Associate Director, Oligonucleotide Drug Substance Manufacturing

Position Purpose: 

The Associate Director of Oligonucleotides Manufacturing will support overseeing all outsourced manufacturing activities for clinical candidates and pre-commercial oligonucleotide products. The right candidate will have significant hands-on experience with cGMP oligonucleotide solid-phase synthesis and purification, support authoring appropriate regulatory filings as required, and interface with the Quality unit to resolve quality events in a timely manner. This position will report to the Director of Oligonucleotide Drug Substance Development and Manufacturing. 

Key Responsibilities: 

• Provide oversight for activities related to cGMP and non-GMP manufacturing of synthetic oligonucleotides at Contract Manufacturing Organizations (CMOs). 

• Troubleshoot manufacturing issues or investigations with a combination of both internal and external resources.   

• Work with CMC, the manufacturing team, and other functional areas to appropriately size manufacturing campaigns to support clinical studies, as well as toxicology materials or other needs as they develop. 

• Develop and maintain strong, positive relationships with external CMOs to ensure alignment with company goals and objectives  

• Act as a technical oligonucleotide expert and help resolve deviations or CAPAs arising from manufacturing campaigns through interactions in collaboration with Quality Assurance. 

• Monitor and communicate CMO performance against agreed-upon metrics and key performance indicators (KPIs), providing feedback and implementing corrective actions as necessary.  

• Support the Development of control strategies for oligonucleotide manufacturing in conjunction with Analytical, Quality, and Regulatory CMC. 

• Ensure timely and accurate invoicing and payment processes with CMOs  

• Execute change controls, deviations, or other Quality items as part of internal QMS. 

• Interface with process validation lead for all API validation activities and serve as technical SME. 

• Ensure process and document compliance in collaboration with Quality teams.  

Required Skills & Experience:  

• PhD and 5+ years of experience supporting GMP ASO manufacturing preferred; Master’s and 8+ years, Bachelor’s degree in life sciences with 10+ years of progressive responsibility in oligonucleotide synthesis and cGMP manufacturing in pharmaceutical, biotechnology, or a related environment required.  

• Have strong Oligonucleotide cGMP manufacturing, PPQ, and Oligo control strategy experience 

• Significant hands-on experience in solid-phase synthesis and downstream processing of oligonucleotides. 

• Application of modern analytical methods as applied to in-process control (IPC) of manufacturing activities. 

• Proven experience managing and working with CMDOs and CROs. 

• Deep knowledge of cGMP requirements as related to manufacturing activities. 

• Experience authoring tech transfer documents, change controls, risk assessments, CAPA plans, and other quality documents.   

• Strong problem-solving abilities and experience with a regulatory environment 

• Familiar with statistical methods applied to manufacturing controls such as Design of Experiments (DOE) and Statistical Process Control (SPC).   

• Ability to work effectively in a fast-paced, dynamic environment with cross-functional teams.  

Culture & Values: 

At Stoke, we believe that innovation, the ability to successfully advance our ground-breaking science and having fun as a team are enhanced by being together in person, at least periodically. We allow for flexibility in work arrangements that balance individual’s needs and preferences with the needs of our business and our desire to foster a culture of collaboration and innovation. 

Our values guide our work to deliver meaningful medicines for people who need them. We are committed to being true to ourselves, to our colleagues, and to the people with severe diseases who are counting on us. We embrace diversity within a unique culture that is defined by our values. Our employee-led Diversity, Inclusion, and Belonging (DIB) Committee underscores the importance of DIB to who we are and what we do.   

Location(s):  

Stoke is located in Bedford, MA, and will be moving to a new location in Waltham, MA by the end of 2026. This position is a hybrid position currently based in Bedford and will later be based in Waltham.  

Travel: 

This position will require approximately 30% travel.  

Compensation & Benefits: 

At Stoke Therapeutics, we are committed to offering a comprehensive, competitive and thoughtfully designed total rewards program.  

The anticipated salary range for this role is $170,000 - $215,000. The final offer will be determined based on a variety of factors, including role scope, experience and qualifications, education, market benchmarks, internal equity, and geographic location. In addition to base salary, Stoke offers an annual bonus and equity participation. 

Our benefits package includes medical, dental and vision insurance; life, long- and short-term disability insurance; paid parental leave; a 401K plan with company match, unlimited vacation time, tuition assistance and participation in our Employee Stock Purchase Program (ESPP).