Sunday, December 13, 2009

Tools for screening and validation

Taqman SNP Genotyping Assays, developed by Applied Biosystems, are a state-of-the-art technology for screening and validation of polymorphisms. Recently Applied Biosystems introduced two new products to complement this offering; the high throughput Taqman Open Array Genotyping System and Taqman Copy Number Assays.


NGP. What is genotyping, and what are its applications in disease prevention?
XC.
Genotyping refers to the process of determining an individual’s genotype. SNPs are currently the most commonly studied genetic variation, although microsatellites and STRs have been widely used in the past and new markers, such as CNV (copy number variants), are of increasing interest to researchers. The ultimate goal of this analysis is to find links between a disease (or group of diseases) and its genetic background. Advances in the technologies available have allowed researchers to analyse thousands, or even millions, of SNPs to discover disease-associated genes, and validate results by replicating studies with larger cohorts of samples using technologies like Taqman SNP Genotyping Assays.

NGP. Why is genotyping important in clinical research?
XC.
Clinical studies aim to discover panels of SNPs or other genetic markers that can be used in the prevention, prognosis or treatment decision of complex diseases. These biomarker panels often include polymorphisms of high clinical relevance, such as those located in DME (drug metabolising enzyme) genes. As they affect an individual’s drug responses, genes that code for the DMEs represent one of the most important classes of genetic variation in drug development studies. Analysis of SNPs in these genes is very important during the drug development phase, as this can indicate how a patient will metabolise the candidate drug. As a simple example, grouping patients into low, medium or high metabolisers can help researchers adjust dosage to improve drug efficiency. This strategy is called pharmacogenetics, and is important for the future of personalised medicine. Applied Biosystems’ DME Taqman SNP Genotyping Assays incorporate over 2,600 high value polymorphisms located in regulatory elements and coding regions of 220 drug metabolism and transporter genes. Later this year, users will be able to customise the Taqman Array Platform (microfluidic card) for DME genotyping research, allowing simultaneous analysis of eight samples for up to 96 SNPs.

NGP. What benefits does Applied Biosystems’ new high throughput genotyping system provide to life scientists? How does it differ from similar systems?
XC.
The recently launched Taqman OpenArray Genotyping System combines Taqman SNP Genotyping Assays with the massively parallel OpenArray technology, allowing researchers to analyse more than 90,000 genotypes per day at low cost and with a simple laboratory set-up. The nanoliter sample volumes required for the Taqman technology permit a very simple workflow, with the excellent call rates critical to the success of this kind of research. Unlike other technologies, the Taqman OpenArray Genotyping System supports full analysis from DNA to results, with customers able to choose from more than 4.5 million pre-designed assays, or custom designed assays to suit any gene for any species. These assays are ready to run on OpenArray, with no hidden costs coming from oligo fees or third party consumables that may hamper the workflow. With this system Applied Biosystems delivers market-leading performance, support, training and services to ensure customer satisfaction for high throughput genotyping applications.

NGP. What do you believe will be the most important developments in genotyping over the next few years?
XC.
Next generation sequencing is an exciting new technology being used by laboratories conducting disease-association studies. Re-sequencing of a large number of individuals will bring more genetic markers (SNPs and CNVs), so there will be increasing demand for simple yet effective technologies for validation and commercialisation of biomarker panels. To complement the SNP assays portfolio, Applied Biosystems has recently launched the Taqman Copy Number Assays. This solution is comprised of more than 1.6 million pre-designed assays, as well as a custom design pipeline, with specific analysis software to provide a platform for all researchers interested in CNV screening and validation of array CGH.

Xavier Cristina Ph.D.
is the European Business Development Manager for the Molecular Biology Systems Division at Applied Biosystems, part of Life Technologies. After completing a Ph.D. in Microbiology and Biochemistry, Xavier joined Applied Biosystems in 2000 and has developed his career in various positions in the company.

The state of validation in the European Union

Since the formation of the European Union (EU) in 1993, each member state has brought along its own regulatory baggage, namely the standards and regulations that their companies are formally required to comply with. These standards and regulations still apply for any pharmaceutical products a native manufacturer decides to market within their homeland. When the same manufacturer markets its pharmaceutical products to consumers in other EU member states, the regulatory directives of the European Commission and the European Agency for the Evaluation of Medicinal Products (EMEA) apply as well.

If this manufacturer plans to export pharmaceutical products to international markets, corresponding regulatory requirements — such as those mandated by the US Food and Drug Administration (FDA) and the Japanese Ministry of Health, Labor, and Welfare (MHLW) — must also be considered. Additionally, global manufacturers must be aware of international guidelines, such as those imposed by the World Health Organization (WHO) and the International Society of Pharmaceutical Engineers (ISPE).

Luckily there is a global effort under way to make all of these regulatory bodies more consistent in their approach to pharmaceutical validation. The European Commission published The Rules Governing Medicinal Products in the European Union, Volume 4, concerning good manufacturing practice (GMP), which is consistent with FDA Good Manufacturing Practices for Finished Pharmaceuticals (21 CFR Parts 210 and 211).1,2

Both European Commission and FDA rules are consistent with the ISPE good automated manufacturing practice (GAMP), an internationally recognized validation guideline. The streamlining of these and other regulatory agency guidelines falls within the scope of the global GMP harmonization efforts brought about by the International Conference on Harmonization (ICH). This has also resulted in sweeping changes to Japan's pharmaceutical affairs law (PAL) to bring it in line with the GMP quality standards of the western world.

The overall intent is to make the process easier and more efficient for manufacturers to consistently produce pharmaceutical products that do not place patients at risk because of inadequate safety, quality, or efficacy by "establishing documented evidence that provides a high degree of assurance that a specific process will consistently produce a product meeting its predetermined specifications and quality characteristics."3 While many regulatory directives and regulations are intentionally vague regarding the specifics of how to conduct pharmaceutical validation, globally-accepted validation processes now seem to be pointing in a similar direction.

Validation pitfalls

The universal rule of thumb still applies: if a particular process or system has been validated previously with a given level of documentation and protocol testing, then it would be reasonable to assume that a comparable level of documentation and testing would be adequate to achieve compliant process validation for a similar manufacturing process or system.

However, this approach can be risky. As the FDA process validation guideline warns: "There is an inherent danger in relying on what are perceived to be similarities between products, processes, and equipment without appropriate challenge."3 The guideline goes on to say: "FDA recognizes that because of the great variety of medical products (drug products and medical devices), processes, and manufacturing facilities, it is not possible to state in one document all of the specific validation elements that are applicable."3 As a result, pharmaceutical companies and consulting firms contracted to help them perform process validation must refer to relevant experience, historical precedents, or other industry guidelines such as the GMP guidelines that apply for their intended markets.

Generally, each piece of equipment used in the manufacturing process — such as computer workstations, servers and controllers — must be qualified by performing and documenting applicable protocol testing. This ensures that the equipment is installed correctly (installation qualification [IQ]), is operating proficiently (operational qualification [OQ]), and is performing satisfactorily according to the required parameters of the overall system (performance qualification [PQ]).

Process validation of a manufacturing system, therefore, requires an entire suite of documents, typically including:

  • A validation plan, which is a written plan stating how the process validation will be conducted, what documents will be included and how they will be approved.
  • Functional requirements specifications that cover the technical aspects of the system.
  • A risk assessment that considers inherent risks of the process and potential contingency plans.
  • Executed IQ, OQ and PQ protocols, traceable to the functional requirements.
  • Validation summary reports stating whether the system is fit to manufacture the product by summarizing results of validation testing and signifying that all required approval signatures have been obtained.4

Collectively, the process validation documentation must prove to a regulatory investigator that the company has built a system that will reliably produce the specified product with the required level of quality.

Once a process is validated, the pharmaceutical manufacturer must show that adequate controls are in place so that the validated state is maintained. European Commission directive 2003/94/EC states: "Principles and guidelines of good manufacturing practice should be set out in relation to quality management, personnel, premises and equipment, documentation, production, quality control, contracting out, complaints and product recall, and self-inspection."5

The EU GMP guideline goes on to say: "Regular periodic or rolling quality reviews of all licensed medicinal products, including export only products, should be conducted with the objective of verifying the consistency of the existing process, the appropriateness of current specifications for both starting materials and finished product to highlight any trends and to identify product and process improvements. Such reviews should normally be conducted and documented annually."6

Regulatory agencies for individual EU member states inspect pharmaceutical manufacturing facilities on a regular basis (e.g., the UK's Medicines Control Agency [MCA] inspects each facility on a two-yearly basis, irrespective of size) to ensure sustained GMP compliance and,

more often, if specific problems are suspected.7 Although inspection results can lead to strongly-worded warning letters, recommendations to revoke a license, and the possibility of prosecution, the overall intent is to promote public safety. As the EMEA emphasizes: "The key aspect of the [Agency's] vision for the coming years is to further strengthen the protection and promotion of public and animal health in the EU, whilst encouraging and facilitating innovation and research in an enlarged EU."8

Challenges or opportunities?

In Road Map to 2010: Preparing the Ground for the Future, EMEA readily admits that the future holds many new challenges resulting from a changing regulatory environment in terms of legislative, institutional and scientific developments. "Amongst them are political factors such as the continuation of the EU enlargement with Bulgaria and Romania joining in 2007 and other countries such as Turkey also seeking membership."8,9 Other issues cited by EMEA to be addressed in coming years include

  • The fall in innovative productivity, despite a sharp increase in global R&D expenditure.
  • Preparing adequately for the introduction of new technologies, from a scientific, legal and regulatory perspective.
  • Taking advantage of new pharmaceutical technologies in the manufacturing and analytical areas, and anticipating the implications of emerging therapies.

There is also a need to adapt to changing health trends such as the impact of an ageing population; the increased demands for medicines in areas of unmet medical need; the possible unavailability of medicines in both the human and veterinary field; the ever-increasing concerns about the development of antimicrobial resistances; the adequate management of bioterrorism and chemical terrorism agents and other major public health issues (such as an influenza pandemic, another SARS outbreak)."8

The EMEA concludes: "These changes are not to be regarded as pure challenges, but rather as new opportunities which, through adequate proactive initiatives, should lead to an enhanced protection and promotion of public and animal health in an enlarged EU."8

The EMEA goes on to contend that each of the future challenges should be increasingly handled in a context of continuing globalization, as stated in the road map: "Faced with these challenges, the EMEA will have to demonstrate that the networking model on which it is based, involving institutional partners, 42 or more national competent authorities (NCAs) and over 3500 scientific experts, is still able to deliver high quality in the areas it is responsible for. In addition, there is a need for greater collaboration with — and for benchmarking against — non-EU regulatory authorities."8


In the area of regulatory compliance (e.g., GxP — good clinical practices, good laboratory practices, good manufacturing practices), the EMEA has plotted the following critical paths in its road map.

  • Effective coordination of GxP inspections performed by the NCAs, particularly those undertaken in non-EU countries, to cover inspections in the framework of centralized licensed medicines with a strong link to decentralized licensed medicines to avoid duplication of work.
  • Ensuring an appropriate quality assurance (QA) system through the work of the joint audit programme for appropriately trained EU GMP inspectorates.
  • Introducing an EU-wide database on manufacturing authorizations, inspection information and GMP certificates to provide better information to regulators, while promoting the best use of community resources and avoiding duplication.
  • Supporting its initiatives through contributions to international discussions on risk management from a quality perspective and through its cooperation with the WHO in relation to regulatory information provided to non-EU countries.

Constant compliance

In the EU, with 456 million people, pharmaceutical manufacturers should strive to maintain a constant state of regulatory compliance by incorporating a company-wide quality system as defined in the relevant GMP guidelines; making all employees aware of the quality system requirements through readily-accessible and open communication channels; and regularly training employees on all regulatory directives, regulations and GMP guidelines that pertain to their areas of accountability.

In addition, pharmaceutical manufacturers may proactively seek the extra guidance obtained through the voluntary use of a third-party quality management system (QMS), such as ISO 9000 or lean six sigma. Combining these efforts and open communication channels with EMEA and local NCA regulatory offices helps to set a favourable climate in trying to maintain a successfully compliant manufacturing environment.

Doug Bonanomi is a consultant at Stelex Inc (USA).

References

1. http://pharmacos.eudra.org

2. www.fda.gov

3. FDA Guideline on General Principles of Process Validation, 1987 (US Food and Drug Administration, 5600 Fishers Lane, Rockville MD 20857-0001, USA).

4. D. Bonanomi, Pharm. Technol. 28(2), 98–102 (2004).

5. European Commission, Commission Directive 2003/94/EC, 8 October 2003 (EMEA, 7 Westferry Circus, Canary Wharf, London, UK).

6. European Commission, Eudralex, The Rules Governing Medicinal Products in the European Union, Volume 4, EU Guidelines to Good Manufacturing Practice, Medicinal Products for Human and Veterinary Use, Part I, Chapter 1, 2005 EMEA, 7 Westferry Circus, Canary Wharf, London, UK).

7. D. Simpson, The Pharmaceutical Journal, 266 (1731), 85–88 (2001).

8. EMEA, The European Medicines Agency Road Map to 2010: Preparing the Ground for the Future, 2005 EMEA, 7 Westferry Circus, Canary Wharf, London, UK).

9. www.emea.eu.int

Validation Life Cycle

Introduction Validation Life Cycle


File:ValidationLifeCycle.jpg

Quality Management

Document Management and good documentation practise for validation documents

  • Check if SOP for "Documentation" within QMS is existing (supplier and client)
  • Generate Validation Templates (version controlled, centralized, easy-to-use)
  • Don't make yourself looking stupid and stop thinking Document Management (DM) is only personnal assistants' stuff...

Make the effort of defining some DM rules at the beginning of your validation effort and you will save a lot of time when your project will be "running for good"...

A good DM SOP should include provisions for the following:


  • Management of Templates (including authority for reviewing and approving; storage; identification; "template for templates" for consistent signature logs, history logs, header, footer, general layout...)
  • Document types
  • Document numbering
  • Document versioning
  • Document lifecycle and general definition of roles (authors, reviewers, approvers)
  • Definition of transversal roles: Document Manager, Document Coordinator...
  • Cross referencing (may provide the maintenance of a central repository of cross-references... A very basic 2 columns Excel file that will make your "impact assessment" so much easier when you will be coming up with the new version of an existing document...)
  • Authorized and respective roles of formats: "native" electronic, electronic / PDF, paper format...
  • Meaning of signatures according to different roles; possible use of electronic signatures and technical requirements for that latter
  • Storage (with respect of formats and "master" Vs. "working" copies)
  • Delegation of authority: temporary and/or permanent
  • Provisions for document updates, relationship with change control SOP (when / under which circumstances can we get rid of a full CC process for updating a document??)

If no "general" DM SOP is available, one can be created for the sake of a specific project. When there is one available, it should be referred into your Validation Plan. Project-specific provisions should be detailed in the VP, especially by further defining the "roles for Doc Management" with respect to the project team / project responsibility matrix.

Validation Management and Planning

Validation Planning

Now, how to describe Validation simple? Ok, there is no simple way, and some start with definitions and standards, and after two hours you have understood, that it is a lot of work - or not very interessting.

In simple words: Validation is nothing special, or adding tons of (unneccesary) tasks to a "normal" project - if any project is being executed with good practices - it is more or less validated. But in normal live, not every project is following good practices....

Please do not forget, that about 60 Percent of IT Projects in general are not in time and budget. So validation is enabling as a quality management discipline a good IT project in general - and in addition regulatory compliance and inspection readiness.

Quality Project Plan

Introduction Like everything in the validation world, a Quality Project Plan (QPP) can be known by several other names (e.g. Quality Plan, Quality Execution Plan, etc.), but essentially its aim is to define a plan for quality assurance activities and outline the regulations and activities to be used by an overall project team (this can / should include the IT and engineering). Rather than replicating the Validation Plan it should supplement and support it. It can also be used to assign people to roles and responsibilities that should have been defined in the Validation Plan.

Who should write a QPP?

The Validation Team - Whilst the Validation Plan should determine the WHAT, WHO and HOW, the QPP should help define these too (the validation team can have a set of roles and responsibilities defined for the project which sit below the overall project Roles and Responsibilities), aswell as adding the WHEN and the WHERE.

Engineering / IT - Sometimes, depending on the company structure and project type, the engineering / IT departments may write their own QPP. This usually focuses on the design, build and install phases, with the emphasis on development and verification of design, test and operability as opposed to the validation teams focus, which should be orientated towards the procedural and regulatory.

The Principal Contractors - The system developers should provice a QPP that shows how they shall meet the requirements of the project based against their Quality Management System? and project plan, detailing their deliverables and timelines.


Section Summary

The aim of a quality plan should be to ensure the following occurs during the system Life Cycle Phases?; the project deliverables are in line with company Standard Operating Procedures and / or the Quality Management System? system is developed against clear requirements (e.g. User Requirements Specifications?) system is developed in line with any regulatory requirements (e.g. 21 CFR Part 11) system is developed using specified guidelines (e.g. GAMP5) before delivery the equipment and software meets specifications (generally through Factory Acceptance Testing) all equipment and software is properly installed (insallation verification and qualification) system is safe to operate (operatonal verification and qualification) documentation for operation and maintenance has been established and all system users and maintainers have been adequately trained system is fully operational in accordance with the functional requirements (based on the original user requirements and generally satisfied by performance qualification)


Suggested QPP Contents

  • Overview Quality Project Plan
  • Quality Approach - QPP
  • Roles and Responsibilities
  • Life Cycle Phases
  • Validation Approach
  • Verification Approach

This should give a brief description of the system and its use. It is usually preferable to cut & paste the overview fom the URS to maintain a consistent description. The overview can also include or be the scope. Some of the following are suggested to be covered;

Example 1. Process Control System Describe what process equipment the system will control (e.g. filter dryer, reactor, centrifuge), the area it is located in and the likely process (or processes if it is multi-functional) that will be ran in the plant.

Example 2. Master Data Management System Describe the data type (GMP, Business, HR), whether historical or archived data needs to be imported, the scale of the system (local or global) and the types of users and access requirements likely (e.g. HR, IT, Engineering).

Example 3. Building Environmental Management System Describe the size and type of building (e.g. manufacturing, storage, laboratory), number of rooms and their dimensions, the classification of spaces and whether the system is to monitor, control or monitor and control the spaces (some end users like to have separate control and monitoring systems but this is not efficient in terms of engineering or valdation effort if the GMP critical areas can be clearly defined using Functional Risk Assessment? of the User Requirements Specifications? and / or Criticality Assessments? of the devices).

Quality Approach

The quality approach should describe the general process for executing the Quality Project Plan. The following should be considered;

The Quality Project Plan can have a section to record the completion of each validation deliverable document. This can be in the form of an Appendix attached to the Quality Project Plan.

Document Description Document Reference Completion Date Validation Signature Validation Plan ABC-09-001-VP User Requirements Specification ABC-09-002-URS


The Quality Project Plan should have a section to record the execution of each phase of the project, reference the Life Cycle Phases?. This can be in the form of an Appendix attached to the Quality Project Plan.

PHASE Completion Date Validation Signature REQUIREMENTS DESIGN SYSTEM BUILD INSTALLATION OPERATION


Define the project review and approval policy. This can differ from project to project (depending on type and size) but generally a 10 day review period is enough. Do not make it too short or people will simply not get time to properly review the documents.

Define system implementation, methodologies and plans against the project roles / responsibilities and the requirements. This can include a document matrix with authors, reviewers and approvers being assigned. Ensure ONLY those absolutely necessary review / approve documents, e.g. Subject Matter Experts review / approve technical design documents - there is no need for QA or validation to spell check or format a document just to add their signature.

Specify what documentation should be assembled in a project documentation repository for the system, along with all the validation documentation outlined in the Validation Plan;

1. System Life Cycle deliverables 2. Audit Plans and Results 3. Design specifications, schedules and drawings 4. Test Plans and Results 5. System Qualification Documentation 6. Training Documentation

Define the project boundaries in terms of document deliverables and change management. Consider if the Performance Qualification? is in or out of the project scope in terms of the system deliverables - especially in relation to the system developer who may possibly be the system suppport and maintainer once the system has gone live (especially if it was an in-house development). Also critical is defining when project change control ends and site change management starts.