp TrNA Family Concentrating Urine Family Patent Term Term to approx. 2035 US provisional app filed Term to approx. 2034 US provisional app filed Term to approx. 2029 US & EU Term 2018 US & EU Small Footprint Family Monitoring Disease Family 20-50 bp TrNA Family Anion Exchange Purification Family Viral and Pathogen TrNA Families  Patent Families TrNA Patent Family Term to approx. 2026 US, EU, JP, China, Australia, Canada, India Term to approx. 2034 US provisional app filed Term to approx. 2034 US provisional app filed Term to approx. 2027 US, EU, Canada

Trovagene Performance Advantages Copyright©2014 Trovagene, Inc.  14 Detection of Rare  Genomic Mutations  Monitoring Response,  Progression & Resistance Robust quantitation to determine number of mutation fragments present Ability to track changes longitudinally Compatible with highly degraded DNA for max dynamic range Type of liquid biopsy dependent on clinical/patient situation and desired utility Single copy detection Compatible with highly degraded DNA for max sensitivity High analytical sensitivity is directly coupled with amount of DNA in sample Analytical sensitivity limited by input Plasma ctDNA Urine ctDNA  3,000 –  15,000 genome equivalent 15,000 –  150,000 genome equivalent Plasma:  Non-frequent sampling Urine: Frequent sampling Home-based sampling 

 Strategy to Drive Clinical Adoption & Reimbursement  Copyright©2014 Trovagene, Inc.  15 Demonstrate concordance of oncogene mutation status between  urine and tumor tissue Clinical Utility:  Determine mutational status of actionable biomarkers in urine when a biopsy is not  an option. Ex. BRAF, KRAS $100-$200M Revenue Expand mutational coverage of  urine-based actionable oncogene mutations for our PCM platform Clinical Utility:  Quantitatively assess mutational status  in urine longitudinally as an indicator  of responsiveness to therapy,  disease status & emergence  of resistance mutations Demonstrate in multi-institutional trials that results from urine-based monitoring of actionable mutations increases patient progression-free survival (PFS) & overall survival (OS)  Demonstrate health economic benefits of  non-invasive oncogene mutation monitoring Clinical Utility:   Quantitatively assess patient mutational status in urine longitudinally for mutational status and early detection of resistance to therapy as  a decision tool for therapy selection $500+M Revenue Multi $B Revenue QUALITATIVE QUANTITATIVE STANDARD OF CARE Tumor Status Stage 1 Tumor Dynamics Stage 2 Improved Patient Outcomes Stage 3

Clinical Utilities of ctDNA Copyright©2014 Trovagene, Inc.  16 Metastatic Cancers Detection of Mutation Monitoring Mutation Level When tissue biopsy  is unavailable Supplement tissue biopsy  to get systemic overview  of the entire heterogeneity  of cancer Tumor load Emergence  of resistant mutations Drug holidays

30+ Collaborations to Validate & Integrate our PCM Platform Copyright©2014 Trovagene, Inc.  17 Disease Ongoing Pending Protocol Dev/Approval Under Evaluation Lung Cancer (NSCLC) 4 3 — Colorectal Cancer 4 3 — Pancreatic Cancer 3 — 1 Melanoma 2 4 — ECD/LCH 2 — 1 Brain Cancer 1 1 — Prostate Cancer — 1 — All-Comers, Metastatic Cancers 2 — — HPV 2 — 3 Total # of Studies 20 12 5

Ongoing Clinical Utility Studies Copyright©2014 Trovagene, Inc.  18 Detection of Mutation Monitoring Tumor Load Emergence of  Resistant Mutations Pancreatic/MDACC Brain/UCSD Lung/MSKCC  KRAS BRAF EGFR Minimal residual disease detection post surgery Detect ctDNA in brain cancer patients Detection and monitoring of EGFR mutations Colorectal/ USC CRC and others/ONG-INB Lung/MSKCC  KRAS KRAS/BRAF EGFR T790M Emergence of mutant KRAS on anti-EGFR Tx Monitor tumor dynamics and acquired resistance T790M detection prior to radiological progression BRAF/KRAS KRAS BRAF EGFR T790M KRAS Faster assessment of therapeutic efficacy Monitor disease burden by ctDNA vs. CA19-9 ctDNA avoids immunotherapy “pseudo-progression” Predict initial/clinical response of new therapeutic Correlate ctDNA to Tx response/PD/recurrence Cancer Type/Institution Biomarker Clinical Utility Examined EGFR KRAS Non-responders to EGFR activating mutations to Tx Correlate ctDNA to Tx response/PD/recurrence All Comers/MDACC Pancreatic/USOR-SH-UCSF Melanoma/DFCI Lung/Pharma Colorectal/GRI  Lung/Catholic Health Initiatives Pancreatic/U. Copenhagen 90 5 200 60 40 25 185 45 40 375 54 # Patients Expected 30 1000

Increasing Volume of Clinical Study Samples Received by Trovagene Copyright©2014 Trovagene, Inc.  19

Clinical Results Presented & Published To Date Copyright©2014 Trovagene, Inc.  20 2014 2 ASCO Presentations Histiocytic BRAF MSKCC/MD Anderson Longitudinal BRAF MD Anderson AACR Poster Concordant BRAF NEXTGEN DX SUMMIT  Oral Presentation, Technology IPV Meeting Poster Presentation  HR-HPV Manuscript submitted Histiocytic BRAF MSKCC/MDACC Q1 Q2 Q3 4/2014 6/2014 8/2014 8/2014  ECD guideline Initial concordance with plasma and tissue Initial longitudinal data—concordance with imaging Publication Histiocytic BRAF MD Anderson Oncotarget 5/2014 Publication ECD clinical guidelines Blood 5/2014

High Concordance of KRAS Status in Urine, Plasma & Tissue  of Advanced Colorectal Cancer Patients Copyright©2014 Trovagene, Inc.  21 20 Advanced Stage Colorectal Cancer Patients KRAS Mutation in Tissue, Treatment Naïve  Matched urine and plasma, archived (3-5 years) Blinded analysis, seven KRAS mutations (G12A/C/D/R/S/V and G13D) 20 Urine 20 Plasma Evaluable urine  n = 16 Non-evaluable urine n = 4 Urine vs. Tissue biopsy Concordant  KRAS mutation 15/16  Urine vs. Plasma Concordant  KRAS mutation 15/16   X Plasma vs. Tissue biopsy Concordant  KRAS mutation 19/20  94% 94% 95%

Monitoring ctBRAF V600E and Treatment Response Copyright©2014 Trovagene, Inc.  22 17 metastatic cancer patients 15 evaluable patients for ctDNA BRAF V600E >4 weeks Evaluate time to progression % tumor change per RECIST 1.1 Urine ctDNA BRAF decrease  Urine ctDNA BRAF increase  Urine BRAF ctDNA correlates to BRAF/MEK targeted therapy (p=0.002) Urine BRAF V600E ctDNA monitoring has clinical utility to track therapeutic efficacy of metastatic cancer patients harboring mutant BRAF V600E Positive urine BRAF V600E 259 days (median)  to progression 95% CI=240-278 days 61 days (median)  to progression 95% CI = 59-63 days p=0.002

ctDNA Improves Genotyping Over Tissue Biopsies in Histiocytic Patients Copyright©2014 Trovagene, Inc.  23 BRAFV600E burden in urine correlates  w/ radiographic response. BRAFV600E Mutant BRAF  Wildtype Urinary ctDNA BRAFV600E genotype Tissue BRAFV600E genotype Indeterminate  Genotype BRAFV600E Mutant BRAF  Wildtype n=9 n=6 n=15 n=14 n=16 1 Abdel-Wahab et al., ASCO Poster Highlight 2014

Dynamic Monitoring Captures Early Progression and Response Copyright©2014 Trovagene, Inc.  24 One week 1 Abdel-Wahab et al., ASCO Poster Highlight 2014 Successful monitoring tumor dynamics independent of drug class used Patient’s tumor progressed within  1 wk of Anakinra withdrawal Demonstration of need for higher frequency urine-based testing to monitor Patient responded to Vemurafenib,  BRAF inhibitor Demonstrates that continually monitoring patient enables optimal therapy over time

Ongoing Clinical Studies Continue to Drive Publications Copyright©2014 Trovagene, Inc.  25 2014 EORTC-NCI-AACR Submit abstracts HISTIOCYTIC SOC.  Submit abstracts Q4 Q1 Q2 Q3 3/2015  10/2015  Submit manuscript Longitudinal and pharmacodynamic BRAF and KRAS multiple cancers MD Anderson ASCO Submit abstracts Melanoma, lung, pancreatic colorectal cancers AACR Poster Submit abstracts  IPV Conference Submit Abstracts 4/2015 5/2015 8/2015 9/2015  Submit manuscript Longitudinal KRAS Colorectal Submit manuscript Longitudinal KRAS Pancreatic ASCO GI Abstract submitted 1/2015 NEXTGEN DX SUMMIT  Submit abstract Technology Submit manuscript KRAS/BRAF colorectal Technology comparison study Submit manuscript EGFR monitoring lung cancer EUROGIN Abstract Submitted 2/2015 16th World Conference  on Lung Cancer Submit abstracts 9/2015 European Lung  Cancer Conference Submit abstracts 4/2015 Chicago Multidisciplinary  Symposium in Thoracic Oncology Submit abstracts 10/2015 ESMO Submit abstracts 9/2015 Q4 Q4 2015 Submit manuscript Longitudinal KRAS Colorectal Submit manuscript Longitudinal KRAS Pancreatic Submit manuscript Detection T790M  Lung EORTC-NCI-AACR Abstract(s) HISTIOCYTIC SOC.  Abstract ECD/LCH BRAF MSKCC/MDACC  Submit manuscript HR-HPV Method Submit manuscript HR-HPV Predictor4 11/2014  10/2014 

Current Development Program for Cancer Monitoring Applications Copyright©2014 Trovagene, Inc.  26  KRAS Exon 2  BRAF V600E  KRAS Exon 2,3,4  NRAS Exon 2,3,4  BRAF V600E  PIK3CA H1047R   EGFR Exon 20 T790M  EGFR Exon 19 Del EGFR Exon 21 L858R  ALK Rearrangements NRAS Exon 2

Trovagene Urine-based High Risk HPV Assay Copyright©2014 Trovagene, Inc.  27 Urine-based High Risk HPV Assay established  in Trovagene’s CLIA lab since 2013 265K Deaths in  2012 Market in  2013 $9B Market in  2020 HPV Testing Market Globally Screening is a viable solution:  75% reduction in incidence in US from 1940 to 1980 w/ National Screening Program Screening not available globally: Cost, Technical expertise, Healthcare infrastructure, Quality Control, Cultural High-risk HPVs cause virtually all cervical cancers New Clinical Evidence Queen Mary, UL:  High sensitivity of test for detecting HPV associated with CIN2+, CIN3 (malignancy) NCI:  Comparative Urine Study J Clin Virol. 2014 Aug;60(4):414-7 UNC:  Urine collection methodology for detecting  HPV associated with CIN2+/CIN3  Cervical Cancer Source: Transparency Market Research 

Developing Trovagene’s HPV Franchise Internal Development  Clinical studies in general screening population Strand Life Sciences  (3,000 patients, enrollment underway) Planning stages for pivotal studies Obtain regulatory compliance Copyright©2014 Trovagene, Inc.  28 Partnering Opportunities Strategic partners to commercialize the test globally  CE Mark  FDA 

Reimbursement Value Based on Clinical Utilities of ctDNA Copyright©2014 Trovagene, Inc.  29 Detection of Mutation Monitoring Tumor Size When tissue biopsy  is unavailable Tumor load Emergence  of resistant mutations Drug holidays  Tier 1 MDx Codes Concordance with SOC Established codes Price/assay Repeat Testing: Novel Utility Not Otherwise Classified Codes (NOC) Unique CPT Codes  Once Clinical Data Established, Reimbursement: Supplement tissue biopsy  to get systemic overview  of the entire heterogeneity  of cancer

Key Component for Commercialization: Market Development Copyright©2014 Trovagene, Inc.   30 Market Development (2013-2014)  Full Commercialization (2015) Target KOLs/ Early adopters Develop IIS  (Investigator Initiated Study) Program Accelerate Adoption within Integrated Healthcare Delivery Networks (IDNs)   Branding,  Market Awareness  and Education   Relationships w/ 30+ top cancer centers   17 National Comprehensive Cancer Network (NCCN) Centers 100+ oncologists engaged in outreach Signed partnership w/ 2 major IDNs  CHI (Catholic Health Initiative)   93 hospitals   Lurie Cancer Center of Northwestern Univ.  

Key Components for Full Commercialization in 2015 Copyright©2014 Trovagene, Inc.  31 Full Commercialization (2015) Drive Adoption of Expanded Menu  Conversion of Research Collaborators to  Clinical Adopters  Expand New  Market Segments New Market for Genomic Monitoring Direct sales team 6 sales reps in Phase 1 Headcount ramp to be initiated in Q1 2015         Direct coverage of top target sites Major academic cancer centers   Entire ECD/LCH treating physician base IDNs where TROV has relationships Geographic focus on key oncology markets  

Targeted Segments for Market Development & Commercialization Copyright©2014 Trovagene, Inc.  32 Data support adoption in clinical academic centers in defined patient populations Pancreatic (Metastatic) Melanoma (Metastatic) Colorectal (Metastatic) Lung (NSCLC) Pancreatic  (Stage 2-3) ECD/LCH

Cash Flow Summary 2012 – YTD Jun 2014 Copyright©2014 Trovagene, Inc.   33 ($ in millions) 2012 2013 YTD Jun 2014 Net loss (11.6) (11.8) (4.3) Cash burn Cash used in operating activities  (4.9)   (7.3)   (5.5)  Cash used in investing  (0.3)   (0.6)   (0.1)                  (5.2)                 (7.9)                 (5.6) Funding Net cash provided by financing activities 15.3  23.0 14.4  Ending Cash  10.8 25.8 34.7

Funding Details 2012 – YTD Jun 2014 Copyright©2014 Trovagene, Inc.  34 ($ in millions) 2012 2013 YTD Jun 2014 Financing activities (net of expenses) Private Placements 6.2  NASDAQ up-listing 9.1  ATM 4.0  Institution Investment 14.8  Exercise of Warrants and options 0.0  3.6  15.3  22.4  -    Net borrowing under debt agreement Equipment line of credit 0.5  (0.5) debt agreement 14.9  -    0.5  14.4  Total 15.3  23.4  14.4 

Near Term Catalysts to Drive Valuation Copyright©2014 Trovagene, Inc.  35 Demonstrate  clinical utility Expand mutation coverage on  PCM platform Initiate new collaborations to establish  clinical utility Establish strategic partnerships to grow market reach  Drive early adoption  in top cancer centers and integrated healthcare networks 20+ abstracts and manuscripts in 2015 8 New Menu Assays 10+ clinical studies in 2015 Top academic centers Geographic expansion  Kit manufacturing Pharma collaboration HPV collaboration Commercial presence in 20 cancer centers with repeat revenue

For further information Please contact: Stephen Zaniboni, CFO szaniboni@trovagene.com   Antonius Schuh, CEO aschuh@trovagene.com  36