EQIPD for Core Facilities

Background

Recommendations outlined in this document has been developed by a task force of members and stakeholders of the EQIPD consortium, the largest private-public partnership completely dedicated to improving data quality in preclinical research.

These recommendations are intended to improve the robustness, reliability, traceability and integrity of the data obtained from the research activities supported by academic core facilities. They aim to:

• improve communication between core facilities and their users of the services and infrastructure provided by the core facilities,
• minimize bias and errors in the collection, reporting or representation of such information, and
• create reliable scientific and supporting evidence in resulting publications, presentations, reports, patents and other types of research output.

The experimental record and its thorough description is the ultimate source of information and documentation regarding the experiment. Therefore, the contents of the experimental record must be accurate and thorough enough to be fully traceable to permit the reproduction of the work conducted. The experimental record is the official data record for each experiment and the most important primary source of data. It is expected that the practices outlined in this document will be applied to experimental planning, record-keeping procedures and reporting, to the fullest extent possible.

Recognizing the diversity of environments and settings in which core facilities operate, the current recommendations can be used in two modes - “Training service” and “EQIPD service”.

It is expected that core facilities and their users discuss both types of services, any ambiguities or conflicts regarding the recommended practices, and ensure alignment and understanding prior to the start of the experiments.

Training Service

1. Core Facility provides information about research practices recommended by EQIPD (items listed below) to the users.
2. It is up to the Core Facility to decide how this information is shared with the users (e.g., made part of a training program, shared as a written summary in paper or electronic form).
3. Unless requested by the users or otherwise enabled by the locally applicable rules and regulations, Core Facility does not assume any further role in supporting or monitoring the implementation of recommended practices.

EQIPD Service

1. Core Facility implements those aspects of EQIPD recommendations that do not depend on the users and that enable support of EQIPD-compliant research.
2. Core facility provides the users with the information about research practices recommended by EQIPD and offers to support in conducting EQIPD-compliant research.
3. If the user accepts the offer (and, as necessary, provides required resources), Core Facility:
   1. together with the user (and supervisor/PI if necessary), identifies the best solution to implement specific recommendations. Shared responsibility over implementation means ""joint decision, knowledge and transparency"" and may still require certain recommendations fully implemented at the Core Facility while others - fully implemented on the user's side.
   2. assumes responsibility over spot checks (requires acceptance by the user if certain recommendations are implemented on the user's side).
   3. confirms to the user that the study was conducted as ""EQIPD compliant"" or not (e.g. to be stated in the report or in a publication)"
4. If the user does not accept the offer, no changes in the routine practice and the studies remain to be not compliant with EQIPD recommendations.

Proposed statements

Training

• Users must be trained by CF members in order to be eligble to use CF
• Users should seek support from CF to design experiments in due time and with with optimal rigor.
  • Users should seek contact with the core facility ahead of time to ensure proper
  • Core facilities should play an educational role in proper planning of projects.
  • CF member together with the PI and the user should perform risk assessment
  • the users should be instructed to record any erros and report them to CFH; the CFH should debrief it; the debrief record should be circulated to all other users in order to minimize the chances for recurrance
  • Users must take responsibility for the appropiate use of reagents, research subjects and equipment they bring into the CF
  • It is up to CF to define which form training should take (including frequency and documentation)

Experimental Record

• Unique study identifiers must be used and defined by the future owner of the raw data for each experiment. Unless this is the CF, the owner of the raw data should communicate the unique study ID to the CF.
  • Best practices should be communicated by the CF during training or by providing a reference to EQIPD Toolbox (e.g. date_User inititals_experiment).
  • CF and PI may generate separate study IDs but there must be a way established to communicate, to connect separate IDs and to enable traceability.
  • For EQIPD, it should be clear who is in charge of generating and storing the Unique Study Identifiers.
  • For complex studies that include more than one experiment, several experiments are typically part of one experimental record under one study ID.
  • Unless known to CF, PI must communicate ethical approval to CF
  • File naming: in order that each data is unique and retrievable we suggest that you adhere to the following file naming convention: [date YYMMDD]-[the first letter of your first name together with your last name]-[free text]. If your surname is long you may use only the first 6 letters of it. e.g. 201108-cpitzer-catwalk with mice zQ98
• Each experimental record should include, directly or by reference, the names of all scientists involved, objectives, ethical approval/number, procedures, methods, materials, equipment, dates, and any other details considered necessary for reproducibility and reconstruction.
  • CF can elaborate a form (excel sheet for instance) listing all the items that are required in an experimental record, and ask users to fill in this form. This could help the user to keep tracking of his/her own detailed experimental record and is likely to increase the traceability of his/her data.
• All raw and any processed data must be retrievable and traceable, directly or by reference. No raw data should be erased.
• An experimental record must describe any significant changes and deviations from the original study protocol.
  • User must report/document if study execution is not in accordance with study protocol and deviations such as changes to study hypothesis, design or analysis must be documented (including the rationale for the changes).
  • Examples of significant changes: Changes in the doses, experimental conditions and groups, sample size, methods of analysis, etc.
  • Any change or deviation from a protocol approved by animal welfare authority would be significant and requires documentation in the experimental record.
  • If uncertain about what constitutes a significant change or deviation, the user should consult with the core facility.
• An experimental record must provide an explanation and justification for exclusion of any data points from analysis.
  • Critical incidents (any unexpected or unplanned events) and errors must be recorded and made part of the experimental record.

Rigor in Study Design

• For every study, there should be a study protocol prepared prior to the study being conducted.
  • Please see a definition of the study protocol above.
  • Study protocols involving more than one experiment should include a dedicated section explaining the sequence and relationships between different experimental operations or procedures.
• The study protocol must include:
  • Title
  • Study hypothesis
  • Ethical approval number and the name of approving body (for research involving animals)
  • Statement / information about controls (with choice justification if necessary)
  • Description of sample size calculation
  • Inclusion / exclusion criteria
  • Description of animal resources, reagents and materials (as applicable)
  • Study design overview for complex studies
  • Detailed description of experimental procedure(s) (or references to standalone descriptions if available)
• The protocol should include:
  • Statement whether study is exploratory or knowledge-claiming
  • Statement about choice of experimental methods
  • Detailed description of measures against risk of bias (randomization, blinding) (or references to standalone descriptions if available)
  • Description of raw data analysis
  • use versioning (or have a section for amendments)
• It is advisable to:
  • Include references to relevant literature
  • Conduct risk assessment
  • Preregister the study protocol

Analysis of Experimental Data

• Experimental / data analysis record and study report (e.g. publication) should include sufficient detail to reconstruct any analysis performed and record all process steps and calculations used.
  • It is very important to define responsbility
  • CF should be in the position/have the possibility to check this or run occasional audits

Data Storage and Traceability

• Experimental records should be kept in an audit-trailed, version-controlled, safe storage environment such as an appropriate bound-paper laboratory notebook with permanent ink or an electronic laboratory notebook (ELN).
• Raw (primary) data must be stored in an un-editable read-only form as soon as it is generated and must be backed-up
  • the raw data should be backed-up
  • reliability of IT resources should be ensured
  • the responsibility for saving and archiving the raw data must be clarified
• Processed (secondary) data must be clearly labeled as such and should contain a reference to raw data

Review and Reporting

• Reported research outcomes should be complete, accurate and findable
  • the location of the data must be identifiable for all data records, e.g. reference with the permanent identifier.
  • Reporting must include for each analysis the exact number of biological units for each condition
• Experimental records should be reviewed by a member of the CF for completeness and accuracy and it is advised to document this review
  • Users should give CF staff the possibility to review data for analysis and reporting
• Report should always provide summaries of all related data, processes, and conclusions, and include justification for excluding any relevant experimental records or individual data points from the summary analyses.
• Any external presentation/publication whether oral or in writing should give credit to the CF where the work was performed.
  • Identify all contributing researchers and reference unique identifiers for the experimental records
  • encourage the use of an unique identifier for reseachers (ORCID)
  • Unique IDs for facilities
• Any external presentation/publication whether oral or in writing should include a statement of conflict of interest.

Resources

Documents for download:

• NEED for CF here
• Guidance for CF users created by EQIPD working group