Cogent Biosciences, Inc. · NASDAQ:COGT

Cogent Biosciences — Technical Presentation (November 2025)

21 slides from Cogent Biosciences's technical presentation, Nov 10, 2025

  1. Slide 1: Peak Trial: Bezuclastinib + Sunitinib in GIST Top-Line Results

    Exhibit 99.1 Peak Trial: Bezuclastinib + Sunitinib in Gastrointestinal Stromal Tumors (GIST) Top-Line Results Investor Webcast November 10, 2025

  2. Slide 2: Forward-Looking Statements and Risk Factors

    Forward-Looking Statements and Risk Factors This presentation and the accompanying oral commentary contain forward-looking statements that involve risks, uncertainties and assumptions. If the risks or uncertainties ever materialize or the assumptions prove incorrect, our results may differ materiall

  3. Slide 3: Agenda and Speakers

    Agenda and Speakers Andrew Robbins Neeta Somaiah, M.D. Jessica Sachs, M.D. President and Chief Executive Officer Professor and Department Chair, Chief Medical Officer Department of Sarcoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center • Introduction

  4. Slide 4: Unmet Medical Need Remains for Patients with Imatinib-Resistant or Intolerant GIST

    Unmet Medical Need Remains for Patients with Imatinib-Resistant or Intolerant GIST ORR ~60% ORR ~7% ORR ~5% ORR ~9% PFS ~19 1L PFS ~5.5 2L PFS ~4.8 3L PFS ~6.3 4L months months months months Imatinib Sunitinib Regorafenib Ripretinib Modest historical performance of novel agents in imatinib-resistant

  5. Slide 5: Peak Phase 3 Top-Line Results

    Peak Phase 3 Top-Line Results Full Results Expected to be Presented at an Upcoming Medical Meeting

  6. Slide 6: Significant Unmet Need Remains for Patients with GIST

    Significant Unmet Need Remains for Patients with Gastrointestinal Stromal Tumors (GIST) • Up to 6,000 GIST cases diagnosed annually in US, over 80% 1,2 of which express KIT mutations, typically exons 11 and 9. • Tumors can start anywhere in the GI tract, but they occur 3 Symptoms most often in the s

  7. Slide 7: Combination of Bezuclastinib + Sunitinib Inhibits the Full Spectrum of Primary and Secondary Mutations

    Combination of Bezuclastinib + Sunitinib Inhibits the Full Spectrum of Primary and Secondary Mutations Exon Exon Exon Exon Exon Exon Treatments D816V 9 11 13 14 17 18 1-11 • No single TKI inhibits all KIT mutations. Imatinib • The combination of bezuclastinib + Regorafenib sunitinib inhibits mutatio

  8. Slide 8: Peak: Randomized Clinical Study Evaluating Bezuclastinib in Combination with Sunitinib

    Peak: Randomized Clinical Study Evaluating Bezuclastinib in Combination with Sunitinib in Patients with GIST Bezuclastinib 600mg QD + Sunitinib 37.5mg QD n=204 Patients 1:1 Randomized C Sunitinib 37.5mg QD n=209 Crossover allowed following BICR confirmed PD Primary Endpoint• Progression Free Surviva

  9. Slide 9: Peak Population is Representative of Second-Line Patients with GIST

    Peak Part 2 Population is Representative of Second-Line Patients with GIST Patient Demographics Bezuclastinib Sunitinib Overall Baseline Characteristics Bezuclastinib Sunitinib Overall + Sunitinib + Sunitinib # Patients 204 209 413 KIT Mutations per molecular pathology report, n (%) Male, n (%) 131

  10. Slide 10: Bezuclastinib Combination Extends PFS with 50% Reduction in Risk of Progression or Death

    Bezuclastinib Combination Extends PFS with 50% Reduction in Risk of Progression or Death Median PFS 100% Bezuclastinib 16.5 months 90% + Sunitinib 95% CI, 13.8 to 19.2 80% 9.2 months Sunitinib 95% CI, 7.2 to 11.0 70% Hazard Ratio = 0.50 60% 95% CI, 0.39 to 0.65; p<0.0001 50% 40% 30% 20% 10% 0% 0 2 4

  11. Slide 11: Bezuclastinib + Sunitinib Demonstrates Unprecedented 46% Objective Response Rate

    Bezuclastinib + Sunitinib Demonstrates Unprecedented 46% Objective Response Rate ORR per BICR , %, n [95% CI] Bezuclastinib + Sunitinib 45.6% (n=204) 93 [38.6, 52.7] Sunitinib 25.8% (n=209) 54 [20.0, 32.3] Difference in ORR, % [95% CI]; P Value 19.8 [10.6, 28.6]; P Value <0.0001 BOR per BICR, n (%)

  12. Slide 12: Bezuclastinib + Sunitinib is Generally Well Tolerated with a Favorable Safety Profile

    Bezuclastinib + Sunitinib is Generally Well Tolerated with a Favorable Safety Profile Study Treatment Bezuclastinib + Sunitinib Sunitinib 1 (n=204) (n=208) • The incidence of TEAEs and TRAEs was similar TEAEs, n (%) 204 (100) 207 (99.5) between treatment arms TRAEs, n (%) 202 (99.0) 204 (98.1) Gr3+

  13. Slide 13: All Grade TEAEs ≥ 20% Demonstrate Balance Between Arms

    All Grade TEAEs ≥ 20% Demonstrate Balance Between Arms Bezuclastinib + Sunitinib Sunitinib 1 (n=204) (n=208) Preferred term, n (%) All Grade Grade 3+ All Grade Grade 3+ • TEAEs reported at a higher frequency (>15%) in 16 (7.8) 15 (7.2) Diarrhea 159 (77.9) 138 (66.3) combination arm: ALT/AST increase

  14. Slide 14: Incidence of Grade 3+ TEAEs (≥2%) Balanced Across Arms

    Incidence of Grade 3+ TEAEs (≥2%) Balanced Across Arms Hypertension 29.4 27.4 • Majority of the Gr 3+ TEAEs were reported at a Neutropenia* 15.2 15.4 similar rate between combination and monotherapy arms; ALT/AST increase and anemia reported at ALT/AST increased* 10.8 1.4 higher incidence in the com

  15. Slide 15: Man with Metastatic GIST with Early and Durable Response to Bezuclastinib + Sunitinib

    66 yo Man with Metastatic GIST who Experienced an Early (PR at C3, CR at C9) and Durable Response to bezuclastinib + sunitinib (ongoing at C26) Relevant Medical History Treatment History 2020 2021 2022 2023 2024 2025 Site of tumor diagnosis: Jejunum/Ileum a Debulking surgery Diagnosis Neoadjuvant Im

  16. Slide 16: Man with Metastatic GIST Responded at Cycle 5 and Continues to Benefit at Cycle 38

    69 yo Man with Metastatic GIST Responded to bezuclastinib + sunitinib Treatment at Cycle 5 (PR) and is Continuing to Benefit at Cycle 38 Relevant Medical History Treatment History 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 Site of tumor diagnosis: Small intestine/bowel a Diagnosis Surger

  17. Slide 17: We Believe Peak Results are Transformative and Practice Changing

    We Believe Peak Results are Transformative and Practice Changing • Bezuclastinib combination establishes first new benchmark for 2L GIST in 20 years • 50% reduced risk of progression or death compared to current standard of care • 16.5 months mPFS compared to 9.2 months for sunitinib alone (p<0.0001

  18. Slide 18: Bezuclastinib GIST Expanded Access Program is Currently Open to Requests

    Bezuclastinib GIST Expanded Access Program is Currently Open to Requests for Access from 1 Treating Physicians in the United States (NCT06948955 ) Aim Methods Designed to provide bezuclastinib coadministered with Patients will receive oral bezuclastinib 600 mg QD plus sunitinib outside of a clinical

  19. Slide 19: Several Additional Near Term Cogent Biosciences Catalysts

    Several Additional Near Term Cogent Biosciences Catalysts Top-line Results: Expected Dec 2025 • ASH 2025 Presentations Single- • Two oral presentations from Summit in Bezuclastinib 150 mg QD arm NonAdvanced Systemic Mastocytosis (NonAdvSM) • Novel selective JAK2 V617F inhibitor Primary endpoint: ORR

  20. Slide 20: Bezuclastinib Emerging as Potential Best-in-Class KIT Inhibitor Across Indications

    Bezuclastinib Emerging as Potential Best-in-Class KIT Inhibitor Across Indications 2025 2026 $3 billion+ Global annual market Positive TLR Announced Registration-directed study in NonAdvSM opportunity; bezuclastinib vs. placebo TLR FDA NDA Best-in-class symptomatic improvement and biomarker data Pos

  21. Slide 21: Cogent

    cogent Real Challenges. Real Solutions. Precision therapies for genetically defined diseases

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