Associate Director, Oligonucleotide Drug Substance Manufacturing

Stoke Therapeutics; Bedford (MA); Hybrid; USD 170,000 - 215,000; Full time

Benefits offered by this job

Medical, dental and vision insurance

Life, disability insurance

Parental leave

401K with company match

Unlimited vacation time

Tuition assistance

Employee Stock Purchase Program

Job summary

Stoke Therapeutics is seeking an Associate Director of Oligonucleotides Manufacturing to oversee all outsourced manufacturing for clinical candidates and pre-commercial oligonucleotide products. The role reports to the Director of Oligonucleotide Drug Substance Development and Manufacturing and requires strong hands-on cGMP synthesis and purification experience.

Based in Bedford, MA, this hybrid position will partner with Quality and Regulatory groups, support tech transfer and CAPAs, and drive

Qualifications

• A PhD with 5+ years in GMP ASO manufacturing or a related role.

Responsibilities

• Oversee cGMP and non-GMP oligonucleotide manufacturing at CMOs.
• Troubleshoot manufacturing issues with internal and external resources.
• Size manufacturing campaigns to support clinical and toxicology materials.
• Manage relationships with CMOs to align with company goals.
• Serve as technical SME for oligonucleotide manufacturing and CAPAs.
• Monitor CMO performance with KPIs and implement corrective actions.
• Develop control strategies with Analytical, Quality, and Regulatory CMC.
• Ensure timely invoicing and payment processes with CMOs.
• Execute change controls and deviations within the QMS.
• Interface with process validation lead for API validation.

Skills

GMP ASO manufacturing

cGMP oligonucleotide synthesis

CMO management

Regulatory filings support

Quality systems (QMS)

Statistical methods (DOE, SPC)

Problem solving

Cross-functional collaboration

Education

PhD in life sciences

Master's degree in life sciences

Bachelor's degree in life sciences

Tools

CMOs management tools

Analytical instruments for IPC

OC/IPC methods

Job description

Stoke Therapeutics (Nasdaq: STOK), is a biotechnology company dedicated to restoring protein expression by harnessing the body’s potential with RNA medicine. Using Stoke’s proprietary TANGO (Targeted Augmentation of Nuclear Gene Output) approach, Stoke is developing antisense oligonucleotides (ASOs) to selectively restore naturally-occurring protein levels. Stoke’s first medicine in development, zorevunersen, has demonstrated the potential for disease modification in patients with Dravet syndrome and is currently being evaluated in a Phase 3 study. Stoke’s initial focus are diseases of the central nervous system and the eye that are caused by a loss of ~50% of normal protein levels (haploinsufficiency). Proof of concept has been demonstrated in other organs, tissues, and systems, supporting broad potential for Stoke’s proprietary approach. Stoke is headquartered in Bedford, Massachusetts. For more information, visit https://www.stoketherapeutics.com/

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.

• 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
• participation in our Employee Stock Purchase Program (ESPP)

All applicants will receive consideration for employment without regard to race, color, age, religion, sex, sexual orientation, gender identity, national origin, physical or mental disability or protected veteran status.

Stoke participates in E-Verify.