If you’re a biostatistician or clinical software developer, you’ve probably felt the weight of trying to meet GxP standards while navigating the FDA/EMA submission process. It’s not just about getting the software right—it’s about ensuring safety, quality, and compliance, all under tight timelines. It can feel like a lot to juggle. 

Curious about GxP validation? Take a look at our guide on how it all starts with the Definition of Done to keep your process on track.

In this post, we’re here to break things down in a way that makes the whole process feel a bit less overwhelming. From GxP guidelines to the best software practices, we’ll help you simplify validation and get your project moving smoothly.

What is an FDA Submission?

An FDA submission is the process through which companies submit the necessary data and documentation to the U.S. Food and Drug Administration (FDA) to seek approval for a new product. This product can be anything from a new drug to a medical device. The goal of this submission process is to demonstrate that the product is safe, effective, and meets the quality standards set forth by the FDA.

Some common types of FDA submissions include:

• New Drug Application (NDA): Used for the approval of new drugs.
• Biologics License Application (BLA): For products like vaccines and blood components.
• Pre-Market Approval (PMA): For medical devices that require approval before marketing.
• 510(k) Submission: Allows manufacturers to demonstrate that their device is substantially equivalent to one already on the market.

The approval process is rigorous and requires companies to comply with various GxP guidelines to ensure the integrity of their products.

Understanding GxP in FDA Submissions

GxP stands for "Good Practice" and refers to the regulations that govern different areas of product development in various industries, including pharmaceuticals, biotechnology, and medical devices. GxP ensures that products are safe, effective, and meet high-quality standards.

Here are some key categories of GxP that are particularly relevant to FDA submissions:

• Current Good Manufacturing Practices (CGMP): Ensures that products are consistently produced and controlled according to quality standards.
• Good Laboratory Practices (GLP): Governs the laboratory testing environment to ensure the quality and integrity of data.
• Good Clinical Practices (GCP): Focuses on ethical standards and the quality of clinical trials.
• Good Distribution Practices (GDP): Ensures the proper distribution and storage of products.
• Good Pharmacovigilance Practices (GVP): Involves monitoring the safety of a drug once it’s on the market.
• Good Automated Manufacturing Practices (GAMP): Ensures the use of automation in manufacturing processes is done correctly and consistently.

The Role of Good Programming Practices in FDA Submissions

Software systems play a critical role in the development and submission process. Ensuring these systems are reliable, secure, and compliant with FDA regulations is where good software engineering practices come into play. Below are some of the key practices that help maintain compliance and quality.

1. Good Development Practices

Good development practices ensure that software is developed systematically and consistently. Some of the practices involved include:

• Definition of Done: This involves defining the criteria that must be met before a piece of work is considered complete. It provides clear guidelines for when a task is fully finished and compliant.
• Version Control: This allows for the tracking of all code changes and maintains an audit trail of modifications. Version control is crucial for ensuring the reproducibility of the code and helping to identify any changes that need review.
• Code Review: Developers review the code after each change to ensure it meets quality standards and doesn’t introduce new issues.
• Build Automation: Automating the process of compiling and packaging software ensures consistent and repeatable builds, reducing the likelihood of errors.

2. Good Reproducibility Practices

In regulated industries, reproducibility is critical. Good reproducibility practices ensure that any software or data can be replicated reliably. Key practices include:

• Version Control: By using version control, you can reproduce the code at any stage, allowing you to analyze, revert, or reproduce changes when necessary.
• Change Control: This involves having a documented process to track all software changes, ensuring that modifications are reviewed, tested, and approved.
• Dependency Management: Managing libraries, packages, and the environment ensures that the software can run consistently across different setups, even years after its initial release.
• Clear Documentation: Manuals, README files, and well-commented code make it easier for development teams to run the software on different machines, even after many years.

3. Good Software Validation Practices

Validation is a critical part of software development in clinical industries. It ensures that the software performs as expected and meets regulatory requirements. This process includes: 

• Verification and Validation (V&V): Software verification ensures that each phase of the development meets the specified requirements (DoD). Validation ensures the final software meets the intended use and performs correctly in real-world conditions.some text
  • Unit Testing: Automated tests that validate the functionality of individual components in the code.
  • Integration Testing: Testing interactions between different software components to ensure they work well together.
  • End-to-End Testing: Ensures that the entire system functions as expected from the user’s perspective.
  • Manual Testing: Quality assurance experts manually test edge cases and scenarios that automated testing may miss.
  • Performance Testing: Tests how the software behaves under extreme conditions, ensuring that it can handle peak loads and stress.
• Risk-Based Validation: Focuses on validating the software components that directly impact product safety, quality, and performance.

4. Good Cybersecurity Practices

Maintaining the security of your software is vital, especially when dealing with sensitive patient data or medical devices. These practices include:

• Vulnerability Management: Regularly scan for vulnerabilities and apply patches to address security risks.
• Open Source Package Validation: Only use validated open-source packages to avoid introducing vulnerabilities into your software.
• Secure Software Development: Follow secure coding practices to prevent common security issues, such as SQL injection and buffer overflow.

5. Good Access Control Practices

Access control ensures that only authorized personnel can access and modify the software and its data. This involves:

• Access Control: Define roles and implement authentication mechanisms to control who can modify, access, or review software code and data.
• Audit Trails: Maintain audit trails to document who accessed or modified the software and system configurations, ensuring traceability and accountability.

6. Good Documentation Practices

Documentation is essential for ensuring that software can be reviewed, validated, and understood by regulatory bodies. Important steps include: 

• Complete Documentation: Every software-related activity, from development to testing, must be thoroughly documented to ensure transparency and reproducibility.
• Understandable: The documentation should be clear and easy to follow, allowing regulators to understand the processes and results. This includes all test results, code changes, risk assessments, and validation reports.
• Helping with Reproducibility: Clear documentation (manuals, readmes, code comments) that allows you to run the code on other machines after many years with different development teams.

Looking to simplify GxP compliance in pharma? Check out our guide on using R Markdown and {officedown} to make good documentation practices easier.

7. Good Data Management Practices (Governance)

Proper data management ensures that the data generated and used in the software is accurate, secure, and compliant with regulatory standards. This process includes: 

• Data Validation: Ensure that data is accurate, complete, without duplicates, and follows one formatting standard.
• Data Integrity: Implement mechanisms such as encryption and hashing to ensure the integrity and security of the data generated by the software.
• Data Security: Implement strong security measures to protect confidential and sensitive data.

Risk Management in Software Development

Risk management plays a key role in ensuring that your software is safe and compliant with FDA regulations. The process involves:

• Risk Assessment: Identify, assess, and mitigate risks related to software development, focusing on patient safety and data integrity.
• Failure Mode and Effects Analysis (FMEA): This technique analyzes potential software failures and mitigates risks associated with its use.

The Software Development Life Cycle (SDLC) in FDA Submissions

The SDLC process ensures that software is developed in a systematic way, with clear phases including:

1. Defining requirements
2. Designing
3. Coding
4. Testing
5. Validation
6. Maintenance

Each phase must be thoroughly documented to provide full traceability from the requirements stage to the final product, ensuring that the FDA can easily follow the development process and verify compliance.

Summing Up GxP Validation in Clinical Software Development

Navigating the FDA submission process and complying with GxP guidelines can be complex, but following good software engineering practices can help you achieve your goals more efficiently. From development and validation to cybersecurity and documentation, maintaining compliance ensures that your product meets the highest standards of safety, effectiveness, and quality.

If your company is facing challenges with GxP compliance or FDA submissions, feel free to reach out to us for expert consultation. We're here to help.

​​Want to speed up your GxP reporting? Check out our case study on how automation cut the process from 5 weeks to just 5 minutes.

Resources

• Principles of Premarket Pathways for Combination Products - Guidance for Industry and FDA Staff
• Current Good Manufacturing Practice (CGMP) Regulations
• Translation of Good Laboratory Practice Study Reports: Questions and Answers Guidance for Industry
• E6(R3) GOOD CLINICAL PRACTICE (GCP) 
• WHO Health products policy and standards - Distribution 
• Current Good Manufacturing Practice (CGMP) Regulations 
• Good Pharmacovigilance Practices and Pharmacoepidemiologic Assessment
• GAMP 5 Guide 2nd Edition
• Good Programming Practice 
• General Principles of Software Validation; Final Guidance for Industry and FDA Staff
• GxP Validation in Software Development starts from the Definition of Done
• Data Integrity and Compliance With CGMP

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