Trial Master File Sr. Manager, Clinical OperationsSouth San Francisco, CA

The Position At Maze Therapeutics, we believe precision medicine has the power to transform the lives of patients with both common and rare diseases. As Trial Master File (TMF) Senior Manager for Clinical Operations, you will serve as the operational leader responsible for the strategy, governance, quality, and execution of the Trial Master File across Maze's clinical development portfolio. You will play a pivotal role in partnering with cross-functional study teams to maintain complete, accurate, and inspection-ready Trial Master Files for ongoing clinical studies. You will also collaborate with Quality Assurance (QA) on the development and implementation of Maze's in-house TMF strategy and operating model for future clinical programs. Working closely with Clinical Operations, Quality Assurance, Clinical Science, Regulatory Affairs, Biometrics and study teams, you will help establish scalable TMF processes, systems, and governance that support the organization's continued growth. You will partner closely with the Head of Clinical Operations and Quality Assurance to drive inspection readiness across the clinical portfolio, ensuring routine TMF quality reviews, timely resolution of document gaps, and sustained compliance with GCP and regulatory requirements. As Maze transitions TMF management in-house, you will lead implementation of the electronic TMF platform, establish sponsor-level standards and workflows, and build the operational infrastructure needed to support current and future studies. This role is ideal for an experienced TMF professional who thrives in a fast-paced biotech environment, enjoys building processes from the ground up, and is passionate about developing high-quality, inspection-ready Trial Master Files. This position will report into the Head of Clinical Operations. As a Senior Manager , we also expect our leaders to demonstrate the following Leadership Competencies: Leadership Competencies Communication and Influence Communicates the reasoning behind decisions to appropriate stakeholders. Promotes open communication with internal and external stakeholders. Fosters healthy and respectful debate. Teamwork and Collaboration Creates opportunities for team members to connect with others outside of team. Manages conflict effectively between teams. Openly values thoughts, opinions, and contributions of employees. Execution and Results Exercises astute judgment to make decisions with only the necessary amount of data. Supports team members in creating their own resolutions to challenges and problems. Works with others to reinforce process compliance, what good looks like, and risk mitigation. Develop Others and Self Articulates what good looks like throughout Maze. Pursues development activities for continuous improvement of self and team. The Impact You’ll Have TMF Strategy & Operational Leadership Lead the strategic transition of TMF management from an outsourced model to an internally managed capability. Partner with Clinical Operations and Information Technology to evaluate, implement, configure, and optimize the organization's electronic TMF (eTMF) platform. Develop and maintain TMF governance, business processes, filing standards, taxonomy, indexing structures, and document management workflows. Co-author and maintain sponsor-level TMF Standard Operating Procedures (SOPs), work instructions, guidance documents, and training materials. Identify opportunities to improve TMF processes, technology, and operational efficiency while promoting organizational best practices. Evaluate, implement, and leverage AI-enabled solutions to improve TMF quality, automate document workflows, enhance inspection readiness, and drive operational efficiency. TMF Management & Program Support Serve as the primary TMF subject matter expert supporting multiple early phase, Phase 2, and Phase 3 clinical programs. Partner with Clinical Operations Study Leads and study teams to develop study-specific TMF management plans and document oversight strategies. Provide guidance to study teams, functional contributors, CROs, and vendors on TMF expectations, document ownership, filing timelines, and quality standards. Ensure TMF documents are filed accurately, completely, and within established timelines throughout the lifecycle of each clinical study. Monitor TMF health through routine completeness, timeliness, and quality reviews, proactively identifying and resolving document gaps. Inspection Readiness & Quality Management Partner closely with Quality Assurance to lead TMF inspection readiness activities across all clinical programs. Develop and maintain a continuous inspection readiness strategy that ensures Trial Master Files remain complete, accurate, contemporaneous, and inspection-ready at all times. Conduct routine TMF quality reviews and completeness assessments in collaboration with Quality Assurance and study teams. Identify TMF deficiencies, inspection risks, and compliance gaps, driving timely resolution through cross-functional collaboration. Support internal audits, sponsor inspections, and regulatory authority inspections by preparing TMF documentation, coordinating responses, and facilitating document retrieval. Ensure Trial Master Files comply with ICH-GCP, FDA, EMA, ALCOA+ principles, and other applicable regulatory requirements. Cross-Functional Collaboration & Training Develop standardized project management tools, templates, meeting frameworks, and operational best practices that improve consistency and scalability across Clinical Operations. Identify opportunities to improve business processes, cross-functional collaboration, and operational efficiency. Collaborate with study teams to monitor key performance indicators (KPIs) that measure study execution, operational effectiveness, and organizational performance. Support onboarding of new Clinical Operations team members through development of training materials, tools, and operational resources. Operational Excellence Develop dashboards and key performance indicators (KPIs) that monitor TMF health, document timeliness, quality, completeness, and inspection readiness. Establish metrics and reporting that provide Clinical Operations leadership with visibility into TMF performance across the clinical portfolio. Evaluate and implement new technologies, automation opportunities, and industry best practices that improve TMF quality and efficiency. Champion continuous improvement initiatives that strengthen document quality, compliance, inspection readiness, and operational effectiveness. Partner with Clinical Operations leadership and Quality Assurance to build a scalable TMF organization capable of supporting future pipeline growth. Champion the adoption of AI and emerging technologies to streamline TMF processes, improve document quality, and drive continuous operational improvement. What We’re Looking For You might be the right fit for this role if you have: Bachelor's degree in Life Sciences, Healthcare Administration, or another scientific or healthcare-related discipline. 6–8+ years of experience in Clinical Operations, Clinical Trial Management, or Trial Master File management within biotechnology, pharmaceutical, or CRO organizations. 4–5+ years of dedicated experience managing electronic Trial Master Files (eTMFs) across multiple global clinical studies. Experience leveraging AI-enabled solutions to improve TMF processes, document quality, reconciliation, inspection readiness, or operational efficiency is preferred. Demonstrated experience supporting early phase, Phase 2, and Phase 3 clinical trials in a GCP-regulated environment. Proven experience leading TMF inspection readiness activities and partnering with Quality Assurance to support audits and regulatory inspections. Experience developing TMF governance, SOPs, business processes, filing standards, and quality management practices. Hands‑on expertise with leading eTMF platforms such as Veeva Vault eTMF, Trial Interactive, or equivalent electronic Trial Master File systems. Strong understanding of ICH‑GCP, FDA, EMA, ALCOA+ principles, and applicable regulatory requirements governing Trial Master Files. Demonstrated ability to identify compliance risks, resolve TMF quality issues, and implement sustainable process improvements. Excellent organizational, communication, and collaboration skills, with the ability to influence cross-functional teams and drive accountability. Experience developing dashboards, KPIs, and operational metrics that support TMF health and inspection readiness is preferred. About Maze Therapeutics Maze Therapeutics is a clinical-stage biopharmaceutical company harnessing human genetics to develop precision medicines for patients with kidney and metabolic diseases. Our clinical pipeline is anchored by two small molecule programs: MZE829, an APOL1 inhibitor for patients with APOL1‑mediated kidney disease, and MZE782, which targets genetic drivers of disease in phenylketonuria (PKU) and chronic kidney disease. We are also advancing a preclinical pipeline through our Compass platform, which links human genetic variants to the biological pathways that drive disease. Our People Maze is comprised of a team of passionate and creative professionals committed to discovering and delivering transformative medicines to patients suffering from both rare and common genetic diseases. We are fostering a culture that encourages vision, initiative and the development of talent. Our supportive work environment inspires creative thinking and freedom of expression, resulting in a stimulating atmosphere where people enjoy coming to work. While we have a passion for advanced science and pride ourselves on excellence in execution, ultimately, everything we do is about patients. Our Core Values Further Together – Our path is paved with challenges, but with resilience and a team‑first mentality, we’ll achieve our mission. Impact Obsessed – We embrace the bold, take calculated risks, and learn from our mistakes to improve the lives of others. Stand True – Our integrity is foundational; it guides us no matter the obstacle. The expected annual salary range for employees located in the San Francisco Bay Area is $175,000 - $215,000. Additionally, this position is eligible for an annual performance bonus. Maze performs position-based compensation benchmarking to industry market data to ensure we pay competitive wages. Determination of starting salary will depend upon a variety of job-related factors, which may include professional experience, skills, and job location. The expected salary range for this role may be modified in the future. Maze offers a robust benefits package to our eligible employees including competitive medical, dental, and vision insurance, mental health offerings, equity incentive plan, 401(k) program with employer match and a generous holiday and PTO policy.

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