What You Should Expect From A High-Functioning CDMO

By Mark Roache, VP of Cell and Gene Therapies for Quality Executive Partners, Inc. and President of BioQ Partners, Inc. and Sarah Boynton, owner of Biopharma Staffing and Consulting Solutions, LLC

For more information, please visit Lianhe Aigen.

For the first time in history, we are entering an era where diseases can be cured, including diseases that have had little to no treatment options available. Unlike small molecule medicines, or even most biopharmaceuticals, cell and gene(C&G) therapies are driving this promise of a functional cure.  This amazing potential has created a goldrush of small companies (we will call them sponsors, since their goal is to sponsor commercial license applications), focused on the development and commercialization of C&G therapies. However, just like that first gold rush in northern California in the middle of the 19th century, this new drive to be first has created huge disruption and has unearthed novel challenges as sponsor companies move towards their goal of license approval.

This is the next topic in a series of articles aimed at discussing that disruption, the challenges that go with it and at least some ideas on how to successfully navigate a development program to approval. The first article presented the key themes at a high level, and the second discussed the challenge of forming a mutually beneficial relationship with early-stage investors.

In this discussion, we will discuss the question of whether to make or buy early GMP material as a sponsor company, how to work effectively with a contract & development manufacturing organization (CDMO) should the decision go in that direction, and how to set the right tone as a CDMO when embarking on a new relationship.  We will cover this broad topic in two parts – this first part will address the process of deciding whether to engage with a CDMO and the subsequent selection process.  The second part (to be published soon) will pick up immediately after selection and will cover how to make the partnership between the client company and CDMO mutually successful.

Make or Buy for Early GMP Supply

In the very early stages of development for a novel therapy, it is typical for small quantities of investigational drug substance to be produced in a development lab.  This material will likely be used for characterization, for small-scale animal studies and for analytical method development.  Data from this initial work may be used to demonstrate the potential of the technology being developed, with the intention of attracting investment funds or collaborating partners.

Following this path, sponsor companies will soon reach the point of needing to scale up or scale out the production process and make it sufficiently robust to be performed reliably in a manufacturing setting. Material demands will increase as test methods are developed and qualified, as early stability studies commence and eventually as plans are established for initial clinical trials. At this point, the technical and scientific need for consistency and process control will become imperative. Moreover, the need to apply appropriate GMP controls for clinical supply will become a regulatory and ethical necessity.  The sponsor must now decide whether to perform process development and GMP manufacture in-house, or to seek a partnership with a CDMO.

We have seen examples of small, startup sponsor companies with no previous experience of process development and GMP operation attempt to keep this process in-house.  In all such cases, it did not go well.  The challenges of at-scale manufacture and the learning curve for GMP operation are too great.  For such companies, the make or buy decision has therefore an inevitable outcome – partner with a CDMO.  This article is written for an audience made up mostly of staff from such companies. We hope you read on and find the content useful.

For commercially established C&G therapy companies (this is a small and exclusive group), the make or buy decision may have more degrees of freedom.  If the company has an existing GMP facility, and if the company has staff with significant process development, analytical and operational expertise in the GMP space, then in-house development is a strong option, all the way to commercial volume and beyond.  While this article is not written primarily for the in-house path, readers involved with in-house manufacturing will find some aspects of the following sections useful when applied in this different context.

It is important to note that when the initial make-or-buy decision leads to a CDMO partnership, it does not, or at least should not, preclude the eventual creation of in-house GMP development and manufacturing capability.  The heavy engineering focus of such projects to build out capacity, with large capital outlay and extended durations, requires separate skill sets and will not be discussed further here.

However, as we consider make-or-buy, we have to recognize the hard facts of establishing new GMP manufacturing facilities.  Such buildouts are expensive, often running to hundreds of millions of dollars.  These projects also take a long time, with the fastest construction and qualification projects coming in around the 2-yearmark.  All of this means that even if a sponsor company fully intends to establish its own production capability for launch or commercial operations, unless that facility exists already, the decision for early development falls by default to CDMO partnership.

CDMO Partnership – Initial decision and strategy

When a sponsor company is faced with the green light of continued development of a novel therapy into early GMP manufacture, there should be celebration. However, some folks may at the same time feel trepidation about the upcoming challenge, i.e. the formation of a relationship with a CDMO. In many cases, the sponsor represents a startup that has a vast amount of technical knowledge and experience yet is lacking the resources and expertise to manufacture their products in-house, so they turn to CDMOs for assistance. If, like the authors, you’ve been around this industry long enough, you might have a story of how a CDMO relationship was difficult or problematic. You will certainly know that the added complexity of shepherding two organizations, the sponsor and the CDMO, with incomplete alignment of goals, will present challenges and complexity. Murphy’s law is waiting in the wings to rear its inevitable head at any moment.

If it is any consolation and speaking of physical laws (Newton’s third – every force has an equal and opposite reactive force), client-side frustration is met and matched at the CDMO. This is the result of the challenges in supporting each of their clients’ programs at that CDMO, for all the same reasons.

But it doesn’t have to be this way!  Just like any relationship, there’s someone for everyone and we all need to equally own our partnerships.  It starts with selection, and moves on with shared goals, effective communication, and awareness and respect for our differences.

Selection of the Right CDMO:

One of the key challenges a sponsor will face is the need to scale their production processes quickly and efficiently. Choosing the right CDMO partner can make all the difference in this regard. Remember the wise words of the grail knight from Indiana Jones, choose wisely. Because as many readers may know, choosing poorly can lead to major issues down the road, that will not be evident until sometimes too late.

When selecting a CDMO partner, small startups must consider a variety of factors, including expertise, capacity, and cost. They must also ensure that the CDMO has experience working with their specific product type, whether it be a small molecule, biologic, or cell and gene therapy. This is especially important in the C&G space, where the manufacturing process is highly specialized and requires novel technologies combined with unique expertise and capabilities.

At this point, it’s important to appreciate a realistic picture of the CDMO business.  In the acronym CDMO, there are two service areas to consider: Development and Manufacturing. Some CDMOs focus on the work of process and analytical development, with a business model that takes the sponsor client up to commercialization and then support for launch, but with a handoff to a larger-scale manufacturing organization.  Other CDMOs focus on a model that optimizes for scale, numbers of batches and ultimately manufacturing throughput as a business model.  In either case, one will see the other as necessary for the main focus, but not an area of prime attention itself.

A third classification of CDMO has the ability, and importantly the cultural intent, to assist a client in process and analytical development, usually from a development-focused location, through commercialization, and then with continued, larger scale services, often from another location focused solely on GMP manufacturing.  A key point here, which is true throughout our industry, is that technology development and routine manufacturing are not easy bedfellows, and in the words of that song by The Offspring, we “gotta keep ‘em separated.” This need for separation comes from the cultural perspective on change (process development is all about iterative change, GMP manufacturing aims to tightly control change) and the need for and presence of scientific experts in the day to day.

It is clearly important therefore that a sponsor company, when seeking a CDMO partner, understands where their own program needs focus and whether that area of focus aligns with the CDMO’s internal interests and emphasis. It’s this alignment, and the realistic clarity thereof, that’s crucial. It is also critical to assess the CDMO's capability in terms of standard processes and equipment for the specific product to be manufactured, as well as their provision of development services. Additionally, understanding the CDMO's market position, whether they prioritize seeking volume or service fees for development, can help sponsors make a more informed decision.

So how does a sponsor know if the CDMO is going to be the ideal partner? In the whirlwind of formulating agreements and timelines, it is important not to lose sight of the main goal: supply patients in need with high quality therapies. The razzle dazzle that comes with reporting to the public about upcoming production and securing additional funding can cause sponsors to miss the CDMO’s red flags. This means it is imperative to ask CDMOs the right questions, that will uncover the inner workings of the organization. The following questions are a good start to get the discussion going, with explanations as to what you should expect from a high-functioning CDMO.

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1. Can you provide us with a breakdown of costs and fees for the project, and how you handle any potential changes or modifications?
2. Another challenge in building a successful relationship with a CDMO is managing the timeline and cost of the project. Delays and cost overruns can quickly derail a startup's plans, so it is important for both parties to have a clear understanding of the project timeline and budget. Effective project management is essential, and sponsors must be proactive in communicating their needs and expectations to the CDMO.
3. Can you describe your quality control processes and how you ensure product quality and consistency?
4. What is your approach to communication and collaboration with clients during the development and manufacturing process?
5. Can you walk us through the timeline and milestones of the project, and how you manage and report progress to clients?
6. These questions will highlight the CDMO’s quality culture mindset. Quality culture and transparency are crucial considerations when selecting a CDMO partner. Sponsors should evaluate the CDMO's willingness to discuss problems in real-time, their ability to admit challenges, and their procedures and technology to support collaboration on quality system elements such as changes to the process, deviations, CAPAs, and complaints. The CDMO should provide details of their approach, such as regular project meetings, project management tools, and transparent reporting of progress. Timely updates and transparency, on both sides, will only strengthen the relationship.
7. Can you provide references or case studies of similar projects you have successfully completed?
8. The CDMO should highlight their achievements and demonstrate their ability to deliver projects on time. Be wary if they have a proven track record of delaying product disposition (i.e. the release/reject decision) since such a trend may indicate a tendency to start before they are truly ready and pay for this on the backend.
9. How do you handle unexpected issues or deviations during the development or manufacturing process?
10. Listen and determine if the CDMO provides clear details of their approach to problem-solving and decision-making, such as their process for root cause analysis and their ability to implement corrective actions.
11. What is your policy regarding intellectual property and confidentiality, and how do you ensure protection of our proprietary information and technology?
12. The CDMO should demonstrate their commitment to protecting their client's proprietary information and technology and provide details of their security measures to ensure data protection and confidentiality.
13. Can you walk us through your process for monitoring and controlling the manufacturing process?
14. It is vital to the future of any early therapy that sponsors understand the manufacturing landscape at a CDMO. This question will uncover a CDMO’s approach to ensuring that the manufacturing process is running smoothly and meeting the desired quality standards. It will also reveal how the CDMO identifies and addresses any issues that arise during the manufacturing process. Startups, especially, may be navigating a complex regulatory landscape that they don’t fully understand, with strict guidelines and regulations governing every aspect of the product development and commercialization process. Having a CDMO that is well-versed in these regulations and working to continuously improve to meet the standards, is a big win.

Once a CDMO partner has been chosen, maintaining open communication throughout the entire process will lead to a fruitful relationship. Communication is the foundation, and the startup must ensure that they have a clear understanding of a CDMO's capabilities and limitations. It is essential to resist the temptation to hoard critical technical knowledge with the CDMO, as the value of sharing outweighs the risk of intellectual property dilution. Establishing these agreements and processes early on can take the decision load off a team dealing with a crisis and ensure a successful partnership with the CDMO.

The CDMO, in turn, must be transparent about their processes and timelines, and work closely with the startup to develop a customized manufacturing plan that meets their specific needs.

Key Messages

It’s clear that CDMOs play a very important role in the delivery on the promise offered by Cell and Gene Therapies and that most sponsor companies will utilize the services of a CDMO at some point in the timeline of product development.  Success of the sponsor/CDMO relationship is heavily dependent on selecting the right partner in the first place, based on a clear understanding of what both companies need and bring to the table.  Asking the right questions and providing truthful, transparent answers will result in choosing the right partners.

Part two of this topic will cover what happens next – issues and advice for both sponsors and CDMOs in terms of operations, responsibilities, and behaviors. We will also cover essential responsibilities of the sponsor, in terms of batch release and overall quality oversight.

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CDMO Selection: The Ultimate Checklist

Copyright © DrugPatentWatch. Originally published at https://www.drugpatentwatch.com/blog/

Part I: Foundational Strategy – Preparing for Partnership

The decision to outsource pharmaceutical development and manufacturing is one of the most critical strategic choices a company can make. In today’s complex and competitive biopharmaceutical landscape, selecting a Contract Development and Manufacturing Organization (CDMO) has evolved far beyond a tactical, cost-saving measure. It is a long-term commitment that profoundly impacts a drug’s journey from concept to commercialization, influencing development timelines, regulatory success, financial viability, and ultimately, patient access to life-changing therapies. This guide provides a comprehensive framework for navigating this high-stakes process, transforming it from a simple vendor selection into the formation of a robust, strategic partnership. Success hinges not on finding the cheapest or fastest provider, but on identifying the right partner whose capabilities, culture, and vision align with the specific needs of the project and the long-term goals of the sponsoring organization. This process begins not with external outreach, but with rigorous internal preparation and a clear understanding of the modern outsourcing ecosystem.

Section 1.1: The Modern CDMO Landscape: Beyond Manufacturing to Strategic Partnership

The pharmaceutical outsourcing sector has undergone a profound transformation. What was once a fragmented industry of specialized service providers has consolidated into a dynamic ecosystem where partners are expected to deliver integrated, end-to-end solutions. Understanding the key players and the strategic value they offer is the first step in formulating an effective outsourcing strategy.

Defining the Ecosystem: Differentiating CDMOs, CMOs, and CROs

Navigating the outsourcing landscape requires a precise understanding of the terminology and the distinct roles played by different organizations.1 While the terms are sometimes used interchangeably, their functions are fundamentally different, and the choice between them has significant strategic implications.2

• Contract Research Organization (CRO): A CRO is a service provider that supports the early stages of the drug development lifecycle, focusing primarily on research and clinical trials.3 Their services do not typically involve manufacturing but are centered on activities such as preclinical research, clinical trial management, patient recruitment, data management, biostatistics, and navigating the complex regulatory submissions required for clinical studies.2 CROs are essential partners for companies needing to execute complex clinical programs and manage the vast amounts of data and regulatory paperwork involved in proving a drug’s safety and efficacy in humans.4 They operate under Good Clinical Practice (GCP) and Good Laboratory Practices (GLP) guidelines.2
• Contract Manufacturing Organization (CMO): A CMO is a specialist in production. These organizations are engaged once a drug has already been developed, its formulation is finalized, and its manufacturing process is established.3 A CMO’s primary role is to manufacture the drug substance or drug product, often at a large commercial scale.4 They provide the physical infrastructure, cGMP-compliant facilities, and operational expertise to produce millions of doses, but they do not typically engage in the early development or process optimization work.3 They are the ideal partner for a company with a market-ready product that simply lacks in-house manufacturing capacity.4
• Contract Development and Manufacturing Organization (CDMO): A CDMO represents the convergence of development and manufacturing services, offering a comprehensive, integrated solution.8 A CDMO partners with a pharmaceutical company much earlier in the lifecycle, providing services that span from initial formulation and process development, analytical method development, and manufacturing of clinical trial materials, all the way through to process scale-up and commercial-scale production.3 This end-to-end capability is their defining characteristic.5

The evolution of the CDMO model is a direct market response to the challenges of a fragmented outsourcing approach. Historically, a company might work with a CRO for clinical trials and then transfer the project to a CMO for manufacturing. This technology transfer step is notoriously fraught with risk, often leading to significant delays, cost overruns, and technical challenges as a new team attempts to replicate and scale a process developed elsewhere.6 The integrated CDMO model mitigates this fundamental risk by keeping the entire development-to-manufacturing continuum under one roof, managed by a single partner.11 This streamlined workflow is a powerful strategic advantage.

Furthermore, the lines are continuing to blur. “Trailblazing CDMOs” are now expanding their service offerings to include clinical research support, effectively integrating traditional CRO capabilities into their portfolio.3 This trend creates a new class of “full-service strategic partner” that can guide a drug from the earliest stages of development to market launch and beyond, representing the ultimate risk-mitigation strategy against the delays and costs associated with managing multiple, siloed vendors.

Table 1: Outsourcing Partner Comparison: CRO vs. CMO vs. CDMO

The Strategic Value Proposition: Cost-Efficiency, Speed-to-Market, and Access to Innovation

Engaging a CDMO is a strategic lever that provides far more than just outsourced labor. The decision to partner with a CDMO unlocks several critical advantages that are particularly vital for small and mid-sized biotech firms but are increasingly leveraged by Big Pharma as well.10

1. Cost Management and Risk Mitigation: The capital expenditure required to build and maintain state-of-the-art, cGMP-compliant manufacturing facilities is prohibitive for most companies, running into hundreds of millions of dollars.3 Partnering with a CDMO provides immediate access to this infrastructure, along with the highly trained chemists, engineers, and quality professionals needed to operate it, for a predictable contract fee.3 This transforms a massive capital expense into a manageable operational expense, de-risking the development process and allowing companies to remain asset-light and focus their capital on core competencies like research and drug discovery.14
2. Accelerated Speed-to-Market: In the pharmaceutical industry, time is one of the most valuable commodities. A CDMO’s established platforms, experienced teams, and global supply chains can significantly accelerate development timelines.12 They have navigated similar projects before and can anticipate risks, avoid common errors, and optimize processes more efficiently than an in-house team starting from scratch.13 This ability to shorten the time-to-market is a crucial competitive advantage, particularly in crowded therapeutic areas.10
3. Access to Specialized Expertise and Technology: The pharmaceutical pipeline is growing increasingly complex, with a shift towards biologics, cell and gene therapies, and other novel modalities that require highly specialized manufacturing technologies.13 CDMOs have become leaders of innovation, investing heavily in cutting-edge capabilities such as continuous manufacturing, advanced aseptic fill-finish lines, and patient-centric dosage forms like sophisticated capsule technologies for controlled release or combination therapies.16 By partnering with a CDMO, a sponsor gains access to this specialized knowledge and technology, which may be unavailable or too costly to develop in-house.12
4. Navigating Global Regulatory Complexity: The regulatory landscape is a daunting and constantly evolving maze of requirements from agencies like the FDA in the U.S. and the EMA in Europe.12 Established CDMOs possess deep regulatory expertise and a proven track record of successful inspections and submissions.9 They ensure that all development and manufacturing activities are performed in strict compliance with cGMP standards, significantly reducing the risk of regulatory setbacks that could delay or derail a program.13

Market Dynamics: Growth Drivers, Consolidation, and the Rise of Specialization

The CDMO market is not static; it is a vibrant and rapidly expanding sector. The global market was valued at over USD 238 billion in and is projected to grow at a compound annual growth rate (CAGR) of around 9%, potentially reaching over USD 465 billion by .19 This robust growth is propelled by several key factors:

• The increasing complexity of drug molecules, especially the surge in biologics, biosimilars, and advanced therapies like cell and gene therapy (CGT), which demand specialized manufacturing capabilities that are often outsourced.13
• The pressure on pharmaceutical companies of all sizes to manage costs and reduce capital expenditures.10
• The strategic imperative to accelerate drug development timelines and achieve faster speed-to-market.13
• The rise of virtual and small biotech companies that rely almost exclusively on outsourcing for their development and manufacturing needs.20

A defining feature of this growth is market consolidation. The CDMO landscape is characterized by significant merger and acquisition (M&A) activity, with larger CDMOs acquiring smaller, specialized firms to broaden their technological capabilities and geographic footprint.16 This trend is driven by the desire to become true end-to-end, “one-stop-shop” providers that can service a client across the entire product lifecycle.11

This M&A activity presents a dual-edged reality for sponsors. On one hand, it creates larger, more financially stable partners with an impressive breadth of integrated services, capable of handling a product from early development through global commercial supply.16 On the other hand, it introduces a new layer of risk that must be carefully managed during due diligence. A CDMO that has recently undergone a merger or is in the process of an acquisition may face internal challenges. These can include the disruption of established project teams, cultural clashes between the merged entities, changes in strategic priorities, and difficulties in integrating disparate quality management systems and IT platforms. A sponsor engaging with such a CDMO must therefore expand their due diligence beyond technical capabilities to assess these integration risks, seeking assurances about the stability of the project management teams, the continuity of the quality systems, and the long-term strategic commitment to their specific project type and scale. The potential for a smaller client’s project to be deprioritized in favor of a larger, more strategic asset from the acquiring company is a tangible risk that must be addressed.

Section 1.2: Internal Alignment: Defining Your Project and Outsourcing Drivers

The success of a CDMO partnership is determined long before the first request for proposal (RFP) is sent. It begins with a rigorous and honest process of internal alignment. A company that does not fully understand its own project, capabilities, and strategic goals cannot effectively evaluate an external partner. Attempting to outsource a poorly defined project is a primary cause of failed partnerships, leading to inaccurate proposals, scope creep, budget overruns, and significant delays.22

The Internal Scoping Process: Assembling a Multidisciplinary Team

The first step is to establish a cross-functional internal team to lead the selection process.22 This is not a task for a single department; it requires a holistic view of the project. The team should include representatives from key functions 23:

• R&D / Scientific Staff: To define the technical and scientific requirements of the molecule and process.
• Operations / Manufacturing (CMC): To define the process development, scale-up, and manufacturing needs.
• Quality Assurance (QA): To establish the quality and compliance standards that must be met.
• Regulatory Affairs: To outline the regulatory strategy and submission requirements for target markets.
• Purchasing / Procurement: To manage the commercial aspects of the bidding and contracting process.
• Finance / Legal: To assess financial stability and negotiate contractual terms.
• Executive Management: To ensure the outsourcing strategy aligns with the company’s overall business objectives.

The primary mandate for this team is to clearly identify the company’s outsourcing drivers.23 Is the primary need to access manufacturing capacity that doesn’t exist in-house? Is it to leverage specific scientific or technological expertise that the company lacks? Or is it a strategic decision to access both? Answering this fundamental question is essential for prioritizing the selection criteria that will be used to evaluate potential partners.23

Defining Project Requirements with Precision: From Molecule to Market

With the team in place, the next task is to create a detailed and precise definition of the project requirements. This internal scoping process is not merely a preparatory step; it serves as a critical diagnostic tool for the sponsoring organization. As the team works through the detailed technical, analytical, and logistical questions, it is forced to conduct an honest assessment of its own internal capabilities. Areas where the team struggles to provide clear answers—for instance, on the robustness of an analytical method or the scalability of a purification step—are precisely the areas where the company has a critical knowledge or resource gap.

This realization fundamentally reshapes the CDMO selection criteria. The search is no longer for a simple “pair of hands” to execute a well-defined work order. Instead, it becomes a search for a true development partner with the deep scientific and problem-solving expertise required to fill those identified gaps. The core question of the evaluation shifts from a tactical “Can you do this?” to a more strategic “Can you help us figure out how to do this?” The level of detail required varies significantly by the type of drug molecule.25

• Considerations for Small Molecules: For small molecule drugs, the project definition should include the current development stage (e.g., preclinical, Phase I, commercial), the specific services required (e.g., process chemistry optimization, analytical method development, stability testing), and the target dosage form (e.g., oral solid dose, sterile injectable, topical).26 Key information to compile includes the physical and chemical properties of the active pharmaceutical ingredient (API), the existing synthesis route, preliminary formulation data, and the required scale of production for clinical trials or commercial supply.28
• Considerations for Biologics: The complexity escalates significantly for biologics, such as monoclonal antibodies or recombinant proteins. The project definition must include detailed information on the cell line to be used (e.g., CHO, E. coli), the upstream process (fermentation or bioreactor conditions and scale), and the downstream process (the sequence of purification steps, such as chromatography and filtration).30 A critical component is the status of the analytical methods required for product characterization, potency, and purity assessment. Key questions that must be answered internally before approaching a CDMO include: How robust and scalable is the current manufacturing process? Are the analytical assays sufficiently developed, sensitive, and reproducible for their intended purpose?.30 For injectable biologics, the need for a partner with proven expertise in aseptic fill-finish operations and lyophilization is often a non-negotiable requirement.33
• Considerations for Cell & Gene Therapies (CGTs): CGTs represent the pinnacle of manufacturing complexity, and the project definition must be exceptionally detailed. This is a field where the manufacturing process is the product. Requirements include defining the starting cellular material (autologous from the patient, or allogeneic from a donor), the need for viral vector production (e.g., AAV, lentivirus), and the specific steps of cell manipulation (e.g., cell selection, gene editing, expansion).34 A critical strategic consideration is the plan to transition the process from manual, open systems often used in academic research to the closed, automated systems required for robust, scalable cGMP manufacturing.34 Due to the nature of these therapies, ensuring an unbroken chain of custody and identity is paramount, as is partnering with a CDMO that possesses deep expertise in cell biology, virology, and genetic engineering.35 The regulatory pathway for CGTs is often novel and evolving, making a partner with direct, successful experience in IND and BLA submissions for these products invaluable.35

Table 2: Modality-Specific Project Requirements Checklist

Establishing the Outsourcing Model: Tactical, Preferred Provider, or Strategic Alliance

Finally, based on the project’s complexity, the company’s long-term pipeline, and the identified outsourcing drivers, the internal team must define the type of relationship it seeks to build.23 This decision will profoundly influence the selection process, as different relationship models demand different levels of due diligence.

• Tactical Outsourcing: This is a transactional, fee-for-service model used for a specific, well-defined, one-off project. The primary focus of due diligence is on the CDMO’s technical ability to execute the task, their capacity, and their cost.
• Preferred Provider Agreement: This model is used when a company anticipates needing similar services for multiple projects over time. It involves selecting one or more “preferred” CDMOs that have been thoroughly vetted. This streamlines future project initiations by eliminating the need for a full selection process each time.
• Strategic Relationship / Alliance: This represents the deepest level of partnership, often spanning years or even the entire lifecycle of a product.19 It can involve co-investment, risk-sharing agreements, and deep operational integration.19 This model is typically reserved for a company’s most critical and complex programs.

The choice of outsourcing model acts as a critical filter for the subsequent due diligence process. For a tactical project, technical capability and cost may be weighted most heavily. However, for a strategic alliance, non-technical factors become equally, if not more, important. The CDMO’s long-term financial stability becomes a paramount concern, as the sponsor is relying on them for years of uninterrupted supply.41 The integrity and resilience of their global supply chain become critical to mitigating geopolitical and logistical risks.44 The compatibility of the two companies’ cultures, communication styles, and project management philosophies moves from a “nice-to-have” to a “must-have” to ensure the long-term health and productivity of the relationship.25 Therefore, the initial decision on the outsourcing model must consciously dictate the weighting of the criteria in the evaluation scorecard that will be used to select the final partner.

Part II: The Selection Process – A Comprehensive Due Diligence Checklist

Once the internal strategy is set and project requirements are meticulously defined, the process of identifying and vetting potential CDMO partners begins. This is a systematic, multi-stage process of due diligence designed to progressively narrow the field from a broad market scan to a single, ideal partner. Each stage builds upon the last, adding layers of scrutiny to ensure the final decision is robust, data-driven, and strategically sound.

Section 2.1: Market Scanning and Longlisting Potential Partners

The initial phase of the selection process involves casting a wide but strategic net to identify a pool of potentially suitable CDMOs. The goal is not to be exhaustive but to efficiently create a qualified “longlist” of candidates for more detailed evaluation.

Leveraging Industry Databases and Reports for Initial Identification

The search begins with a broad survey of the CDMO market, leveraging publicly available and commercial intelligence resources. Industry-specific databases are an invaluable starting point. For example, BioPlan Associates offers the Top300Bio CDMO Database, which actively tracks and ranks hundreds of dedicated biopharmaceutical CDMO facilities worldwide, providing details on their bioreactor capacity, services offered, and areas of expertise.46 Similarly, platforms like PharmaSource allow for filtering of CDMOs based on capabilities such as small molecule API manufacturing, biologics, aseptic fill-finish, and regulatory approvals (e.g., FDA, EMA).48

In addition to databases, market research reports from firms like Fortune Business Insights or Precedence Research provide high-level analysis of market size, growth trends, key players, and regional dynamics.14 These reports can help identify major, established CDMOs and understand the competitive landscape.20 This initial sweep provides the raw material for building a preliminary list of candidates whose stated capabilities appear to match the project’s high-level requirements.

Strategic Use of Patent Intelligence to Align Technical Capabilities

A more sophisticated and powerful method for identifying and qualifying potential partners involves the strategic use of patent intelligence. Platforms like DrugPatentWatch offer a window into the true research and development activities of CDMOs, moving beyond marketing claims to objective evidence of innovation.50

This approach serves as a form of proactive technical due diligence. A primary risk in CDMO selection is the potential mismatch between a partner’s advertised capabilities and their actual, hands-on expertise.53 While a CDMO’s website may list a wide range of services, patent filings provide concrete, legally scrutinized proof of their work in a specific area. By searching for patents filed by a CDMO, or patents that cite a CDMO’s work, a sponsor can verify genuine innovation in a highly specific domain. For example, if a project involves a complex lipid nanoparticle (LNP) formulation for an mRNA therapeutic, a patent search can identify CDMOs that have not just manufactured LNPs, but have invented novel LNP formulations or manufacturing processes.50

This allows a sponsor to prioritize CDMOs on their longlist who are not just operational “doers” but are also scientific “thinkers” and “innovators.” This is particularly crucial for complex development programs where unforeseen scientific and technical challenges are almost certain to arise. Partnering with a CDMO that has a demonstrated history of solving tough problems in the relevant field significantly de-risks the technical aspects of the project before the first conversation even takes place.

Creating the Initial Longlist: Balancing Geography, Scale, and Specialization

The information gathered from databases, reports, and patent analysis is then synthesized to create a curated longlist of potential partners. The objective is to identify approximately 6-8 CDMOs that will receive the Request for Proposal (RFP).55 This list should be carefully filtered based on the non-negotiable criteria established during the internal scoping phase:

• Technical Specialization: The CDMO must have proven expertise in the specific modality (e.g., small molecule, biologic, CGT) and dosage form (e.g., oral solid, sterile injectable).41
• Scale of Operations: The CDMO’s capacity must align with the project’s needs, whether it’s for small-scale clinical trial material production or large-scale commercial manufacturing. A key consideration is their ability to scale up as the project progresses.27
• Geographic Location: The location of the CDMO has significant implications for logistics, supply chain management, communication, and regulatory strategy.27 A sponsor must decide whether to prioritize proximity for easier collaboration or consider partners in different regions (e.g., North America, Europe, Asia) for potential cost advantages, while being mindful of the associated regulatory and logistical complexities.38

Section 2.2: The Request for Proposal (RFP) and Initial Screening

With a qualified longlist in hand, the next step is to initiate formal contact through a well-structured RFP. This stage is designed to gather consistent, comparable information from each potential partner, enabling an objective initial screening and the creation of a final shortlist.

Crafting a Comprehensive RFP: Key Components and Best Practices

The RFP is a critical strategic document, not merely a request for a price quote.58 Its quality and completeness directly reflect the sponsor’s preparedness and will dictate the quality and accuracy of the proposals received. A vague or incomplete RFP will lead to proposals based on incorrect assumptions, necessitating significant rework and renegotiation later.58

Based on the detailed requirements defined in Part I, a comprehensive RFP should include the following sections 24:

• Project Overview and Objectives: A clear summary of the drug, its therapeutic indication, and the overall goals of the outsourcing project.
• Detailed Scope of Work: An explicit list of the services required from the CDMO (e.g., process development, analytical validation, cGMP manufacturing, stability studies, regulatory support).
• Technical Information Package: As much detailed technical data as possible, including information on the molecule (e.g., structure, stability), the current manufacturing process, existing analytical methods, and a summary of the development history.58
• Capacity and Scale Requirements: The required batch size, number of batches, and projections for future scaling needs.
• Timeline and Key Milestones: A realistic project timeline with critical deadlines for material delivery, regulatory filings, or clinical trial initiation.58
• Quality and Regulatory Requirements: The target markets for the drug and the corresponding regulatory standards that must be met (e.g., FDA, EMA cGMP compliance).
• Evaluation Criteria: A brief outline of the key criteria the sponsor will use to evaluate the proposals.

Managing the RFP Process and Shortlisting Candidates

The finalized RFP is distributed to the 6-8 CDMOs on the longlist.55 Before the proposals are received, the sponsor’s internal multidisciplinary team should establish a standardized review process and a scoring template or scorecard.33 This ensures that each proposal is evaluated consistently against the same set of prioritized criteria, which limits subjectivity and facilitates a true “apples-to-apples” comparison.33

A crucial, often overlooked, part of this process is evaluating the nature of the CDMO’s response to the RFP. The quality of a CDMO’s questions is just as revealing as the quality of their final proposal. A complex RFP will inevitably contain areas that require clarification. An experienced and diligent CDMO will proactively seek this clarification, asking thoughtful questions about the sponsor’s technical data, process assumptions, or timeline constraints.32 This inquisitiveness is a strong positive signal; it demonstrates deep engagement, a collaborative mindset, and a genuine effort to de-risk the project and provide the most accurate proposal possible.

Conversely, a CDMO that accepts a complex RFP at face value without any substantive questions may be a red flag.32 This could indicate a lack of deep expertise, an overeagerness to win the business without fully understanding the scope, or an intention to use a generic, non-tailored approach. Sponsors should therefore view the Q&A phase of the RFP process as a key evaluation point for assessing a CDMO’s diligence and partnership potential.

Once the proposals are received, the internal team conducts its review, scoring each CDMO against the predefined criteria. This process will narrow the field to a shortlist of the top 3-4 candidates who will proceed to the most intensive phase of due diligence.33

Section 2.3: Technical and Operational Due Diligence

With the shortlist established, the due diligence process deepens significantly, moving from paper-based proposals to a hands-on evaluation of the CDMO’s technical and operational capabilities. This phase is about verifying claims, assessing tangible assets, and confirming that the CDMO has the scientific expertise and physical infrastructure to execute the project successfully.

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Evaluating Technical Expertise: Process Development, Scale-Up, and Technology Transfer

This is a fundamental assessment of the CDMO’s core scientific and engineering competencies. The evaluation must confirm that the CDMO has direct, demonstrable experience with the specific type of processes required for the sponsor’s project.33 This includes:

• Process Development and Optimization: The CDMO should have a strong team of scientists and engineers capable of optimizing existing processes for robustness, yield, and scalability. For early-stage projects, they must be able to develop a manufacturing process from scratch.22
• Scale-Up and Scalability: The CDMO must prove it can successfully scale the process from the laboratory or pilot scale to the required clinical or commercial scale. This involves not just larger equipment, but a deep understanding of the engineering principles that govern how processes behave at different volumes.27
• Technology Transfer: The CDMO should have a well-defined, systematic process for technology transfer, ensuring that processes and knowledge are seamlessly transferred into their facility from a sponsor or another CDMO.22
• Specialized Technologies: For projects with unique challenges, the sponsor must verify expertise in specific advanced technologies, such as spray drying, hot-melt extrusion, particle engineering for small molecules, or high-containment facilities for highly potent compounds.40

The evaluation should not only confirm that the CDMO can perform these tasks but also how they perform them. A key differentiator is a CDMO’s ability to proactively troubleshoot and provide innovative solutions to the inevitable technical hurdles that arise during development.23

Assessing Analytical Services: The Cornerstone of Quality Control

Robust analytical capabilities are the foundation of all quality and regulatory compliance in pharmaceutical manufacturing.60 A product cannot be released without definitive analytical proof that it meets all specifications for identity, strength, quality, purity, and potency. Therefore, the assessment of a CDMO’s analytical services department is non-negotiable and must be exceptionally thorough. A top-tier CDMO will offer a comprehensive, phase-appropriate suite of analytical services 29:

• Method Development and Validation: The ability to develop, optimize, and formally validate analytical methods in accordance with ICH guidelines is essential. The methods must be robust, reproducible, and fit for their intended purpose (e.g., release testing, in-process control, stability monitoring).60
• Raw Material Testing and Qualification: The CDMO must have systems in place to test and qualify all incoming raw materials and components to ensure they meet predefined specifications before use in manufacturing.60
• In-Process and Release Testing: They must be equipped to perform all necessary testing during the manufacturing process (in-process controls) and on the final drug substance and drug product to ensure every batch meets its release specifications.61
• Stability Testing: The CDMO must have dedicated, ICH-compliant stability chambers to conduct long-term and accelerated stability studies, which are required to establish the product’s shelf-life and storage conditions.29
• Advanced Characterization: For complex biologics, the evaluation must confirm the availability of advanced characterization technologies. This includes mass spectrometry for identity and post-translational modification analysis, various forms of chromatography for purity and impurity profiling, and sophisticated techniques for particle characterization and aggregation analysis.39

During this evaluation, it is valuable to probe the CDMO’s analytical development philosophy. Some CDMOs have invested in creating “platform” analytical methods, particularly for common modalities like monoclonal antibodies.61 These are pre-developed, well-understood analytical procedures that can be quickly adapted and customized for a new but similar molecule. This platform approach can significantly accelerate the initial stages of a project compared to a purely “custom” approach where every single method must be developed from the ground up. A CDMO’s investment in such platforms is a strong indicator of their commitment to efficiency and speed.

On-Site Audits: Best Practices for Facility and Equipment Evaluation

A physical, on-site audit is an indispensable part of due diligence. It provides the opportunity to verify the claims made in the RFP response and to assess the tangible reality of the CDMO’s operations.32 A reluctant CDMO is a major red flag.63 The audit should be a structured, planned event, not an informal tour. Best practice is to develop an audit plan that follows the systems-based inspection technique used by the FDA, which covers six major systems: Quality, Facilities & Equipment, Materials, Production, Packaging & Labeling, and Laboratory Controls.63

Key activities during the on-site audit include 64:

• Touring the Facility: A guided tour of the manufacturing plant, laboratories, and warehouse areas to assess cleanliness, material flow, and general state of control.
• Evaluating Equipment: Inspecting the key pieces of equipment to be used for the project to ensure they are suitable, properly qualified, and well-maintained. This includes reviewing maintenance, calibration, and qualification records.
• Assessing Infrastructure: Evaluating the suitability of the warehouse and storage infrastructure, including controlled-temperature storage capabilities.
• Observing Operations: Observing staff at work to gauge their level of training, adherence to procedures, and the overall quality culture on the shop floor.
• Meeting the Team: Conducting interviews with key technical, quality, and operational staff to assess their experience and expertise.

The on-site audit provides a wealth of information that cannot be gleaned from documents alone. It offers a direct sense of the CDMO’s commitment to quality, their operational discipline, and the competence of their team.

Section 2.4: Quality and Regulatory Due Diligence

Parallel to the technical audit, a deep dive into the CDMO’s quality systems and regulatory history is essential. This part of the due diligence process is focused on risk assessment and ensuring that the potential partner operates in a state of control that can withstand regulatory scrutiny from global health authorities.

Dissecting the Quality Management System (QMS)

A CDMO’s Quality Management System (QMS) is the documented framework that defines how they ensure quality and compliance in every aspect of their operation.66 It is the heart of a cGMP-compliant organization. The on-site audit must include a thorough review of the QMS, which is typically anchored by the CDMO’s Quality Manual and its index of Standard Operating Procedures (SOPs).64 The sponsor’s audit team should scrutinize the core subsystems of the QMS, including 64:

• Deviation and Investigation System: How does the CDMO document, investigate, and resolve deviations from established procedures? This includes their process for handling Out-of-Specification (OOS) and Out-of-Trend (OOT) laboratory results.
• Corrective and Preventive Action (CAPA) System: A robust CAPA system is a sign of a mature quality culture. The audit should assess how the CDMO uses investigations to identify true root causes and implements effective CAPAs to prevent recurrence.
• Change Control System: How does the CDMO manage changes to processes, equipment, materials, or methods? The system must ensure that all changes are properly justified, documented, assessed for impact, and approved before implementation.
• Supplier and Subcontractor Qualification: How does the CDMO approve and monitor its own suppliers of raw materials and services? They must have a system to ensure their suppliers meet the same high standards.64
• Training Program: The audit should review documentation for staff training programs to ensure that all personnel are qualified for their assigned roles.

Evaluating the Regulatory Track Record: A History of Compliance

A CDMO’s history of interactions with regulatory agencies is a direct indicator of its compliance posture and a critical factor in risk assessment. This evaluation should include 27:

• Review of Inspection History: The sponsor should request a summary of the CDMO’s inspection history with major regulatory bodies like the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA). A long history of successful inspections is a powerful indicator of a reliable, compliant operation.37
• Analysis of Inspectional Observations (FDA Form 483s) and Warning Letters: It is crucial to request and review any regulatory observations or warning letters the CDMO has received. A perfect inspection history is rare for facilities that have been operating for a long time. Therefore, the key is not necessarily the absence of observations, but how the CDMO responded to them.68 A CDMO that is transparent about past issues and can provide a detailed, convincing narrative of the root cause analysis and the systemic corrective actions they implemented demonstrates a healthy, learning-oriented, and mature quality culture. In contrast, a CDMO that is defensive or evasive about past issues, or provides evidence of only superficial fixes, signals a reactive culture that is likely to encounter future compliance problems. This focus on the
  process of correction rather than just the presence of errors provides much deeper insight into the true quality culture of the organization.
• History of Product Approvals: A track record of successfully manufacturing products that have gone on to receive regulatory approval is another strong testament to the CDMO’s capabilities and compliance.56

Data Integrity as a Non-Negotiable Criterion

In the modern era of pharmaceutical manufacturing, regulatory agencies place an enormous emphasis on data integrity.69 All data supporting a product’s quality and a regulatory submission must be reliable and accurate. The due diligence process must confirm that the CDMO has robust systems and procedures in place to ensure data integrity, often summarized by the acronym ALCOA+ (Attributable, Legible, Contemporaneous, Original, Accurate, plus Complete, Consistent, Enduring, and Available).

This evaluation should cover 59:

• Compliance with 21 CFR Part 11 (for the US) and EudraLex Annex 11 (for the EU): These regulations govern the use of electronic records and electronic signatures. The CDMO must demonstrate that its computerized systems are validated and compliant.
• Audit Trails: Critical laboratory and manufacturing systems must have secure, computer-generated, time-stamped audit trails that record all actions, such as the creation, modification, or deletion of data.
• Data Governance Policies: The CDMO should have clear policies and training programs that define expectations for data management and emphasize the importance of data integrity to all employees.

A failure in data integrity can undermine an entire regulatory submission, and therefore, a CDMO’s commitment and capability in this area must be considered a non-negotiable criterion for partnership.

Section 2.5: Business and Relational Due Diligence

Beyond the technical and quality assessments, a comprehensive due diligence process must evaluate the business health and relational compatibility of a potential partner. A technically brilliant CDMO that is financially unstable or impossible to work with is not a viable long-term partner. These “softer” factors are often the ultimate determinants of a successful, enduring relationship.

Assessing Financial Stability and Long-Term Viability

A CDMO partnership, particularly a strategic one, is a long-term commitment that can span years or even decades.27 The financial health of the CDMO is therefore a critical consideration.41 A financially unstable partner poses a significant risk to supply chain continuity. They may be unable to make necessary investments in new technology, struggle to maintain their facilities and quality systems, or, in a worst-case scenario, face bankruptcy, leaving a sponsor’s project stranded.41

The due diligence should include:

• Review of Financial Reports: Where possible, the sponsor should review the CDMO’s financial statements and annual reports to assess their profitability, cash flow, and debt levels.28
• Industry Reputation: Inquire within industry networks about the CDMO’s reputation for financial stability and reliability.28
• Quantitative Financial Metrics: For publicly traded CDMOs, financial data is readily available. Key liquidity and leverage ratios can be calculated and compared to industry medians to provide an objective measure of financial health. Important metrics include 70:

• Current Ratio (Current Assets / Current Liabilities): Measures short-term liquidity.
• Quick Ratio ((Current Assets – Inventory) / Current Liabilities): A more stringent measure of immediate liquidity.
• Total Debt to Equity Ratio: Indicates financial leverage and risk.
  A CDMO that is significantly underperforming industry benchmarks on these metrics warrants deeper investigation.

Evaluating Supply Chain Integrity and Geopolitical Resilience

The global pharmaceutical supply chain is increasingly vulnerable to disruption from geopolitical events, trade policy shifts, natural disasters, and pandemics.44 A sponsor’s product is only as secure as the weakest link in the CDMO’s supply chain. Therefore, evaluating the CDMO’s supply chain management capabilities is a critical risk mitigation activity. The assessment should cover 37:

• Raw Material Sourcing: How does the CDMO qualify and manage its suppliers of critical raw materials? Do they have a diversified supplier base to avoid single-source dependencies?.45
• Risk Mitigation Strategies: Does the CDMO have proactive strategies to manage supply chain risks? This could include maintaining safety stocks of critical materials, dual-sourcing key components, or investing in domestic manufacturing capabilities to reduce reliance on volatile regions.45
• Logistics and Distribution: Does the CDMO have a global logistics presence and expertise in navigating cross-border shipping, customs clearance, and the complexities of cold-chain management for temperature-sensitive products?.27
• Geopolitical Awareness: In the current environment, a sophisticated CDMO should demonstrate an awareness of trade policies (e.g., potential tariffs, the BIOSECURE Act) and have strategies to mitigate their impact on the supply chain.45

Assessing Project Management, Communication Protocols, and Cultural Fit

This is arguably the most crucial element for the long-term health of the partnership. The daily interactions, the flow of information, and the ability to solve problems collaboratively will ultimately define the success of the project.

• Project Management Structure: A sponsor should probe deeply into the CDMO’s project management framework.73 Does the CDMO assign a dedicated Project Manager (PM) who will serve as a single point of contact and accountability for the project?.27 For smaller biotech companies, the seniority and dedication of the assigned PM are leading indicators of how their project will be prioritized within the CDMO’s broader portfolio. A CDMO that assigns a senior-level, dedicated PM to all projects, regardless of size, is signaling a strong, client-centric commitment.76 Conversely, a structure where project management is a part-time or matrixed responsibility for a technical lead suggests a higher risk of the project being deprioritized when resource conflicts arise.
• Communication Plan: Effective communication is the foundation of a successful partnership.22 The CDMO should be able to articulate a clear plan for regular communication (e.g., weekly team meetings, monthly progress reports) and, critically, a well-defined escalation pathway for handling deviations, delays, and other unforeseen issues.22 This plan should include a 24/7 contact list so that critical issues on the manufacturing floor can be addressed immediately.22
• Cultural Fit: This “soft” factor is a powerful predictor of long-term success.25 The sponsor must assess whether the CDMO’s working style, values, and corporate culture align with their own. Is the CDMO collaborative and transparent, or formal and siloed? Do they share a similar sense of urgency and approach to risk-taking? A strong cultural fit fosters trust and creates a smoother, more productive, and less adversarial working relationship that can endure for years.27

To synthesize these multifaceted due diligence findings into a clear, defensible decision, the use of a weighted scorecard is highly recommended. This tool transforms a complex evaluation into a more objective, data-driven process. It forces the internal team to formally agree on the strategic importance of each criterion before the evaluation begins, ensuring the final choice is aligned with the project’s core drivers.

Table 3: The Comprehensive Due Diligence Scorecard

Instructions: The internal team assigns a Weighting Factor to each criterion based on strategic importance (1=Low, 5=Critical). Each shortlisted CDMO is scored on a scale of 1-5 for each criterion based on due diligence findings. The Weighted Score is calculated by multiplying the Score by the Weighting Factor. The CDMO with the highest Total Weighted Score is the leading candidate.

Part III: Finalizing the Partnership – From Proposal to Contract

The final phase of the CDMO selection process involves translating the intensive due diligence into a concrete business relationship. This stage moves from evaluation to negotiation, focusing on interpreting the nuances of the CDMO proposals and codifying the terms of the partnership into robust legal agreements. This is where the foundation for a successful long-term collaboration is formally laid.

Section 3.1: Comparing Proposals: Reading Between the Lines

After the site audits and deep-dive discussions, the sponsor team must reconvene to make a final comparison of the shortlisted candidates, using the detailed proposals as a primary data source. This comparison must go far beyond a simple analysis of the price tag.77

Beyond the Bottom Line: Deconstructing Pricing Models

The lowest price is often a siren’s call that can lead to significant long-term costs and is frequently a red flag indicating an incomplete or risky proposal.32 To make a true “apples-to-apples” comparison, sponsors must first understand the different pricing models and their implications for budget predictability and risk allocation 19:

• Fee-for-Service (FFS): The sponsor pays for specific, defined activities. This is a common, straightforward model but requires a very well-defined scope of work.
• Time and Materials (T&M): The sponsor pays for the hours worked and the materials consumed. This model offers flexibility for projects with uncertain scopes but carries significant budget risk for the sponsor if the project encounters delays or inefficiencies.19
• Fixed-Price: The sponsor pays a single, fixed price for a defined package of work. This offers budget certainty for the sponsor, but the CDMO will build a significant risk premium into the price to cover potential unforeseen challenges.19
• Cost-Plus: The sponsor pays the CDMO’s actual costs plus an agreed-upon markup. This model offers transparency but requires strong auditing capabilities on the sponsor’s part to ensure costs are legitimate.19
• Performance-Based/Milestone Payments: Payments are tied to the achievement of specific, predefined milestones (e.g., successful batch completion, regulatory filing). This model aligns the incentives of both parties and shares the risk.19

A critical element of the proposal comparison is demanding a detailed, line-item breakdown of all costs, including raw materials, labor, analytical testing, and project management fees.32 This transparency is essential to uncover potential “hidden” costs and to understand the assumptions behind each CDMO’s quote.78

Identifying Red Flags and Green Flags in CDMO Proposals

The proposal document itself is a rich source of information about a CDMO’s professionalism, diligence, and partnership philosophy. Sponsors must learn to “read between the lines” to identify signals of a strong or weak potential partner.32

A crucial litmus test for a mature, partnership-oriented mindset is the CDMO’s willingness to discuss and define a process for handling failures. Development and manufacturing are complex, and setbacks are inevitable.53 A transactional CDMO might have contractual language that absolves them of responsibility or heavily penalizes the sponsor in the event of a batch failure, regardless of fault. A true strategic partner, however, will be willing to proactively discuss and negotiate fair and clear terms for how deviations will be investigated, how root cause will be determined, and how costs for remediation or repeat work will be shared.79 A proposal that transparently addresses this “unhappy path” is a strong green flag, signaling a commitment to a true partnership rather than a simple transactional relationship.

Table 4: CDMO Proposal Evaluation: Red Flags vs. Green Flags

Using a Weighted Scorecard for Objective Comparison

The final step in the comparison is to formally populate the Due Diligence Scorecard (from Table 3) with the scores derived from the proposals, site audits, and team discussions. This quantitative tool provides a structured and defensible rationale for the final selection, moving the decision away from gut feeling or a single factor like cost, and toward a holistic assessment of which partner best aligns with the project’s weighted strategic priorities.33

Section 3.2: Negotiating the Master Service Agreement (MSA)

Once the preferred CDMO partner has been selected, the legal teams engage to draft and negotiate the contracts that will govern the relationship. The primary contract is the Master Service Agreement (MSA), a comprehensive document that outlines the overarching legal and commercial terms of the partnership.81 Specific projects or work packages are then typically defined in separate Statements of Work (SOWs) or Project Orders that fall under the umbrella of the MSA.

Critical Clauses: Scope of Work, Governance, and Timelines

The MSA must be a meticulously drafted document, as it serves as the roadmap for the entire collaboration.81 Key clauses that require careful negotiation include:

• Scope of Services: The agreement must clearly and unambiguously define the scope of the services to be provided by the CDMO. This includes not only the core manufacturing tasks but also responsibilities for ancillary activities like sourcing raw materials, generating regulatory documentation, and ensuring compliance with the laws of the final market destination.82
• Governance Structure: The MSA should formalize the governance framework for the partnership. This often includes establishing a Joint Steering Committee (JSC) with representatives from both parties to provide strategic oversight, resolve issues, and ensure alignment.74 The roles and responsibilities of each party’s team members must be clearly delineated.83
• Timelines and Change Control: The agreement must specify key timelines and milestones. Critically, it must also include a robust change control process that defines how any changes to the scope, timeline, or manufacturing process will be requested, evaluated, approved, and documented.82

For early-stage, cash-constrained biotech companies, flexibility in the MSA can be a powerful strategic tool. A standard, all-encompassing MSA may require an upfront financial commitment that a startup, reliant on milestone-based funding, cannot make.24 A savvy sponsor can and should negotiate for a more flexible, staged contractual structure. For example, they could negotiate an initial SOW under the MSA that covers only the first phase of work, such as cell line development, without committing to the full, multi-million dollar clinical manufacturing campaign.85 This “pay-as-you-go” approach allows the startup to achieve a critical, value-inflecting milestone that can be used to secure the next tranche of funding. It allows the program to move forward and saves months on the overall timeline without requiring a massive, premature capital outlay. A CDMO’s willingness to accommodate such a fractionated approach is a strong indicator of their flexibility and their understanding of the unique challenges of the biotech ecosystem.85

Liability, Indemnification, and Dispute Resolution

These clauses are often the most heavily negotiated and contentious sections of the MSA, as they deal with the allocation of risk and financial responsibility.81

• Liability and Defects: The agreement must specify who is liable in the event of a manufacturing defect, a batch failure, or a product recall.82 This includes defining who bears the costs associated with the event (e.g., cost of materials, investigation, repeat work) and the extent of liability (e.g., are consequential damages or lost profits covered?).
• Indemnification: Indemnification clauses require one party to compensate the other for specific losses or damages. These are critical for protecting the sponsor from third-party claims arising from the CDMO’s negligence or breach of contract.81
• Dispute Resolution: To avoid costly and time-consuming litigation, the MSA should establish a clear, tiered process for resolving disagreements. This typically starts with escalation through the governance structure (JSC) and may then proceed to formal mediation or binding arbitration.51

Section 3.3: The Quality Agreement (QA): The Blueprint for Compliance

The Quality Agreement (QA) is a separate, legally binding document that is mandated by cGMP regulations and is a focus of regulatory inspections.87 While the MSA governs the commercial relationship, the QA governs the quality and cGMP-related activities. It is the primary operational blueprint for ensuring compliance.

Essential Components of a Robust QA per FDA and ICH Guidelines

According to FDA guidance, the QA is a comprehensive written agreement that defines and establishes each party’s manufacturing activities in terms of how each will comply with cGMP.87 It should be a standalone document, separate from the MSA, to allow for review by regulatory inspectors without disclosing sensitive commercial terms.87

The essential components of a robust QA include 87:

• Purpose and Scope: Defines the products and services covered by the agreement.
• Definitions: Ensures both parties agree on the meaning of key quality and technical terms.
• Dispute Resolution: Outlines the process for resolving disagreements on quality-related matters.
• Delineation of Manufacturing Activities: This is the most critical section, detailing the specific cGMP responsibilities of both the sponsor (owner) and the CDMO (contract facility).

Defining Roles, Responsibilities, and Change Control Procedures

The QA must be exceptionally clear and detailed in assigning responsibility for every cGMP activity. It is not just a regulatory formality; it is the primary operational tool for managing the day-to-day relationship and preventing the most common sources of partnership friction, such as misaligned expectations and poor communication.53 By creating a pre-agreed “rulebook,” the QA transforms abstract expectations into concrete, auditable procedures.

Key areas where responsibilities must be explicitly defined include 69:

• Quality Unit Activities: Defining responsibilities for batch review, final product release (the sponsor’s quality unit always retains ultimate responsibility for release to market), auditing, and handling of regulatory inspections.
• Laboratory Controls: Who is responsible for method validation, stability studies, OOS investigations, and release testing.
• Materials Management: Who is responsible for qualifying suppliers, testing incoming materials, and managing inventory.
• Documentation: Who is responsible for creating, reviewing, approving, and maintaining all cGMP documents, including batch records and validation reports.
• Change Control: The QA must establish a formal, robust process for managing any proposed changes to facilities, equipment, processes, or specifications. This ensures that no changes are made unilaterally and that the impact of every change is thoroughly assessed and documented before implementation.

The time and effort invested in negotiating a detailed, comprehensive QA is a direct investment in the long-term health and risk mitigation of the entire project.

Section 3.4: Safeguarding Innovation: Intellectual Property (IP) Protection

For any pharmaceutical company, but especially for innovation-driven biotechs, intellectual property is the most valuable asset. Protecting this IP within a CDMO partnership is a paramount concern and a highly complex area of contract negotiation. The agreement must establish a clear framework for IP ownership and prevent the unauthorized use or “contamination” of the sponsor’s proprietary technology.86

Defining Background vs. Foreground IP

The foundational step in any IP negotiation is to clearly define the different categories of intellectual property in the contract 82:

• Background IP: This is all intellectual property that is owned or controlled by either the sponsor or the CDMO before the start of the project. Each party retains ownership of its own background IP.
• Foreground IP (or Developed IP): This is all new intellectual property that is invented or created during the course of the project collaboration. The ownership of this newly created IP is the primary subject of negotiation.

Strategies for IP Ownership, Licensing, and Contamination Prevention

There are several common models for assigning ownership of foreground IP, and the choice depends on the nature of the project and the negotiating leverage of each party 90:

1. Ownership Follows Inventorship: IP is owned by the party whose employees invented it. This may seem fair, but since the CDMO’s employees are performing the work, this model often results in the CDMO owning most of the foreground IP.
2. Customer Owns All Foreground IP: The sponsor, as the paying client, takes ownership of all IP developed during the project. CDMOs may resist this as it prevents them from using process improvements developed on one project for other clients.
3. Split Ownership: This is a common compromise where the sponsor owns foreground IP that is solely related to their specific product or molecule, while the CDMO owns foreground IP that relates to general improvements in their own manufacturing platform or technology. This can lead to disputes over inventions that relate to both.
4. Customer Owns, CDMO Licenses Back: The sponsor owns all foreground IP but grants the CDMO a broad, royalty-free, perpetual license to use that IP. This gives the CDMO the operational flexibility it needs while securing ownership for the sponsor.

Beyond ownership, the contract must include robust clauses to prevent IP contamination.86 This includes strong confidentiality obligations and representations and warranties from the CDMO that they will not use any third-party IP in the project without authorization, nor will they use the sponsor’s confidential information or IP for any other client’s project.

A critical, yet often overlooked, risk mitigation tool for the sponsor is the negotiation of a “springing license” to the CDMO’s essential background IP.90 A sponsor’s product can become inextricably linked to a CDMO’s proprietary manufacturing process. If the partnership fails or the CDMO runs into capacity or quality issues, the sponsor can be effectively “trapped,” unable to move their product to another manufacturer who lacks the CDMO’s specific know-how. A springing license addresses this vulnerability. It is a pre-negotiated license to the CDMO’s necessary background IP that only “springs” into effect under specific, pre-defined trigger conditions, such as a material breach of contract or a sustained failure to supply.90 This provides the sponsor with a crucial “escape hatch,” giving them the operational flexibility to transfer their manufacturing process to another partner if the relationship becomes untenable. It is a necessary component of a robust risk management strategy for any long-term manufacturing agreement.

Part IV: Managing the Partnership and Future-Proofing Your Strategy

Selecting a CDMO and signing the contracts is not the end of the process; it is the beginning of a long-term relationship that requires active management, continuous communication, and a forward-looking perspective. The health of this partnership will directly impact the success of the product. Furthermore, the CDMO landscape itself is in constant flux, and sponsors must stay abreast of key trends to ensure their outsourcing strategy remains competitive and effective.

Section 4.1: Common Pitfalls in CDMO Relationships and Mitigation Strategies

Even with the most rigorous due diligence, CDMO partnerships can fail. Understanding the common reasons for failure is the first step toward proactive mitigation. Failures rarely stem from a single event but rather from an accumulation of interconnected issues that erode trust and impede progress.53

Case Studies: Learning from Successful and Failed Partnerships

Analysis of industry case studies and expert commentary reveals several recurring themes in both successful and failed partnerships.

Common Failure Modes:

• Misaligned Expectations and Poor Communication: This is the most frequent cause of failure. When the scope of work, deliverables, and timelines are not clearly defined and agreed upon in the contract, both parties may operate under different assumptions, leading to frustration and conflict.53 Infrequent or unclear communication allows small problems to escalate into unmanageable crises.53
• CDMO Overpromising and Underdelivering: In a competitive market, a CDMO’s business development team may be incentivized to win contracts by overstating their technical capabilities or promising unrealistic timelines.53 A particularly damaging pitfall is the internal disconnect within a CDMO, where the business development team enthusiastically accepts a project that the technical operations team later rejects due to a lack of technical fit or capacity.92 This not only wastes the sponsor’s valuable time but also destroys trust in the CDMO’s professionalism and internal communication.92
• Inadequate Quality Systems or Regulatory Compliance: A CDMO with a weak quality culture or a poor compliance record can lead to severe consequences, including product quality failures, regulatory setbacks, costly recalls, and damage to the sponsor’s reputation.54
• Cultural Mismatch: This is a more insidious but equally critical pitfall. A fundamental misalignment in the working culture, risk tolerance, and sense of urgency between the sponsor and the CDMO can create constant friction. For example, a nimble, fast-moving startup may be perpetually frustrated by the perceived bureaucracy and slower pace of a large, process-driven CDMO. The startup values speed and is willing to accept calculated risks to hit milestones, while the large CDMO prioritizes process adherence and risk aversion to ensure compliance across its vast portfolio.53 This mismatch in core values can make effective collaboration nearly impossible. During due diligence, sponsors must probe beyond technical capabilities and ask pointed questions about decision-making under pressure and the balance between speed and risk. The answers are often more predictive of long-term success than a list of equipment.

Hallmarks of Successful Partnerships:

• Deep Collaboration and Transparency: Successful partnerships are characterized by open, honest, and frequent communication. The CDMO is treated not as a vendor, but as a true extension of the sponsor’s internal team.54
• Strong Governance and Project Management: A well-defined governance structure with regular meetings and clear escalation pathways ensures that both parties remain aligned and that issues are addressed proactively.74
• Mutual Trust and Respect: The relationship moves beyond a purely transactional agreement to one of colleagues working toward a shared goal.93 There is a shared understanding that challenges will arise and a commitment to resolving them collaboratively.79

Proactive Risk Management and Building a Resilient Partnership

Mitigating the risks of partnership failure is an ongoing activity that begins with the rigorous due diligence process outlined in Part II. After selection, risk management continues through several key practices:

• Robust Governance: Actively use the governance framework established in the MSA and QA. The Joint Steering Committee should meet regularly to review progress, address challenges, and ensure strategic alignment.74
• The “Trust But Verify” Approach: A sponsor should empower the CDMO to operate with autonomy within the agreed-upon parameters, but this trust must be balanced with verification. This includes conducting regular performance reviews against key performance indicators (KPIs) like batch success rates and on-time delivery, as well as exercising the right to conduct periodic audits.74
• Contingency Planning: For critical commercial products, the ultimate risk mitigation strategy is to qualify a second-source or backup CDMO.95 While this involves additional cost and effort, it provides an essential fail-safe against a catastrophic supply disruption at the primary partner.

Section 4.2: The Future of CDMO Partnerships: Key Trends to Watch

The CDMO industry is continuously evolving, driven by scientific advancements, technological innovation, and shifting market demands. Sponsors must monitor these trends to ensure their outsourcing strategies remain effective and to identify forward-thinking partners who can provide a competitive edge.

The Impact of Pharma 4.0: Digitalization, AI, and Smart Manufacturing

The most significant transformative trend is the adoption of Pharma 4.0, the application of Industry 4.0 principles to pharmaceutical manufacturing.96 This involves the integration of digital technologies, automation, and data analytics across the entire manufacturing process. CDMOs are increasingly investing in these capabilities to improve efficiency, transparency, and quality.97

Key Pharma 4.0 technologies include:

• Artificial Intelligence (AI) and Machine Learning (ML): AI/ML algorithms are being used to analyze vast datasets from manufacturing processes to optimize parameters, predict potential deviations before they occur, and enhance quality control.42
• Cloud-Based Data Platforms and Digital Twins: The transition to the cloud enables real-time data sharing and accessibility.98 This allows a sponsor to have unprecedented, real-time visibility into their manufacturing process running at a CDMO’s facility through shared data platforms or even “digital twins”—virtual models of the process.20
• Automation and Robotics: Automation is being used to reduce manual interventions, improve consistency, and handle complex processes with greater precision.42

This digital transformation is creating a new, critical due diligence category for sponsors: digital readiness and data governance. A CDMO’s digital maturity is no longer just a “nice-to-have”; it directly impacts a sponsor’s ability to have real-time oversight and control over its own product and supply chain. The selection checklist must now include a thorough evaluation of a CDMO’s IT infrastructure, cloud capabilities, data sharing platforms, and cybersecurity policies.45 Choosing a digitally lagging CDMO in the current environment is a strategic misstep that will limit a sponsor’s operational agility and competitive standing.

The Rise of Sustainability (ESG) as a Selection Criterion

Environmental, Social, and Governance (ESG) considerations are becoming an increasingly important factor in corporate strategy, and this is extending to the CDMO selection process. Pharmaceutical companies are under pressure to improve their sustainability footprint, and they expect their supply chain partners to contribute to these goals. Forward-thinking CDMOs are responding by adopting green chemistry principles, investing in energy-efficient equipment, reducing waste, and implementing sustainable manufacturing practices.14 As this trend grows, a CDMO’s ESG performance will likely become a more formalized and weighted criterion in the selection process.

Patient-Centricity and the Growth of Personalized Medicine

The pharmaceutical industry’s pipeline is shifting dramatically towards more complex and targeted therapies. The growth of biologics, biosimilars, and highly personalized medicines like cell and gene therapies is a primary driver of the CDMO market.14 This trend has profound implications for CDMOs and the capabilities sponsors must seek in a partner.

This shift demands greater flexibility and specialization from CDMOs. Instead of manufacturing massive batches of a one-size-fits-all drug, they must be able to handle smaller, more frequent production runs, manage highly complex and sensitive biological processes, and support intricate “vein-to-vein” supply chains for autologous cell therapies.42 This reinforces the need for sponsors to partner with highly specialized, technologically advanced CDMOs that have invested in the specific platforms and expertise required for these novel modalities. The era of the generalist CMO is giving way to an era of the specialist CDMO, and the selection process must reflect this new reality. The right partner is no longer just one who can manufacture a product, but one who can master its complexity.

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