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In our last blog on Master protocols, we discussed the definition of master protocol, the types and advantages of using Master Protocol in clinical trials. In today’s article, we will like to present before you the parameters that are kept in consideration while designing a master protocol for oncology drugs and biologics. During the preparation of master protocols, different parameters are kept in consideration like:

  • Specific Design Considerations
  • Biomarker Development Considerations
  • Statistical Considerations
  • Safety Considerations
  • Regulatory Considerations


  1. Use of a single common control arm

FDA recommends the use of a single control arm with the current System Organ Class (SOC) while developing a master protocol where multiple drugs are assessed in a single disease.SOC for the target population can be changed during the conduct of the trial if there is a new drug approval or scientific evidence that makes it unethical to randomize patients based on the previous SOC. During such a situation, FDA recommends the sponsor to suspend patient enrollment until the protocol, the SAP, and the protocol informed consent document are modified to include the new SOC as control.

  1. Novel combination of two or more investigational drug

While writing a master protocol, where two or more investigational drugs are involved as a combinational product, the sponsor should summarize the following.

  • Safety of the combinational product
  • Pharmacology of the combinational product
  • Preliminary efficacy data for each investigational drug
  • Rationale for the use of the drugs as a combination product
  • Evidence of any synergistic effect (if any) of the two or more investigational drugs when given in combination.

The FDA strongly recommends that the sponsor ensure that the Recommended Phase II Dose (RP2D) for each drug having antitumor activity should be identified in all cases.

  1. Studies with drugs targeting multiple Biomarkers

Early discussion of biomarker research strategies is highly encouraged by the FDA when the sponsor plans to use one or more biomarkers to guide patient preference for trials. A defined plan for the allocation of eligible patients should be present. Patient selection studies must be analytically checked with well-defined parameters for master protocols involving drugs that target multiple biomarkers.

  1. Adding and stopping treatment arms

Before beginning the trial, the sponsor should make sure that the master protocol and its corresponding SAP identify conditions that would contribute to adaptations, such as introducing a new experimental arm or arms to the study, re-estimating the sample size based on the interim analysis results, or discontinuing the experimental arm on the rules of futility.

  1. Independent Data Monitoring Committee (IDMC)

The master protocol should provide the details of the IDMC that is involved in monitoring the efficacy results and the details of Independent Safety Assessment Committee (ISAC) that is involved in monitoring the safety results. However, the IDMC can perform both the functions of safety and efficacy. For marketing an oncology drug, if the basis of marketing application involves one or more sub studies, FDA recommends the inclusion of independent radiologic review committee to perform blinded tumor-based assessments.


            Master protocols assessing biomarker-defined populations should explain the rationale behind the use of that particular biomarker.The sponsor should employ in vitro diagnostic (IVD) tests that are analytically validated, establish procedures for sample acquisition, handling, and the testing and analysis plans as early as possible. The sponsor may need to submit the IVD’s analytical validation data for FDA(CDRH or CBER) to determine whether the clinical results will be interpretable.


If a sponsor introduces randomization into the design of an umbrella trial, the FDA advises that a standard control arm to be used where possible.Bayesian statistical method or other methods for dropping an arm, modifying sample size, or implementing other adaptive strategies can be used in preparation of master protocols. The SAP should include details on implementation of Bayesian or other methods as described in the FDA guidance for industry Adaptive Design Clinical Trials for Drugs and Biologics and the guidance on Enrichment Strategies for Clinical Trials to Support Approval of Human Drugs and Biological Products.Statistical considerations for master protocols can be strategized in four different ways:

  1. Nonrandomized, Activity-Estimating Design
  2. Randomized Designs
  3. Master Protocols Employing Adaptive/Bayesian Design
  4. Master Protocols With Biomarker-Defined Subgroups


The sponsor should implement a structured team of ISAC or an IDMC to assess the safety as well as the efficacy of all master protocols.The constitution of this committee and the definition of its responsibilities should be well defined in the IND. A sponsor should not begin a clinical trial until the master protocol has been reviewed and approved by an IRB or IEC. The FDA encourages the use of a central IRB to promote the IRB analysis of master protocols. The sponsor is required to perform a safety review of master protocols more regularly than on an annual basis and supply the investigator with the details.If the master protocol contains proposals to include pediatric patients in the study, the FDA advises that the IRB include a pediatric oncology expert in its team who has expertise with the regulatory criteria for the enrollment of pediatric patients in clinical investigations, including parental approval and consent. The informed consent document should be submitted to the IRB for review.


Each master protocol should be submitted as a new IND to the FDA. This is done to avoid miscommunication owing to the sophistication of master protocols that may hamper patient safety.If the sponsor is conducting a clinical trial on more than one indication for oncology drugs or biologics, the IND should then be forwarded to the Office of Hematology and Oncology Products at CDER or CBER for approval.


Master Protocols: Efficient Clinical Trial Design Strategies to Expedite Development of Oncology Drugs and Biologics, Guidance for Industry, Draft Guidance.U.S. Department of Health and Human Services, Food and Drug Administration, September 2018.

With many new therapeutics approved annually, the demand for biologics has seen exponential growth in the pharmaceutical market. In the bioanalytical community, the study of large molecules is now a hot topic of discussion.

The snowballing importance of peptides and proteins as therapeutic agents, combined with the colossal opportunities offered by new MS-based technology, has unlocked a new world for bioanalytical scientists.

Ligand-binding assays (LBAs) such as enzyme-linked immunosorbent assays (ELISA) or UV identification of individual peptides using high-performance liquid chromatography (HPLC) are the standard methods for the quantification of biologic drugs.

However, these methods are typically expensive, time-consuming to develop, and have limited selectivity and antibody cross-reactivity.

This results in a lack of interference specificity and high background levels that are not appropriate for fulfilling the specifications of the biopharmaceutical industry to identify different proteins and peptides with increasing sensitivity and reproducibility.

Liquid chromatography combined with tandem mass spectrometry (LC-MS-MS) has been widely used for small molecule bioanalysis in pharmaceutical laboratories since the 1980s.

As like smaller molecules, LC-MS-MS also carry advantages for biologics:

  • It is not susceptible to cross-reactivity of the antibody because LC-MS-MS involves direct assessment of the analyte’s chemical properties.
  • It provides excellent selectivity, being able to discern and quantify extremely homologous isoforms with precision and accuracy over a large linear dynamic range, even at low levels.
  • Due to its high analytical sensitivity and selectivity, in addition to its high-throughput capability, LC-MS/MS has been considered the primary technique to measure the concentrations of first-generation and second-generation antipsychotics in schizophrenia patients.

Mass spectroscopy has gained increased interest for peptide and protein analysis over LBA because:

  • LBA detects molecules based on binding affinity and 3D conformational structure, but they may not be able to distinguish between a protein and its metabolites.
  • In contrast with LBA, MS-based approaches have the potential and would be able to produce more precise data on unchanged peptide/protein levels in situations where metabolism hampers reliable LBA data.
  • MS techniques usually offer absolute concentrations of medications. This can depend on the form of an assay for LBA methods, and they may provide either absolute or free concentration of drugs.

However, LC-MS-MS-based bioanalysis for large molecule drugs poses a range of new obstacles, like difficulties in sample processing and extraction measures for the quantification of large molecules.

The reasons include the following:

  • The background peptides and proteins in the biological matrices compete with the biotherapeutic molecule of interest, creating interference problems and impacting accuracy.
  • The lack of significant evidence during quantification arises for being unable to catch free drugs that may circulate in serum.

Recently, many LC-MS-MS technological advancements have been made that can help solve all of these concerns.

In particular, the increase of ionization efficiency and ion transmission in recent triple quadrupole instruments has greatly enhanced sensitivity, allowing biologics to be detected at picogram or sub-femtogram levels.

Advances in technologies inside the LC-MS-MS include improved ion collision focusing, which brings more ions to the detector, as well as upgrades to the dynamic range of the detector to increase bioanalysis sensitivity and efficiency.

Recently, there has been a growing interest in integrating LBA immunoaffinity enrichment with LC-MS-MS quantification to integrate LBAs with the sensitivity and selectivity of LC-MS-MS technologies with greater precision and wider immune capture capabilities.

Automated Column-switching LC–MS/MS, Microextraction packed sorbent (MEPS)/LC-MS/MS, and Disposable Pipette extraction (DPX)/LC-MS/MS are some of the recent techniques that have been used to quantify large molecules.

Two major methods are widely used when using LC-MS/MS based technologies for the bioanalysis of large molecules:

1. Intact analyte LC–MS(/MS) approach

This approach is predominantly used for peptides, small proteins, and oligonucleotides with a molecular weight typically below 4–8 kDa.

2. LC–MS/MS approach using a digestion step

This approach is more complex and mainly used for proteins or larger peptides. This approach involves an (enzymatic) digestion step in addition to the intact analyte approach, where the protein/peptide is digested into smaller peptides.

Today, it is most common to use traditional LC-MS/MS triple quadrupole instruments for quantification for both the intact and the digested analyte approaches.

According to the existing standards, 4-6-15 (four out of six QC samples should be within 15% of the nominal value) is used as an approval criterion for large molecular LC-MS/MS assays. 4-6-20 approval requirements are proposed for larger intact analytes, in particular, if a hybrid LC-MS/MS approach is used.

A labeled peptide for peptide analysis or either a labeled intact protein or a labeled signature peptide can be used as an Internal Standard (IS) to establish a successful LC-MS/MS method.

Several guideline documents have been issued by the ICH and FDA to help standardize large molecule bioanalysis studies. These recommendations can be found on the website of the appropriate regulatory agency.

While LC-MS-MS technologies have progressed to be more appropriate for biological bioanalysis, for non-experts who need to create and measure new biologics, the variety of mass spectrometry technologies and techniques, sample preparation methods, and reagents could be overwhelming.

The new advances in instrumentation and software will bring substantial changes in the consistency and efficiency of bioanalysis tests, providing more accurate and compliant results with significant patient safety consequences.


  1. Suma Ramagiri, Trends in Bioanalysis Using LC–MS–MS. The Column, The Column-12-07-2015, Volume 11, Issue 22.
  2. Magnus Knutsson, Ronald Schmidt & Philip Timmerman, LC–MS/MS of large molecules in a regulated bioanalytical environment – which acceptance criteria to apply? Future Science, BIOANALYSIS VOL. 5, NO. 18,

Will Brexit Have Any Impact on CROs?


The United Kingdom comprises of England, Scotland, Wales, and Northern Ireland. It is an island nation in northwestern Europe. The exit of the United Kingdom from the European Union to become a ‘third country’ on February 1, 2020, is termed as Brexit.

The withdrawal agreement that provided a transition period of one year came to an end on December 31, 2020. Thus, the Medicines and Healthcare Products Regulatory Agency (MHRA) has been the UK’s independent authority for medicines and medical devices since January 1, 2021.

The Brexit will have both direct and indirect effects on the future of UK and EU clinical trials. The impact of Brexit on pharmaceutical companies will be seen at the levels of regulatory alignment with respect to the forthcoming implementation of the EU Clinical Trial Regulation (EU CTR).

As the best universities for research in the study of clinical pre-clinical, and medicine are present in the UK with strong regulatory and IP safety structures, the United Kingdom has become globally a major centre for the pharmaceutical industry.

In addition, most generic pharmaceutical companies are registered with a UK address. The departure from the EU would thus lead to hectic structural shifts, with a huge amount of time and investment on both sides.

Impact of Brexit on Outsourcing of Clinical Trial

Till now, many pharmaceutical companies based out of Europe were outsourcing their projects to contract research organizations (CROs) and contract manufacturing organizations (CMOs) based in the UK.

Post-Brexit, these scenarios may change. As of now, the European Commission has given its decision that the UK authorities will have partial access to Article 57 and will also have partial access to the EudraVigilance database.

Because of Brexit, CROs and CMOs located in the United Kingdom are no longer members of the EU, and this will have a dramatic impact on the European portion of the clinical trials for the delivery of investigational medicinal products (IMPs).

The effect of clinical trials on the supply chain post-Brexit will totally disrupt the new drug development process due to major negative financial and economic effects. Brexit can influence the clinical trial and drug discovery scenario that may involve access to drugs and Investigational Medicinal Products (IMPs), results, financing, and the workforce of clinical trials.

For BE studies carried out in the EU, the reference product can be made to a RefMP (UK Reference product) that has been granted in the Union in accordance with Articles 8(3), 10a, 10b, or 10c of Directive 2001/83/EC.

It is important to understand for the sponsor and the CRO that bioequivalence studies conducted with a medicinal product sourced in the UK can be used by EMA if the new MA using those BE studies have been granted before January 31, 2020.


United Kingdom is the 2nd destination of Indian Pharmaceutical exports after the USA. Some CROs have an internal Brexit Task Force comprised of talented individuals who very well know their roles and responsibilities.

CROs are preparing themselves to engage and capitalize on the new regulatory process in the UK and EU so as to avoid costly delays and disruptions of clinical trials. However, many questions still remain unanswered.

One of the biggest issues refers to complaints regarding the shipping of materials from the UK to the EU for clinical trials. Will the volunteers involved be at any risk? Or will international boundaries lead to delays in clinical trials and difficulty in site management? Or will there be any imposition of tariffs that could lead to disinterest among pharmaceutical sponsors in the UK in carrying out clinical research?

Thus, it will be interesting to see what is in store for the CROs post-BREXIT. However, because the UK and the EU account for less than 15-18 percent of total Indian pharmaceutical revenues, BREXIT is expected to have little impact on Indian pharmaceutical firms.


  1. The Landscape for CROs post-Brexit: An Update. Accessed at
  1. Brexit Solutions, Clinigen Clinical Supplies, and Management. Accessed at
  1. Questions and answers to Stakeholders on the implementation of the Protocol on Ireland/Northern Ireland, 11 December 2020. European Medicine Agency (EMA/520875/2020)
  2. Future of clinical trials after Brexit. Cancer Research UK, School of International Futures (SOIF).