The ITR is a cost recovery shared resource, therefore we charge all investigators for all services rendered. The ITR executes services professionally, with the appropriate controls performed at each experimental step. It is our goal to provide quality, cost effective, and timely service to both Vanderbilt and non-Vanderbilt investigators.
1. Project Initiation
The ITR encourages all investigators to discuss their project(s) with the ITR Director prior to completing a project application form. If the Principal Investigator decides to initiate work with the ITR, the Principal Investigator must complete a project application form found on the ITR website. Once this form is submitted, the ITR Director will work closely with the Principal Investigator to develop a comprehensive outline of experiments and budget to achieve the project goals. Projects that equal or exceed 20% ITR personnel effort will be subject to final approval by the ITR Advisory Board. This Advisory Board is made up of VICC leadership who ensures that ITR resources are allocated to high-impact, translational research. Upon final approval by the Principal Investigator, ITR Director, and/or ITR Advisory Board the ITR will initiate the project. If your project is not approved the ITR Director may work with you to locate a collaborator or to address the concerns of the ITR Advisory Board. Services are performed on a first-come first-serve basis.
2. Sample Submission
All samples sent to the ITR must be properly prepared, labeled, handled, stored, packaged, and shipped. All samples must be accompanied by an electronic manifest providing a detailed list of samples submitted for processing (including sample identifier that matches what is written on the tube(s), type of sample, DNA or RNA concentration, and % tumor DNA if applicable). This electronic manifest (click here to download file) should be submitted to the ITR Director.
The study Principal Investigator (PI) is responsible for removing identifying information from the tissue, or vessel housing the tissue, before releasing the samples to the ITR. It is the responsibility of the study Principal Investigator (PI) to assign each sample a unique identifier and label the sample accordingly. If approved by the Institutional Review Board, the study PI can possess a “key” that links the unique identifier with the clinical information associated with that patient. In the event that the ITR Director is a study co-investigator, the ITR Director may have access to this key and patient information. The ITR staff will not keep a record of the identifying information.
Individually identifiable health information is defined as any information collected from an individual (including demographics) that is created or received by a health care provider, health plan, employer, and/or health care clearinghouse that relates to the past, present or future physical or mental health or condition of an individual, or the provision of health care to an individual or the past, present or future payment for the provision of health care to an individual and identifies the individual and/or to which there is reasonable basis to believe that the information can be used to identify the individual (45 CFR 160.103).
These identifiers include:
- Any geographic subdivisions smaller than a State, including street address, city, county, precinct, zip code, and their equivalent geocodes, except for the initial three digits of a zip code
- All elements of dates (except year) for dates directly related to an individual (e.g., date of birth, admission)
- Telephone numbers
- Fax numbers
- Electronic mail addresses
- Social security numbers
- Medical record numbers
- Health plan beneficiary numbers
- Account numbers
- Certificate/license numbers
- Vehicle identifiers and serial numbers, including license plate numbers
- Device identifiers and serial numbers
- Web Universal Resource Locators (URLs)
- Internet Protocol (IP) address numbers
- Biometric identifiers, including finger and voiceprints
- Full-face photographic images and any comparable images
3. Data Use Restriction
Congress passed the Clinical Laboratory Improvement Amendments (CLIA) in 1988 establishing quality standards for clinical laboratories to ensure the accuracy, reliability and timeliness of patient test results regardless of where the test was performed (57 FR 7139, Sec. 493.1). This provision defines clinical laboratory as a facility for the “biological, microbiological, serological, chemical, immune-hematological, hematological, biophysical, cytological, pathological, or other examination of materials derived from the human body for the purpose of providing information for the diagnosis, prevention, or treatment of any disease or impairment of, or the assessment of the health of, human beings”. Under these amendments, if researchers wish to provide diagnostic results to subjects or use test results to alter care, they should have laboratory tests performed under the auspices of a clinical laboratory that has been certified in accord with CLIA. The ITR is NOT a CLIA-certified laboratory; therefore data generated in the ITR cannot be used for the diagnosis, prevention, or treatment of any disease or impairment of, or the assessment of the health of, human beings.
4. Custom Services
The ITR encourages diversity in experimentation to meet the needs of Vanderbilt investigators. The ITR performs experimentation tailored to the needs of investigators which are often outside the realm of the ITR Core Services listed in C.O.R.E.S. The ITR uses Vanderbilt Shared Resources and outside resources to complete studies. Please discuss your project(s) with the ITR Director prior to completing a project application form to determine your options. The ITR will use reasonable efforts to perform the experiments outlined by the ITR Director and the Principal Investigator. Expenses incurred by performing additional experiments, discussed by the ITR Director and Principal Investigator, will be the responsibility of the Principal Investigator. The Principal Investigator is not exempt from charges incurred due to failed experiments through no fault of the ITR.
5. SNaPshot Services
SNaPshot services can be performed on DNA extracted from frozen tissue/cell lines/blood and on DNA extracted from formalin-fixed paraffin embedded (FFPE) samples. All DNA must be of human origin. In some circumstances DNA extracted from FFPE tissue is not of high quality and can affect the performance of the SNaPshot assay. In these cases, the ITR will use reasonable efforts to perform the SNaPshot analysis. Expenses incurred by performing additional experiments, discussed by the ITR Director and Principal Investigator, will be the responsibility of the Principal Investigator. The ITR cannot guarantee that a complete set of data will be rendered from the SNaPshot assay using DNA derived from FFPE tissue. The Principal Investigator is not exempt from charges incurred due to failed experiments through no fault of the ITR.
All samples submitted are assessed for DNA concentration and quality to determine if the samples meet minimum criteria for SNaPshot analysis. Furthermore, all samples must have a minimum of 15% tumor DNA for accurate mutation analysis. If the ITR prepares the DNA sample, measures will be taken to assure this minimum tumor DNA content is achieved and expenses will be charged to the Principal Investigator. If the Principal Investigator submits DNA directly to the ITR, he/she should confirm that the sample contains > 15% tumor DNA.
6. PCR and Sequencing Services
PCR primer design, PCR, and sequencing services can be performed on gDNA or cDNA from frozen tissue/cell lines/blood and on DNA extracted from formalin-fixed paraffin embedded (FFPE) samples. DNA can be of human or murine origin. In some circumstances DNA extracted from FFPE tissue is not of high quality and can affect the performance of the PCR. In addition, DNA extracted from certain tissues is not of high quality and can contain contaminating factors that affect the performance of the PCR (e.g. melanin in melanoma). In these cases, the ITR will use reasonable efforts to perform the PCR. Expenses incurred by performing additional experiments, discussed by the ITR Director and Principal Investigator, will be the responsibility of the Principal Investigator. The ITR cannot guarantee data delivery from samples that are not prepared appropriately or that have these contaminating factors. The Principal Investigator is not exempt from charges incurred due to failed experiments through no fault of the ITR.
All samples submitted are assessed for DNA concentration and quality to determine if the samples meet minimum criteria for PCR. Furthermore, all samples must have a minimum of 20% tumor DNA for accurate mutation analysis. If the ITR prepares the DNA sample, measures will be taken to assure this minimum tumor DNA content is achieved and expenses will be charged to the Principal Investigator. If the Principal Investigator submits DNA directly to the ITR, he/she should confirm that the sample contains > 20% tumor DNA.
7. Data Delivery
Once the experiments outlined in the project application are completed, a data report will be delivered to the Principal Investigator by email in a timely fashion. This data report will contain the raw data, figures, interpretation of the data, and the materials and methods used (for manuscript preparation). Upon request, the ITR Director will meet with the Principal Investigator to discuss the data and their interpretation. In addition, when project milestones are reached, the ITR Director will provide the Principal Investigator with a progress report and any relevant data*. After the analysis is complete, all remaining samples will be returned to the Principal Investigator upon request.
*Relevant data are released to non-Vanderbilt investigators only when they pay for services (see Payment for Services below).
8. Data Retention
Definition of data: The ITR generates original, primary data and utilizes other Vanderbilt Shared Resources and non-Vanderbilt vendors to generate primary data. These primary data include, but are not limited to, nucleic acid quantification Excel and PDF files, agarose gel images, SNaPshot genotyping and triplex sizing assay electropherograms and accompanying Excel files, Sanger sequencing electropherograms, high-throughput (next-generation) sequencing BAM and FASTQ files, western blots and accompanying films, identity testing electropherograms and accompanying Excel files, real-time PCR files, cytokine quantitation files, and flow cytometry files. In addition, the ITR may generate valuable research derivatives from these data that include but are not limited to Excel, Word, PDF, PowerPoint, or Photoshop files that include data calculations, graphs, tables, summaries, and images/figures. Since the ITR may perform custom experimentation for individuals who do not have their own laboratories, the ITR also generates protocols and notebooks with detailed experimental procedures. These written protocols and notes are also herein considered data.
Minimal operational data retention period: The ITR will transfer all original, primary data and those data derivatives generated in the ITR to the project Principal Investigator (PI) when those experiments are complete and will retain those data for 6 months from project completion, unless a written agreement states otherwise. Custom experimentation protocols and notes will be transferred to the PI upon request. The ITR will retain experimental notebooks for at least 5 years and copies of those notes can be requested at any time during that time period; however any data retrieval performed 6 months after project completion will be charged to the PI at the current ITR hourly rate. The cost of ITR original, primary data and data derivative storage is included in the service rate.
Data generated by other Vanderbilt Shared Resources or non-Vanderbilt vendors will be transferred to the project Principal Investigator when those experiments are complete and will be retained in the ITR for 6 months from project completion, unless a written agreement states otherwise. An exception to this policy is high-throughput sequencing data which will be immediately transferred to the project Principal Investigator and will not be retained in the ITR. High-throughput sequencing data and derivatives are the sole responsibility of the project PI and are subject to the Data Retention and Management policies outlined by the Shared Resource(s) or non-Vanderbilt resources in which they were generated.
Data transfer: Data and its derivatives generated in the ITR will be transferred to the project PI upon project completion. Data will be transferred electronically by email, unless otherwise specified by the PI. If not electronically available, notebook data and experimental notes will be transferred to the PI as hard-copies. If the data set is too large to be transferred to the PI via email, the ITR will request an external hard drive from the PI to enable the transfer of data. The cost of the external hard drive will be the PI’s responsibility. The transfer of high-throughput sequencing data will be performed by mechanisms currently utilized by the Vanderbilt Shared Resource or non-Vanderbilt vendor that generated the data.
9. Sample Retention
Definition of research sample: The ITR may be given valuable biological material or derivatives of biological material by the PI, in the course of project initiation and execution. The ITR, other utilized Vanderbilt Shared Resources, or non-Vanderbilt vendors may also generate derivatives from the initial biological materials given. These biological materials include, but are not limited to human, mouse, and rat tissue (e.g. tumor, blood, plasma, serum, cell line). The derivatives of these biological materials include, but are not limited to nucleic acid, protein, and tissue/cell fractions (e.g. isolated peripheral blood mononuclear cells or plasma from whole blood), and stained or unstained formalin-fixed paraffin embedded tissue sections on slides or in tubes. These biological materials and their derivatives are herein considered research samples. Sample intermediates that include, but are not limited to, sample dilutions and samples used for taking measurements (e.g. nucleic acid or protein quantitation assays) are not considered research samples in this policy and will not be given to the PI. In addition, sample derivatives that were not specified by the PI will not be retained by the ITR.
Minimal operational research sample retention period: The ITR will transfer all remaining original research samples and those sample derivatives generated in the ITR to the PI when those experiments are complete. The PI will have up to 1 year from project completion to retrieve the samples before the samples are destroyed, unless a written agreement states otherwise. During this one year period, the PI will be notified at least three times that their samples need to be retrieved by the 1-year mark or they will be destroyed. If a written agreement allows for sample storage longer than 1 year, the cost associated with that storage (past 1 year) will be the responsibility of the PI. Return of the samples and their derivatives generated by another Vanderbilt Shared resource or non-Vanderbilt vendor will be subject to that Shared Resource or vendor policy. The ITR is not responsible for research samples or derivatives submitted to these non-ITR resources. Following Vanderbilt University policy, if the PI leaves the institution and fails to retrieve their research sample(s) prior to vacating their position, the PI’s supervisor will be contacted to inform him/her of the project and to pick-up the sample(s). In that case, the PI’s supervisor or designated investigator will have up to 1 year from ITR contact to retrieve the samples before the samples are destroyed, unless a written agreement states otherwise. If a written agreement allows for sample storage longer than 1 year, the cost associated with that storage (past 1 year) will be the responsibility of the PI’s supervisor or designated investigator/department. In the event orphan samples are formalin fixed paraffin embedded blocks (FFPE) and the specimens belong to the Vanderbilt University Pathology Department, those samples will be returned to Pathology. If the FFPE blocks belong to a non-VU pathology department and the ITR has the mailing address, the ITR will mail the blocks back to that department. The ITR reserves the right to utilize samples to be destroyed for internal validation and troubleshooting of new protocols.
Research sample return: It is the sole responsibility of the PI or the PI designee to retrieve research samples and their derivatives from the ITR, Shared Resource, or vendor upon project completion. If the samples and/or derivatives were processed by a non-ITR resource, but facilitated by the ITR, the ITR will attempt to retrieve the samples and return them to the PI, where possible. If the PI is a non-Vanderbilt University investigator, the PI will be responsible for the shipping charges and associated materials to return the samples.
10. Payment for Services
As a cooperative laboratory, the ITR relies on investigator-initiated projects and Principal Investigator associated funding for those projects. However, the facility and its personnel are wholly managed and operated by the VICC and the ITR Director. Although the ITR has some basic laboratory equipment, other needed equipment, supplies, and personnel effort related to your project must be funded by the investigator initiating the project(s). Personnel costs may be covered by a direct Core charge or by inclusion of the appropriate ITR personnel effort on a grant. The ITR will acquire the needed expertise, instrumentation, and utilize Vanderbilt University Shared Resources or outside resources to complete the experimental studies.
Billing of core services is performed through the Vanderbilt C.O.R.E.S. billing system. When a project is initiated, the ITR Director will provide the Principal Investigator a cost estimate based on the experiments outlined in the project application form. Costs exceeding those outlined in the project initiation form will be paid for by the Principal Investigator of the project. These costs may result from an increase in sample number or unexpected experimental results. Any excess costs will be discussed with the investigator prior to moving forward with the project.
Samples that fail to yield data due to circumstances beyond the control of the ITR are not the responsibility of the ITR. The ITR does not guarantee results. The Principal Investigator is not exempt from charges incurred due to failed experiments through no fault of the ITR.
Not all services rendered by the ITR are "Core" services. As a collaborative laboratory, we perform experiments based on the need(s) of the Principal Investigator. Depending on the scope of the project, supplies and special equipment may be purchased directly off of the Principal Investigator's center number provided in the project application form. A billing arrangement will be discussed with the Principal Investigator prior to project initiation.
Vanderbilt investigators must provide a valid center number to cover the quoted expenses before the project is initiated. In some cases, different center numbers may be utilized for personnel, supplies, or special equipment and must be specified on the project application. VICTR vouchers/funding can be applied to ITR services if the ITR was specified in the application. Scholarship vouchers cannot be applied to ITR services at this time.
Non-Vanderbilt investigators must provide a purchase order or payment must be received prior to the release of data. A check, money order, or credit card is an acceptable form of payment. If a purchase order is provided, an invoice will be sent along with a request for payment for services after the work is completed and the data are released. For projects that take over 1 month to complete, payments can be made in installments for an early release of partial data. Please contact the ITR Director about payment installments prior to project initiation.