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Quality of science is often improved when study objectives and methods are clearly thought through and described. A written protocol facilitates high quality science and is an invaluable tool to investigators as they develop and conduct studies.

Regardless of the scientific discipline in which the study is undertaken, the same scientific method is used. Further, while the scientific content will differ across studies, the general elements of the study protocol will be similar.

The Excellence in Science committee has developed a general protocol checklist and companion guide to assist scientists in preparing protocols. The checklist is intended as an aid in suggesting a format for writing protocols and in identifying issues that scientists should consider as they design the study.

With many scientific disciplines represented by CDC scientists, the checklist was developed to have utility in conducting laboratory and basic science studies, epidemiological studies, and behavioral and social science studies employing a variety of study designs. In using the checklist, investigators should select the items that apply to their types of studies. It is unlikely that any protocol would include every item on the checklist.

A number of studies are conducted at CDC that are not classified as research or do not involve humans as participants. To make the checklist applicable to the widest range of studies, the general protocol checklist does not contain requisite protocol items for review by an institutional review board. A separate addendum checklist for Protection of Human Research Participants is available.


This checklist is intended as an aid in suggesting a format for writing protocols and in identifying issues that scientists should consider as they design a study or surveillance system. When using the checklist, investigators should select the items that apply to their specific project. It is not expected that every item on the checklist is applicable to each protocol for a study or surveillance system.

Protocol summary
Investigators/collaborators/funding sources

Literature review/current state of knowledge about project topic
Justification for study
Intended/potential use of study findings
Study design/locations
Hypotheses or questions
General approach

How study design or surveillance system addresses hypotheses and meets objectives
Audience and stakeholder participation
Cost benefit/prevention effectiveness
Study time line
Expedited protocol review request


Description and source of study population and catchment area
Case definitions
Participant inclusion criteria
Participant exclusion criteria
Justification of exclusion of any sub-segment of the population
Estimated number of participants
Sampling, including sample size and statistical power

Study instruments, including questionnaires, laboratory instruments and analytic tests
FDA Investigative New Devices (IND) information
Intervention or treatment
Outcomes and minimum meaningful differences
Training for all study personnel

Data analysis plan, including statistical methodology and planned tables and figures Data collection
Information management and analysis software
Data entry, editing and management, including handling data collection forms,
different versions of data and data storage and disposition
Quality control/assurance
Handling results in the absence of a reference test
Measurement/estimation and adjustment for cross reactivity
Verifying independence of tests used to confirm results of new test being studied
Bias in data collection, measurement and analysis
Intermediate reviews and analyses
Limitations of study

Response to new or unexpected findings and to changes in the study environment
Identifying, managing and reporting adverse events
Emergency care


Notifying participants of their individual results
Notifying participants of study findings
Anticipated products or inventions resulting from the study and their use
Disseminating results to public


Data collection forms
Proposed tables and figures
Other relevant documents



Title: Summarize the main idea under investigation. The title should be able to stand alone as an explanation of the study.

Protocol summary: Give a concise overview of the project. Describe the purpose of the study, including problem to be investigated and hypothesis(es) to be tested, the population, and the methods that will be used. Avoid the use of acronyms. Include the expected benefit of the study.

Investigators/collaborators/funding sources: Include the names and degrees of all investigators and their roles in the project. Note any conflict of interest for each investigator and acknowledge all funding sources.


Literature review/current state of knowledge about project topic: Discuss relevant information about the subject of the project based on a review of the literature. In the Reference section, attach a bibliography of the sources used.

Justification for study: Explain the public health and scientific importance of the study. In the context of previous studies, describe the contribution this study will make.

Intended/potential use of study findings: Define the primary target audiences and discuss the expected applicability of study findings.

Study design/locations: Describe the study design and the locations where the study will be conducted.

Objectives: Clearly and concisely list the objectives that the project will address.

Hypotheses or questions: List the clear and focused question(s) that the study will answer. State the type of hypothesis(es) that will be explored or tested.

General approach: Describe whether the approach used will be descriptive, exploratory (hypothesis-generating), confirmatory (hypothesis testing), or developmental (focused on corrective action).

How study design or surveillance system addresses hypotheses and meets objectives: Explain the appropriateness of the study design to the project and to the questions and objectives previously outlined. Distinguish between procedures that are experimental and those that involve routine care. Identify specific design attributes that characterize the study design (e.g., cross- sectional survey, case/control, cohort, focus group, chart review, etc.) or surveillance system
(e.g., description of the system as active or passive, defining reported cases as individual versus aggregate and as laboratory confirmed or not).

Audience and stakeholder participation: Define the primary audiences for the project. Assess the major stakeholders and describe ways they can (and cannot) participate in the study. Explain the process by which those affected by the study can express their views, clarify their needs, and contribute to the project.

Cost benefit/prevention effectiveness: Describe how these measures will be addressed.

Study time line: Provide a calendar with estimated dates for implementing and completing key activities.

Expedited protocol review: If appropriate, describe the need for an expedited review of the protocol (e.g., because it is for an ongoing outbreak or emergency disaster).


Description and source of study population and catchment area: Demographically and in terms of the specific public health conditions to be studied, define the population from which the participants, sample or surveillance subjects will be drawn and to what population inferences will be made.

Case definitions: Provide descriptions of illness, condition or health event which defines a study participant as having that condition.

Participant inclusion criteria: Describe conditions or characteristics applicable to the identification and selection of participants in the study and the conditions necessary for eligible persons to be included.

Participant exclusion criteria: Describe characteristics that would disqualify otherwise eligible participants from the project.

Justification of exclusion of any sub-segment of the population: If a sub-population as defined by gender, race/ethnicity, or age is excluded, provide reasons. In accordance with CDC's policy for inclusion of women and minorities in research, state how these populations are included in the sponsoring CIO's overall program of research if excluded in this particular study.

Estimated number of participants: State the estimated number of participants for the study.
For a project establishing or using data from a surveillance system, this may include the expected number of reported cases per reporting period for epidemic and non-epidemic periods.

Sampling, including sample size and statistical power: Describe the sample (e.g., the sample will be one of convenience, a population-based representation or systematically chosen for some other purpose). State the sampling units and units of analysis. Estimate required sample sizes to answer questions and test statistical hypotheses (based on available information from pilot studies or previous reports). Include statistical power estimates. Explain the conditions under which sampling estimates would be revised. If group-level or aggregate information will be
collected (e.g., from focus groups), explain how the groups will be comprised, or what procedures will be followed to create appropriate groups.

Enrollment: Describe the manner in which potential participants will be contacted, screened, and registered in the study. Describe procedures for tracking the number of persons who withdraw from the study. Explain the procedures for assigning participants to different groups.


Variables: List and briefly describe the categories, topics, or domains of information to be explored and variables to be collected. Address consistency of definition of variables for data collected from multiple sources. Traditionally, for outbreak investigations, “time”, “place” and “person” would be collected to construct the epidemiologic curve. Explain how the variables will be utilized and the process by which variables will be defined.

Study instruments, including questionnaires, laboratory instruments, and analytic tests: Describe strategies to elicit information, including specific techniques and study and laboratory instruments, and explain how they will be used. Describe the attributes of those strategies/ instruments as demonstrated in other studies, including appropriateness, validity and reliability within the particular study populations, sensitivity and specificity of instruments, and how well they yield reproducible results.

FDA Investigative New Device (IND) information: If the study involves the use of an investigational new drug or investigation new device, provide IND number.

Intervention or treatment: Describe the types of interventions or treatments that will be tested in detail, including dosing, schedules of administration, etc.

Outcomes and minimum meaningful differences: List the possible results of exposure or intervention of interest in the study (i.e., the outcomes) and what clinical or epidemiologic differences in measurement of the outcomes are important to detect.

Training for all study personnel: Describe training, such as interviewer techniques, data collection and handling methods or informed consent, provided to study personnel.


Data analysis plan, including statistical methodology and planned tables and figures: Describe the sampling methods, information collection procedures, methods to maximize response rates, test procedures and relevant statistical quantities (e.g., variance, confidence intervals and power based on data from the study) in sufficient detail that the methods are reproducible. This includes calculation of relevant quantitative measures for tests and
instruments, such as sensitivity and specificity. In outbreak investigations, it is common to employ an iterative process in the analysis (consisting of developing and testing hypotheses and planning and evaluating interventions) to identify the source of the outbreak and control it. For projects establishing or utilizing data from a surveillance system, this could include how and how often the surveillance system will be evaluated. Describe what tables and figures are planned to present study results.

Data collection: Describe data collection procedures, processes and documentation. For data emanating from a surveillance system, this would include frequency of reports.

Information management and analysis software: Provide the names of data entry, management and analysis software packages and computer programming languages to be used for the project.

Data entry, editing and management, include handling of data collection forms, different versions of data, and data storage and disposition: Describe the overall procedures for management the data collected. Include in the description the process for entering and editing data. Describe how study materials, including questionnaires, statistical analyses, unique reagents, annotated notebooks, computer programs and other computerized information, whether used for publication or not, will be maintained to allow ready, future access for analysis and review. Document operating procedures for managing and accessing different versions of data sets. State who the data belong to and any rights to and limitations to access for any primary and secondary data analyses and publications. Document procedures regarding confidentiality of the data, including how confidentiality will be preserved during transmission, use and storage of the data and the names of persons or positions responsible for technical and administrative stewardship responsibilities. Document what the final disposition of records, data, computer files, and specimens will be, including location for any relevant information to be stored. Records must be stored in compliance with CIO or Agency guidelines.

Quality control/assurance: Describe the steps that will ensure no unintended consequences that could affect the quality of the data. Those steps might include methods to capture all reported data exactly as received, assuring logical consistency among all parts of a record and ensuring that manipulation or transformation of the data (e.g from audio tape to transcribed text) produces no unintended changes. For outbreak investigations, this would include verifying diagnosis and confirming the outbreak. Describe procedures for ongoing data quality monitoring to assure that

information of appropriate depth, breadth, and specificity is collected and remains consistent within and among staff over time, and acceptable levels of such attributes as validity, reliability, reproducibility, sensitivity and specificity are achieved.

Handling results in the absence of a reference test: Describe how tests will be used and results interpreted in the absence of a referent test and/or consensus of multiple test results. Include how sensitivity and specificity are affected.

Measurement/estimation and adjustment for cross reactivity: Describe how cross reactivity will be measured, its potential effects on test results and how it will be accounted/adjusted for in the analysis.

Verifying independence of tests used to confirm results of new test being studied: Describe process to validate results and use of new test, including verification of independence of tests or adjustments made for non-independence.

Bias in data collection, measurement and analysis: Describe the kinds of bias that may occur in collecting the data or in the measurement or analysis phases, and the steps that will be taken
to avoid, minimize and compensate for the bias. Include factors in the study population or in study personnel that could bias results, as well as the steps that will be taken to assure valid self- reporting or recording of observations. Include any randomization and blinding procedures that
will be used to eliminate/minimize bias by investigators, other study staff or participants (e.g., in selection of participants, allocation to treatment groups, providing/receiving treatment).

Intermediate reviews and analyses: Describe the ways that progress will be tracked and the study will be evaluated prior to assessing final results.

Limitations of study: Explain factors that might reduce the applicability of study results.


Response to new or unexpected findings and to changes in the study environment: Describe procedures for identifying and handling new or unexpected findings, and responding to changes in the study environment.

Identifying, managing, and reporting adverse events: Describe the types of adverse events that might be encountered and how study personnel will be trained to react. Describe methods that will be used to track adverse reactions and their potential impact on the study.

Emergency care: Explain the actions that would be taken in the event that an emergency develops during a study participant’s involvement in the research.


Notifying participants of their individual results: Describe the process used to notify

study participants of their results, including those of immediate importance. Include precipitating circumstances and whether or not counselors will be used.

Notifying participants of study findings: Explain whether the participant will be offered the option of receiving overall study findings and the form they will take.

Anticipated products or inventions resulting from the study and their use: List any products, including inventions, derived from the study, and how those will be used.

Disseminating results to public: Define effective communication channels and best formats for presenting information that will be used to disseminate project results to specific target


List bibliographic references used to create and delimit all aspects of the study.


Data collection forms: Include any forms or documents used to collect data or from which data are abstracted. Examples of these are questionnaires, medical records and other abstraction forms.

Tables and figures: Provide table shells and examples of figures for presentation of data and study results.

Other relevant documents: Include any other relevant supplementary materials.
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