Reporting recommendations for tumor marker prognostic studies (REMARK): explanation and elaboration

The REMARK (Reporting Recommendations for Tumor Marker Prognostic Studies) guideline includes a checklist which aims to improve the reporting of these types of studies. Here, we expand on the REMARK checklist to enhance its use and effectiveness through better understanding of the intent of each item and why the information is important to report. Each checklist item of the REMARK guideline is explained in detail and accompanied by published examples of good reporting. The paper provides a comprehensive overview to educate on good reporting and provide a valuable reference of issues to consider when designing, conducting, and analyzing tumor marker studies and prognostic studies in medicine in general.

section_content: Unprecedented advances in biomolecular technology in recent years have greatly increased the power and precision of analytical tools used in cancer research and accelerated the drive toward personalized medicine. Human specimens that serve as analytes for these new and developing technology platforms have emerged as a critical resource for basic and translational research in cancer as they are a direct source of molecular data from which targets for therapy, detection, and prevention are identified and molecular taxonomies of cancer are derived. The reliability of molecular data derived from these new analysis platforms is dependent on the quality and consistency of the biospecimens being analyzed. As a result of the increased requirement for biospecimen quality, standardization of biospecimen resources using state-of-the-science approaches has become a pressing need across the research enterprise. The lack of standardized, high-quality biospecimens is widely recognized as a significant roadblock to cancer research. 

Over the past several years, the National Cancer Institute (NCI) has undertaken an intensive due diligence process to understand the state of its funded biospecimen resources and the quality of biospecimens used in cancer research. This process began in 2002 with NCI surveys and community forums. In 2003, the National Biospecimen Network Blueprint and Case Studies of Existing Human Tissue Repositories were published, and an extensive examination of the current state of NCI's biospecimen resources was conducted the following year. 1,2 During 2004-2005, the NCI first established a trans-divisional Biorepository Coordinating Committee (BCC) and then created the Office of Biorepositories and Biospecimen Research (OBBR) to lead and coordinate a strategic plan to confront and resolve the issues in a stepwise fashion. The BCC was expanded to advise and assist in OBBR initiatives. The primary purpose of the BCC is to work with the OBBR to coordinate the NCI's biospecimen resources in a manner that optimizes the quality and accessibility of biospecimens for the broad cancer research community. In addition, the NCI held two major workshops that further informed the development of specific recommendations. The two workshops, organized by the OBBR and the BCC in the summer of 2005, brought together diverse representatives from the cancer research community as well as ethics, legal, and policy experts to discuss and propose approaches that could help unify, integrate, and improve biospecimen resource activities. The recommendations that resulted from the workshops identified future areas of research and unresolved issues and are summarized in the report Harmonizing Processes and Policies for NCI-Supported Biorepositories. 3 These efforts culminated in 2005 with the development of the First-Generation Guidelines for NCI-Supported Biorepositories, a first-iteration document published in the Federal Register on April 28, 2006 (71 FR 25184) and on the Web site of the NCI OBBR. The NCI requested public comments on the Guidelines both through the Federal Register posting and the OBBR Web site. The Guidelines were subsequently revised, based on public comment and input from content experts, and renamed the NCI Best Practices for Biospecimen Resources ("NCI Best Practices"). 

Through this due diligence process, the NCI has identified salient guiding principles that define state-ofthe-science biospecimen resource practices, promote biospecimen and data quality, and support adherence to ethical and legal requirements. The current NCI Best Practices do not comprise detailed laboratory procedures; rather they consist of principles by which such procedures should be developed by biospecimen resources. The recommendations contained within this document are intended to be adapted, as appropriate, based on the mission and scientific needs of individual biospecimen resources. While adoption of the NCI Best Practices is voluntary, the Institute believes that the principles outlined in this document support the goal of optimizing biospecimens for cancer research. 

In addition to developing principles of best practice for biospecimen resources, the NCI has taken a stepwise, multifaceted approach to addressing the needs of biospecimen resources across the cancer research community. First, through the cancer Biomedical Informatics Grid (caBIG™), an enterprise designed to create infrastructure that will facilitate the exchange of data and access to programs among cancer investigators, the NCI is developing informatics tools to support the collection, annotation, storage, and dissemination of high-quality biospecimens. 4 caBIG™ is working to provide guidance on uniform, nonredundant sample nomenclature for biospecimen annotation; comprehensive, technologydriven biospecimen tracking procedures; and informatics systems interoperability that will allow queries across multiple biospecimen resources or networks. These tools will be publicly available to all biospecimen resources, regardless of their source of support or scientific objectives. 

Second, the NCI is developing evaluation tools based on the NCI Best Practices that will allow biospecimen resources to assess and monitor the quality of their resource. The self-evaluation process also will facilitate the development of quality management systems that are essential for the improvement and maintenance of biospecimen quality. 

Third, recognizing the importance of moving toward evidence-based standards for the collection, processing, and storage of biospecimens, the NCI has launched the Biospecimen Research Network (BRN) to generate the biospecimen data needed for evidence-based methodologies. 5 The BRN comprises intramural, extramural, military, and commercial participants from both clinical centers and research laboratories. The BRN will conduct research to determine how the results of deoxyribonucleic acid, ribonucleic acid, and protein analyses are affected by individual preacquisition and postacquisition variables. Data generated by the BRN will be available to the scientific research community through a searchable, Web-based tool. Concordant with the BRN initiative, the NCI encourages the development of standard operating procedures (SOPs) based on objective scientific data. Biospecimen resources should develop their individual protocols for biospecimen processing based on the goal of preserving the quality of the analytes of interest to the greatest degree possible. 

The NCI Best Practices will continue to evolve as the field of biospecimen biology advances; novel scientific, technological, and clinical practices develop; and new ethical and legal policies and regulations emerge (e. g., National Institutes of Health and Department of Health and Human Services policies). Results from BRN initiatives and other similar research efforts will inform future versions of the NCI Best Practices as the community moves toward the development of evidence-based SOPs that are both specimen type specific and analysis platform specific. The NCI is committed to maintaining current and scientifically accurate best practices for biospecimen resources and will continue to solicit input from stakeholders in the cancer research community. collection may occur in field locations such as hospitals or research participants' homes (Eiseman and Haga 1999). 6 B. 1. 2. 1. All data relevant and necessary to research goals, including the collection and processing procedures used, are recorded by biospecimen resources. As appropriate for the study, the amount of time elapsed during collection and processing is recorded and tracked in the biospecimen resource informatics system for all types of biospecimens. 

• For solid tissue biospecimens, the time for collection is minimized and biospecimen temperature is reduced as soon as possible after collection. Biospecimen processing time is minimized if freezing is the stabilization endpoint. • Rapid processing may not be as critical for other types of biospecimens, such as blood, and optimal processing times may vary depending on the analysis method for which a biospecimen is used. 

B. 1. 2. 2. The processing method that preserves the greatest number of analytes is used, unless the aim of a particular study specifically requires alternative processing.
section_name: INTRODUCTION

section_content: Personnel involved in biospecimen resource management and use, including researchers, technicians, nurses, surgeons, pathologists, anesthesiologists, and assistants, are aware of the purpose and goals of the biospecimen resource. To ensure the collection of highquality biospecimens for research, personnel are well qualified and trained to adhere to applicable standard operating procedures (SOPs). A pathologist or his/her designee is involved in collecting and processing surgical and autopsy biospecimens. It is important that a pathologist determines which biospecimen, or portion thereof, is necessary for pathologic diagnosis and which is excess and can be given to the biospecimen resource for research purposes. This is crucial in ensuring that patient care is not compromised.
section_name: B.1.3. Biospecimen Resource Personnel

section_content: The following general best practices apply to all types of biospecimens, such as wet tissue, frozen tissue, paraffin-embedded tissue, glass slides, blood, serum, and urine. Individual types of biospecimens are handled according to SOPs specific to each biospecimen type and to the biomolecules to be analyzed in that biospecimen type (e. g., ribonucleic acid [RNA], deoxyribonucleic acid [DNA], protein, and lipid). In selecting biospecimen storage temperature, consideration is given to the biospecimen type, the anticipated length of storage, the biomolecules of interest, and whether study goals include preserving viable cells (Hayes et al. 2002, ISBER 2005, Holland et al. 2003). Paraffin blocks are stored at temperatures below 80 °F (27 °C) in an area with pest and humidity control. In the case of liquids, such as blood and urine, biospecimen components are separated before storage to preserve each constituent under its optimal condition. Whole blood (rather than fractional) cryopreservation is considered an efficient and cost-effective option for processing viable cells in large-scale studies (Hayes et al. 2002). When in doubt as to possible future uses, tissues are stored in the vapor phase of liquid nitrogen freezers to ensure long-term viability. Lower storage temperatures and cryoprotectant (such as dimethyl sulfoxide) are used to maintain viable cells for long periods of time (ISBER 2005). The difference in temperature between the bottom and top of a liquid nitrogen freezer is considered in planned analyses; the temperature at the top of a liquid nitrogen is consistently below -140 °C. 

B. 1. 4. 3. Storage vessels are stable under planned storage conditions (Caporaso and Vaught 2002, Grizzle 2004 ). Biospecimen containers are chosen with analytical goals in mind. Vial size and number are suitable for typical aliquots, anticipated investigator uses, and number of investigators. Volume and type of containers prevent sample loss and minimize the costs of collection and storage. Screw-cap cryovials are used for long-term, low-temperature storage; glass vials or vials with popup tops are unsuitable for long-term storage (Caporaso and Vaught 2002). Snap-frozen biospecimens are wrapped in aluminum foil or placed in commercial storage containers to minimize desiccation (Grizzle 2004 ). Labeling and printing systems are stable under the long-term storage conditions appropriate for the biospecimen. Face shields and appropriate gloves are worn for worker protection. 

B. 1. 4. 4. Each biospecimen storage container has a unique identifier or combination of identifiers that is firmly affixed to the container, clearly and legibly marked, and able to endure storage conditions. All other relevant information is tied to this identifier, bearing in mind research participant confidentiality, security, and informed consent provisions. Inventory systems relate the presence of each aliquot to its position in a specific freezer, refrigerator, or shelf. This applies primarily to biospecimen collections established after publication of this document. 

B. 1. 4. 5. Automated security systems continuously monitor the function of storage equipment. Backup equipment, such as an alternative power source, is automatically activated when necessary. Procedures are in place to respond to freezer failures, weather emergencies, and other emergency situations (Friede et al. 2003, Landi and Caporaso 1997, Caporaso and Vaught 2002, Eiseman et al. 2003). 

B. 1. 5. Shipping Samples B. 1. 5. 1. Retrieval. Samples are retrieved from storage according to biospecimen resource SOPs that safeguard sample quality. 

B. 1. 5. 2. Shipping conditions. When seeking to regulate sample temperature during shipping, the shipping time, distance, climate, season, method of transportation, and regulations as well as the type of samples and their intended use are considered (Landi and Caporaso 1997, ISBER 2005). To maintain proper temperature during shipping, appropriate insulation, gel packs, dry ice, or liquid nitrogen (dry shipper) is used. To maintain refrigerated temperatures (2 °C to 8 °C), gel packs conditioned at -15 °C or phase change material rated for refrigerated transport are used. To maintain frozen temperatures, gel packs conditioned at or below -20 °C are used. For frozen temperatures at -70 °C, dry ice pellets or sheets are used. Dry ice is considered a hazardous substance for shipping purposes. For maintaining temperatures at or below -150 °C, a liquid nitrogen dry shipper is used (ISBER 2005). Insulated packaging is used to protect biospecimens from extremely hot or cold ambient conditions. Whenever intending to maintain samples below ambient temperature, enough refrigerant is included to allow for a 24-hour delay in transport (ISBER 2005). 

Temperature-sensitive material is handled by a courier with resources to replenish the refrigerant in case of a shipping delay (ISBER 2005). 

Paraffin blocks and slides are shipped at room temperature in an insulated package via overnight carrier. The use of insulated packages is considered important to minimize the effect of temperature fluctuations and to protect the blocks from temperatures higher than 80 °F (27 °C). Flat biospecimens, such as dried blood samples on absorbent pads or cards, are enclosed in watertight plastic bags and shipped in a sturdy outer package or commercial envelope. Samples on glass or plastic slides are cushioned and shipped inside a sturdy (not flexible) outer package. Triple packaging is used for liquid samples. 

The number of biospecimens per package also affects whether the appropriate temperature can be maintained for all biospecimens in the shipment. A test shipment (e. g., frozen water samples) is sent before shipping extremely valuable samples to check the adequacy of coolants and any potential obstacles to a successful shipment. In addition, conditions throughout a critical shipment are monitored by enclosing a device that records temperature during transport. Samples are placed in sealed bags with a desiccant to control humidity. 

B. 1. 5. 3. Documentation. The biospecimen resource notifies a recipient before shipping to confirm that the recipient can accept the package and properly store the samples. A shipping log, either written or computerized, tracks shipments from and to the biospecimen resource (ISBER 2005). The following information is included: Shipment/invoice number, recipient (or source), date shipped (or received), courier name and package tracking number, sample description, number of samples shipped (or received), condition on arrival, study name and number (if available), key investigator's name, and signature of biospecimen recipient (ISBER 2005). 

Standardized paperwork accompanies shipments. Biospecimen resource personnel send a shipping manifest, a list of sample identification numbers, and descriptions of samples electronically to the biospecimen recipient and include a hard copy of the manifest inside the shipment. Identifying data are available for the use of shipping or customs agents as well. Some shipping agents require an itemized list of contents between the secondary and outer packaging of diagnostic biospecimens. 

Biospecimen resource personnel verify biospecimen labels and pathology reports against the packing list for consistency and correctness. 

A feedback questionnaire requesting feedback about the quality of samples received is enclosed in each shipment for QA/QC purposes (Eiseman et al. 2003). 

B. 1. 5. 4. Regulatory considerations. ISBER Best Practices and International Air Transport Association (IATA) regulations (ISBER 2005, IATA 2006 ) are consulted for information concerning international transport regulations and classifying samples for shipment. Variation in national and regional standards regarding biospecimen transport is considered when shipping biospecimens to or from an international location. 

Occupational Safety and Health Administration (OSHA) regulations on toxic and hazardous substances (29 CFR 1910 Subpart Z) are consulted to determine whether a substance requires a biohazard label. 

B. 1. 5. 5. Training. Biospecimen resource personnel are trained to ship samples appropriately (ISBER 2005).
section_name: B.1.4. Biospecimen Storage

section_content: Appropriate annotation of biospecimens is crucial to the overall usefulness of the biospecimen resource as a tool for scientific research (Eiseman et al. 2003). Biospecimen resources store biospecimens collected using multiple methodologies and procedures. Researchers rely on banked biospecimens for a wide variety of purposes, including target discovery and validation, research on prevention, early detection, genetic studies, and epidemiologic analyses. The data recorded by investigators and biospecimen resources depend on the types of biospecimens collected and the studies' objectives.
section_name: B.2. Collecting and Managing Clinical Data

section_content: Laboratories and biospecimen resources that handle biospecimens expose their employees to risks involving infectious agents and chemicals as well as the general dangers of a laboratory. A predictable yet small percentage of biospecimens will pose a risk to biospecimen resource personnel who process them. Consequently, all biospecimens should be treated as biohazards (Grizzle and Fredenburgh 2001). In addition to taking biosafety precautions, biospecimen resources should adhere to key principles of general laboratory safety. 

B. 4. 1. Biohazard Precautions B. 4. 1. 1 Laboratories and biospecimen resources assume that all human specimens are potentially infective and biohazardous (Grizzle and Fredenburgh 2001). OSHA regulations (29 CFR § 1910. 1030(f)) require that employers "make available the hepatitis B vaccine and vaccination series to all employees who have occupational exposure, and post-exposure evaluation and follow-up to all employees who have had an exposure incident. " Dried blood, tissue, and saliva are handled according to universal precautions and labeled according to OSHA requirements. Biospecimen resource work practices are based on universal precaution practices similar to those used in laboratories and clinical settings. Two basic safety precautions are followed in laboratories and biospecimen resources that handle biospecimens: (1) Wash hands frequently and (2) always wear face protection and gloves when handling biospecimens or working within or around freezers. Additional good general laboratory work practices are outlined by Grizzle and Fredenburgh (2001). 

B. 4. 1. 2 A biospecimen resource establishes clear policies regarding the inclusion or exclusion of high-risk biospecimens. For example, depending on the potential for exposure by splash or aerosol, human specimens of unknown infectivity are handled according to Biosafety Level-2 (BSL-2), as outlined in the Centers for Disease Control and Prevention (CDC)/National Institutes of Health (NIH) booklet "Biosafety in Microbiological and Biomedical Laboratories" (BMBL) (CDC and NIH 1999). According to BSL-2, when biospecimen containers are opened for processing, they are handled in a BSL-2 biological safety cabinet (hood). All biospecimen resources that handle human specimens operate under the OSHA bloodborne pathogens standard and develop an exposure control plan (29 CFR § 1910 (29 CFR §. 1030)). Additional precautions apply, as outlined in the BMBL. Some activities may require higher containment, and in other cases, less stringent practices may be acceptable. Therefore, biospecimen resource staff members are trained to perform risk assessments and determine appropriate levels of containment.
section_name: B.4. Biosafety

section_content: In addition to biosafety, biospecimen resources follow strict general safety regulations and procedures regarding chemical, electrical, fire, physical, and radiological safety (ISBER 2005; 29 CFR 1910).
section_name: B.4.3. General Laboratory Safety

section_content: Driven by the scale of data in genomics and proteomics, informatics systems have become critical to the research enterprise. Informatics systems that support biospecimen resources should be robust and reliable to sustain day-to-day operations. Informatics systems should be able to meet changing scientific needs. Interoperability of systems is key to exchanging data and biospecimens. 

An informatics system should support all aspects of biospecimen resource operations, including (but not limited to) research participant enrollment and consent; biospecimen collection, processing, storage, and dissemination; QA/QC; collection of research participant data; data security; validation documentation; and management reporting functions. In addition, the system should manage clinical annotations to the biospecimens. 

Biospecimen resource informatics systems are a key tool in providing accountability of biospecimens (e. g., location) and related data uses to research participants. Biospecimen resources should implement and operate their informatics systems with security mechanisms such that this demand is met. 

The NCI Center for Bioinformatics (NCICB) is developing caBIG™, a voluntary network or grid connecting individuals and institutions to enable the sharing of data and tools across the NCIsupported research continuum, especially clinical and translational research. 7 Biospecimen resources are encouraged to draw upon caBIG™ to implement the informatics recommendations in this section. For more information on NCI infrastructure to support these best practices and caBIG™, refer to Appendix 1. 

B. 5. 1. Functionality-General B. 5. 1. 1. At the biospecimen resource level, informatics systems are focused on inventory functions, tracking all phases of biospecimen acquisition, processing, handling, QA/QC, and distribution from the collection site (research participant) to utilization (researcher). Restocking of returned, unused samples from the researcher also is tracked. Tracking includes documenting multiple, preexisting, and/or external physical biospecimen identifiers, such as barcodes with nonidentifying information. 

B. 5. 1. 2. The informatics system has the capability of linking the labels on the physical biospecimen container (e. g., paper labels/barcodes) to other information in the system. 

B. 5. 1. 3. Informatics systems track clinical data associated with a biospecimen and link biospecimen data with external sources of clinical data, where applicable. 

B. 5. 1. 4. Tools used to extract structured information from free-text data such as surgical pathology reports are validated as to their accuracy in performing that task. 

Biospecimen resources routinely monitor the performance of such tools. 

B. 5. 1. 5. All biospecimen resource databases at an individual institution are in a secure site monitored by the institution. Plans are in place for data storage and retrieval in response to a wide variety of conditions that could affect the performance of an informatics system. Biospecimen resources eliminate unsecured, ad hoc databases and manage data through the central informatics system. Resources without the capabilities to provide such infrastructure seek external hosting arrangements for their informatics system. 

B. 5. 1. 6. Biospecimen resource informatics systems monitor and report on biospecimen quality in terms of the scientific best practices described elsewhere in this document. 

B. 5. 1. 7. Biospecimen resource informatics systems provide vital system statistics and audit logs of all access to protected health information (PHI) in the database. 

B. 5. 2. Functionality-Identification of Biospecimens B. 5. 2. 1. Each biospecimen is assigned a unique identifier or combination of identifiers, such as a number and/or barcode. This recommendation is most applicable to future biospecimen collections as implementation in existing collections would be laborious. In this context, the scope within which identifiers are unique applies to an individual system and the biospecimen resources it supports. 

B. 5. 2. 2. The informatics system is able to track a biospecimen from collection through processing, storage, and distribution as well as associated clinical and epidemiological data. In 2005, the NCI hosted a workshop to bring together diverse representatives from the cancer research community as well as ethics, legal, and policy experts to discuss and propose approaches that could help unify, integrate, and improve biospecimen resource activities. The recommendations that resulted from this workshop as well as additional NCI-sponsored meetings and work conducted between 2002 and 2005 formed the basis of the NCI Best Practices. The ethical, legal, and policy best practices in this document identify key regulations relevant to biospecimen resources and provide additional recommendations for biospecimen resources. These best practices are not an exhaustive list of issues and solutions; rather, they are principles to be carefully considered in conjunction with the mission of the biospecimen resource to determine the most appropriate operational policies. The regulations and standards discussed in this document are for research using biospecimens in the United States. Many countries have their own ethical and legal standards for human subjects research including, in some cases, specific provisions for the use of biospecimens. Investigators and biospecimen resources should be aware of foreign standards that may be applicable and address any differences between foreign and U. S. requirements prior to the initiation of a new collaboration or collection.
section_name: B.5. Biospecimen Resource Informatics: Data Management and Inventory Control and Tracking

section_content: Responsible custodianship requires careful planning and transparent policies to ensure the longterm physical integrity of the biospecimens while maintaining the privacy and confidentiality of research participants. C. 1. 3. Biospecimen resources establish and document transparent policies governing the retention of biospecimens, data, and records pertaining to informed consent and the identity of research participants. In addition, usage agreements, such as MTAs, specify the retention policy of the recipient investigator. 

• The retention of clinical biospecimens is governed by Federal and/or State laws related to the retention of medical records. • For research biospecimens, permanent storage generally is preferred, subject to sufficient resources and storage space and foreseeable research utility (i. e., QA/QC, dated datasets). • Biospecimen resources are reviewed periodically (e. g., at the time of funding renewal) to determine the utility of existing biospecimens, the need for new biospecimens, etc. • In the event that biospecimen resources close because of lack of funding or otherwise cannot maintain or use the biospecimens, the availability of the biospecimens for transfer, if permitted, is announced to the research community by means appropriate for reaching a wide audience. The transfer of such biospecimens is conducted in a manner consistent with human subjects regulations. 

C. 1. 4. One aspect of responsible custodianship is the appropriate management of conflicts of interest. Biospecimen resources adhere to regulations regarding conflict of interest at 42 CFR Part 50 Subpart F, as well as other applicable regulations. 

C. 1. 5. Biospecimen resources have transparent policies for maintaining the privacy and security of the biospecimens and associated clinical data, if applicable. Specifically, biospecimen resources that store coded samples and data have established policies regarding how the link or code that allows identification of research participants will be maintained.
section_name: C.1. Principles for Responsible Custodianship

section_content: Informed consent (pursuant to the human subjects regulations at 45 CFR Part 46 Subpart A) is designed to present potential human subjects with sufficient information-including anticipated procedures, risks, and benefits-to make an informed decision to participate in research studies. 

Obtaining informed consent for the collection and storage of biospecimens and for their use in future research is challenging since the specifics of the future research often are not known at the time of biospecimen collection. Despite this challenge, the informed consent information describing the nature and purposes of the research should be as specific as possible. The specific type of research that will be conducted in the future on contributed biospecimens may be sufficiently anticipated and described in the original informed consent to satisfy DHHS regulations. In • A clear description of the operation of the biospecimen resource. This description could include details that may be of interest to human subjects, such as whether identifiable information will be maintained in the biospecimen resource and/or whether research results will be linked to the biospecimen. 

• The conditions under which data and samples will be released to recipient-
section_name: C.2. Informed Consent

section_content: The extent to which a biospecimen resource is involved in obtaining informed consent varies widely and depends on the mission of the resource. Many biospecimen resources collect biospecimens and participate in the informed consent process, whereas other biospecimen resources store biospecimens originally collected for alternate purposes or by researchers not affiliated with the resource. Regardless of the level of involvement in the informed consent process, biospecimen resources should ensure that the research uses of biospecimens are consistent with the informed consent of the research participant and develop policies for responding to requests for discontinuation of participation. 

C. 2. 2. 1. The NCI recommends informed consent whenever possible, consistent with applicable regulations. Respect for individuals who have provided data or biospecimens for research is of paramount concern; therefore, their preferences should be considered when deciding whether informed consent should be sought. Some individuals may prefer use of unidentified samples or a waiver of consent to being recontacted to obtain consent for additional research or future uses. 

C. 2. 2. 2. For biospecimens collected during the course of medical care, the timing of consent (e. g., before or after a medical procedure) to use biospecimens for research purposes should not be imposed rigidly but instead informed by a number of important considerations, including ethical guidelines and logistical constraints. 

Generally, consent should be obtained prior to the medical procedure, but postmedical procedure consent may be appropriate in some circumstances. These decisions should be made on a case-by-case basis with sensitivity to the situation a patient faces when undergoing a medical procedure or a test for a serious disease. For example, post-medical procedure consent may be acceptable for the use of remnant human specimen beyond what is needed for diagnostic purposes if it was not possible to previously consent the patient due to considerations about illness, undue stress, or the ability of the patient to fully comprehend what is being asked. However, in all cases where biospecimens are collected from the individual for research purposes or the procedure for collecting a biospecimen for clinical purposes is changed to meet a research need, informed consent must be obtained prior to the collection of the biospecimen. 

C. 2. 2. 3. The informed consent document should employ clear and specific language to address the use of biospecimens and/or data by private or for-profit entities and the possibility of research leading to future development of commercial products, as appropriate. 

C. 2. 2. 4. The informed consent document should state whether or not individual or aggregate research results will be released to the human subject, the subject's health care provider, or the subject's family. 

C. 2. 2. 5. The informed consent document should describe how human subject data will be used and stored. Where applicable, the informed consent document should state whether identifiable or coded information will be maintained in the biospecimen resource and if research results will be linked to other data about the human subject, such as clinical data obtained from anatomic pathology and clinical pathology laboratory information systems and cancer registries. (Refer to B. 5. 3. 1. for further recommendations on the integration of informatics systems. ) If longitudinal data will be collected, the informed consent document should state that the subject's medical records will be accessed for this purpose. 

Informed consent documents also should describe whether the biospecimens and/or the data associated with or derived from biospecimens will be shared with other investigators and, if so, the oversight mechanisms for such sharing. 

C. 2. 2. 6. If a study includes genetic sequencing or analysis, the informed consent document should include information about the potential risks to the subject posed by such research. While the frequency of harm is not known, possible consequences could include paternity determinations or potential employment or insurance discrimination if the research reveals the individual to be at increased risk for certain diseases. In the case of genetic analyses, such risks also could pertain to the subject's family members. 

C. 2. 2. 7. If appropriate to the study design or the biospecimen resource's mission, human subjects may be allowed to specify the types of research for which the contributed biospecimens will be used via a tiered system of consent. 

Examples:

• My tissue may be kept for use in research to learn about, prevent, or treat cancer. 

• My tissue may be kept for use in research to learn about, prevent, or treat other health problems (e. g., diabetes, Alzheimer's disease, or heart disease). 

While a tiered system of consent will provide the human subject with greater specificity about future research, it also can lead to ambiguities in terms of how to classify certain types of inter-or multidisciplinary research. Tiered consent also may be inappropriate if the purpose of the biospecimen resource is to provide biospecimens for a very broad range of research, in which case providing human subjects with a list of potential types of research would be burdensome and uninformative. Tiered consent only should be used if a sophisticated system capable of tracking the levels of consent for each human subject already is in place. The logistics of monitoring the various levels of consent in a tiered system are complex and should be attempted only if the biospecimen resource has experience with a suitable tracking system. 

C. 2. 2. 8. If appropriate, informed consent documents should provide an option for human subjects to select whether they would be willing to be recontacted about the use of their biospecimens and/or data in future research studies. 

C. 2. 2. 9. Biospecimen resources should develop policies and procedures to track records for human subjects who discontinue participation. Informed consent documents should highlight the human subject's ability to discontinue participation and describe what will take place should this occur. 

• In the event that participation in the research study is discontinued, any remaining identifiable biospecimens and associated clinical data should be withdrawn from the biospecimen resource. However, samples and/or clinical data that have been transferred from the biospecimen resource to investigators and research data already generated from samples need not be withdrawn. Instead, if a biospecimen resource learns about the discontinuation of participation of a human subject, the NCI considers the biospecimen resource ethically obligated to inform investigators who received specimens derived from that individual. For additional information about IRBs and the requirement for OHRP-approved assurance of compliance, see the OHRP Web site at http://www. hhs. gov/ohrp/.
section_name: C.2.2. NCI Recommendations Pertaining to Informed Consent

section_content: Research depends on protecting the privacy of individuals who contribute biospecimens to biospecimen resources and on maintaining the confidentiality of associated clinical data and information (Eiseman et al. 2003). Applying the highest possible ethical standards is necessary to ensure the support and participation of research participants, physicians, researchers, and others in biospecimen resource activities (Friede et al. 2003). With the recent advances in genomic and proteomic technology, the sequencing of the human genome, and the increasing reliance of biospecimen resources on electronic and Web-based databases for data tracking, it is even more crucial to address the risk of breaches in privacy. The unintended release or disclosure of sensitive information can place individuals at risk for discrimination and related groups at risk for stigmatization, although the frequency of these types of harms is unknown.
section_name: C.3. Privacy Protection

section_content: The DHHS-issued regulation titled "Standards for Privacy of Individually Identifiable Health Information," commonly known as the HIPAA Privacy Rule (see 45 CFR Part 160 and Subparts A and E of Part 164), was created to protect the privacy of health information that identifies an individual while still allowing other activities of benefit to society, such as research. While the Privacy Rule does not apply to biospecimens directly, it may affect some biospecimen resources in that human specimens often are accompanied by identifiable health information that is necessary for tracking or longitudinal research. When determining if the Privacy Rule applies to an individual biospecimen resource and its research activities, the following points are considered:

• Protected health information. The Privacy Rule applies to PHI, defined as "individually identifiable health information transmitted by electronic media, maintained in electronic media, or transmitted or maintained in any other form or medium. PHI excludes education records covered by the Family Educational Rights and Privacy Act, as amended, 20 U. S. C. 1232g, records described at 20 U. S. C. 1232g(a) (4) (B) (iv), and employment records held by a covered entity in its role as employer" (45 CFR § 160. 103). As stated in 45 CFR § 164. 502, "Health information that meets the standard and implementation specifications for de-identification under §164. 514(a) and (b) is considered not to be individually identifiable health information. " • Covered entities. The Privacy Rule regulates the use and disclosure of PHI by covered entities. Under the Privacy Rule, a covered entity is defined as "a health plan, a health care clearinghouse, or a health care provider who transmits health information in electronic form in connection with a transaction for which DHHS has adopted a standard" (Protecting Personal Health Information in Research: Understanding the HIPAA Privacy Rule, available at: http://privacyruleandresearch. nih. gov/pr_02. asp). 

In general, a biospecimen resource is not considered a covered entity "unless the organization maintaining the tissue repository conducts some other activity that makes it a covered entity. For example, tissue repositories that conduct testing of specimens for the benefit of transplant recipients based on another health care provider's orders would be covered providers under HIPAA if they conduct electronic transactions for which the DHHS has adopted standards" (Research Repositories, Databases, and the HIPAA Privacy Rule, available at: http://privacyruleandresearch. nih. gov/research_repositories. asp). Even if a biospecimen resource is not a covered entity, it still is important to understand what constitutes PHI and the conditions under which it can be released by a covered entity, as these factors may affect what types of data will accompany a biospecimen and therefore what types of studies may be conducted using the biospecimen. 

• Privacy Rule Authorization. "A valid Privacy Rule Authorization is an individual's signed permission that allows a covered entity to use or disclose the individual's PHI for the purposes, and to the recipient or recipients, as stated in the Authorization. When an Authorization is obtained for research purposes, the Privacy Rule requires that it pertain only to a specific research study, not to nonspecific research or to future, unspecified projects. The Privacy Rule considers the creation and maintenance of a research repository or database as a specific research activity, but the subsequent use or disclosure by a covered entity of information from the database for a specific research study will require separate Authorization unless the PHI use or disclosure is permitted without Authorization… An Authorization differs from an informed consent in that an Authorization focuses on privacy risks and states how, why, and to whom the PHI will be used and/or disclosed for research. An informed consent, on the other hand, provides research subjects with a description of the study and of its anticipated risks and/or benefits, and a description of how the confidentiality of records will be protected, among other things.
section_name: C.3.1. Federal Regulations Pertaining to Privacy

section_content: Access to human specimens and data for research purposes is crucial for fields such as genomics, proteomics, metabolomics, molecular imaging, and nanotechnology. Researchers in these areas often rely on federally funded biospecimen resources for high-quality biospecimens and associated data. To best serve the needs of the research community, biospecimen resources should establish guidelines for sample distribution and clinical data sharing consistent with ethical principles, governing statutes and regulations, and, if applicable, informed consent language. These guidelines should be:

• Clear to ensure their comprehension and adoption;

• Flexible so that biospecimen resources may be responsive to changing scientific needs;

• Amendable to facilitate their adaptability over time; and

• General enough so they may be applied to different kinds of biospecimen resources. 

In C. 4. 4. 1. Access levels are described in the protocol for operation of the biospecimen resource and approved by an IRB and/or a bioethics/scientific advisory board, as appropriate. 

C. 4. 4. 2. Access to research participants' identities and medical, genetic, social, and personal histories is restricted to only those biospecimen resource staff members who need to access such records as part of their assigned duties or to those persons permitted access by law. 

C. 4. 4. 3. The number of personnel allowed to access links and re-identify information is kept to a minimum, and access is appropriately monitored to ensure compliance. 

C. 4. 5. Charges for samples, if any, are used only to recover reasonable costs associated with operation of the biospecimen resource.
section_name: C.4. Access to Biospecimens and Data

section_content: Inventions and data arising from research using annotated biospecimens may have commercial value. As researchers and industry sponsors have sharply increased their demand for properly prepared and clinically annotated biospecimens, some institutions have begun to assert control over biospecimens, associated data, and research findings. For reference, Appendix 2 contains a sample MTA addressing the transfer of human unidentifiable or coded biospecimens. 

The following Internet sites are relevant to this issue:

• http://ott. od. nih. gov/policy/research_tool. html • http://www. autm. net/aboutTT/aboutTT_umbta. cfm • http://grants. nih. gov/grants/policy/data_sharing/ C. 5. 2. Biospecimen resource staff, as custodians of biospecimens, are not considered a priori inventors under patent law for inventions made using materials distributed by the biospecimen resource. In general, one whose sole contribution to an invention consists of the routine collection, handling, storage, and disbursement of biospecimens might not rise to the level of "inventor. " Inventorship is determined by patent law and is considered on a case-by-case basis by trained legal personnel. 

C. 5. 3. Biospecimen resources have no inherent rights to future IP, such as reach-through rights in inventions made by investigators using samples obtained from the biospecimen resource. 

C. 5. 4.
section_name: C.5. Intellectual Property and Resource Sharing

section_content: This glossary is included to provide instruction as to how terms used in the NCI Best Practices for Biospecimen Resources should be interpreted. Wherever possible, standardized definitions from Federal documents and/or the NCI Thesaurus were used. 11 Where such sources were not available or appropriate, definitions were selected from widely used texts, such as Black's Law Dictionary (8 th ed. ), Taber's Cyclopedic Medical Dictionary (20 th ed. ), Merriam-Webster Dictionary [online]; reports specific to biospecimen resources, such as ISBER Best Practices for Repositories I (2005), and RAND Corporation's Case Studies of Existing Human Tissue Repositories (2003) or relevant Web sites such as the OSHA Web site. The citation "NCI Best Practices working definition" refers to definitions drafted specifically for this document by the NCI in consultation with appropriate experts. In some cases, two definitions may be listed for a single term to convey both a general and a biospecimen resource-specific meaning or to provide definitions from two Federal regulations. Where two definitions are listed, the first definition contains the meaning most relevant to the NCI Best Practices. 

Accident. An unforeseen and unplanned event or circumstance frequently causing loss or injury (NCI Thesaurus). 

Aerosol. A fine mist or spray which contains minute particles (Centers for Disease Control and Prevention Special Pathogens Branch, Glossary of Terms, http://www. cdc. gov/ncidod/dvrd/spb/mnpages/glossary. htm). 

Aliquot. Pertaining to a portion of the whole; any one of two or more samples of something, of the same volume or weight (NCI Thesaurus).
section_name: GLOSSARY OF TERMS

section_content: Annotation. Explanatory or additional information associated with a particular biospecimen. Annotations may be added by either the pathologist or the resource collector (NCI Best Practices working definition).
section_name: Analyte. The sample being analyzed (NCI Best Practices working definition).

section_content: See Biospecimen associated data.
section_name: Associated data.

section_content: A documented review of procedures, records, personnel functions, equipment materials, facilities, and/or vendors to evaluate adherence to written standard operating procedures or government laws and regulations (ISBER 2005). 2. To perform an audit (Merriam-Webster Dictionary). 

Best practices. Standard operating procedures that are considered state-of-the-science consistent with all applicable ethical, legal, and policy statutes, regulations, and guidelines (NCI Best Practices working definition). 

Biohazard. A combination of the words biological hazard. Organisms or products of organisms that present a risk to humans (Occupational Safety and Health Administration, http://www. osha. gov/doc/outreachtraining/htmlfiles/hazglos. html). 

Biorepository. An organization, place, room, or container (a physical entity) where biospecimens are stored. In the context of the NCI Best Practices, only biorepositories containing human specimens collected with an intention to use them for research purposes (research biorepositories) are addressed. The physical structure, policies, and the biospecimens and data contained within it are defined collectively as a biospecimen resource, defined below (NCI Best Practices working definition). 

Biosafety. Biological safety, or biosafety, is the application of knowledge, techniques, and equipment to prevent personal, laboratory, and environmental exposure to potentially infectious agents or biohazards. Biosafety defines the containment conditions under which infectious agents can be safely manipulated. 

The objective of containment is to confine biohazards and to reduce the potential exposure of the laboratory worker, persons outside of the laboratory, and the environment to potentially infectious agents (U. S. Environmental Protection Agency, Terminology Reference System, http://oaspub. epa. gov/trs/trs_proc_qry. navigate_term?p_term_id=1317&p_term_cd=TERM). 

Biosafety level. Specific combinations of work practices, safety equipment, and facilities, which are designed to minimize the exposure of workers and the environment to infectious agents. Biosafety level 1 (BSL-1) applies to agents that do not ordinarily cause human disease. Biosafety level 2 (BSL-2) is appropriate for agents that can cause human disease, but whose potential for transmission is limited. Biosafety level 3 (BSL-3) applies to agents that may be transmitted by the respiratory route which can cause serious infection. Biosafety level 4 (BSL-4) is used for the diagnosis of exotic agents that pose a high risk of life-threatening disease, which may be transmitted by the aerosol route and for which there is no vaccine or therapy ( Custodianship. The caretaking responsibility for a biospecimen collection, including management and documentation, as well as rights to determine the conditions under which biospecimens are accessed and used (NCI Best Practices working definition). 

Data. 1. Factual information (e. g., measurement, statistic, numerical value) derived from scientific experiments or diagnostic procedures organized especially for scientific analysis in a numerical form suitable for digital transmission or processing by computer, digitally transmitted or processed and used as a basis for reasoning, discussion, or calculation. The information may include both useful and irrelevant or redundant information that must be processed to be meaningful (NCI Best Practices working definition). 2. A collection or single item of factual information, derived from measurement or research, from which conclusions may be drawn (NCI Thesaurus). 

Demographic data. The statistical characterization of human populations or segments of human populations; e. g., characterization by age, sex, race, or income (NCI Thesaurus). 

Disposal. Systematic destruction of medical waste and other biohazardous waste (NCI Best Practices working definition). 

Disposition. Transfer to the care or possession of another (Merriam-Webster Dictionary). 

Distribution. 1. A process that includes receipt of request for samples, selection of appropriate samples, and final inspection, in conjunction with subsequent shipment and delivery of samples to another biospecimen resource, biospecimen collection center, or laboratory (NCI Best Practices working definition). 2. The act of distributing, spreading, or apportioning (NCI Thesaurus). 

End user. The ultimate consumer of a finished product (Merriam-Webster Dictionary). 

Epidemiologic. Of or relating to epidemiology, the study of the causes, incidence and distribution of disease in the population and its application for prevention or control (NCI Thesaurus). Genomics. The study of genes and their function; the study of all or a substantial portion of the genes of an organism as a dynamic system, over time, to determine how those genes interact and influence biological pathways, networks, and physiology (Eiseman et al. 2003).
section_name: Audit. 1.

section_content: Honest broker. An individual, organization, or system acting for, or on behalf of, a covered entity to collect and provide health information to research investigators in such a manner whereby it would not be reasonably possible for the investigators or others to identify the corresponding patients-subjects directly or indirectly. The honest broker cannot be one of the investigators. The information provided to the investigators by the honest broker may incorporate linkage codes to permit information collation and/or subsequent inquiries (i. e., a "re-identification code"); however, the information linking this reidentification code to the patient's identity must be retained by the honest broker and subsequent inquiries are conducted through the honest broker (NCI Thesaurus).
section_name: Extramural

section_content: A living individual about whom an investigator (whether professional or student) conducting research obtains (1) data through intervention or interaction with the individual or (2) identifiable private information (45 CFR § 46. 102(f)). 

Identifiable. 1. The identity of the subject is or may readily be ascertained by the investigator or associated with the information (45 CFR § 46. 102(f)). 2. Able to identify the individual; or with respect to which there is a reasonable basis to believe the information can be used to identify the individual (Protecting Personal Health Information in Research: Understanding the HIPAA Privacy Rule, http://privacyruleandresearch. nih. gov/pr_02. asp). 

Individually identifiable health information. A subset of health information, including demographic information collected from an individual, and: (1) is created or received by a health care provider, health plan, employer, or health care clearinghouse; and (2) relates to the past, present, or future physical or mental health or condition of an individual; 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 (i) that identifies the individual; or (ii) with respect to which there is a reasonable basis to believe the information can be used to identify the individual (45 CFR § 160. 103)

Informatics. An occupational discipline which unites information science with computer science. It is concerned with the development of techniques for the collection and manipulation of data, and the use of such data (NCI Thesaurus). 

Informed consent. The legally effective consent of the human subject or the subject's legally authorized representative. An investigator shall seek such consent only under circumstances that provide the prospective subject or the representative sufficient opportunity to consider whether or not to participate and that minimize the possibility of coercion or undue influence. The information that is given to the subject or the representative shall be in language understandable to the subject or the representative. No informed consent, whether oral or written, may include any exculpatory language through which the subject or the representative is made to waive or appear to waive any of the subject's legal rights, or releases or appears to release the investigator, the sponsor, the institution or its agents from liability for negligence (45 CFR § 46. 116(a) ). 

Institutional review board (IRB). An institutional review board reviews and has authority to approve, require modifications in (to secure approval), or disapprove all research activities at the institution covered by this policy. Each IRB shall have at least five members, with varying backgrounds to promote complete and adequate review of research activities commonly conducted by the institution. The IRB shall be sufficiently qualified through the experience and expertise of its members, and the diversity of the members, including consideration of race, gender, and cultural backgrounds and sensitivity to such issues as community attitudes, to promote respect for its advice and counsel in safeguarding the rights and welfare of human subjects. In addition to possessing the professional competence necessary to review specific research activities, the IRB shall be able to ascertain the acceptability of proposed research in terms of institutional commitments and regulations, applicable law, and standards of professional conduct and practice (45 CFR § 46. 107-109).
section_name: Human subject.

section_content: A commercially valuable product of the human intellect, in a concrete or abstract form, such as a copyrightable work, a protectable trademark, a patentable invention or a trade secret (Black's Law Dictionary). 

Interoperability. The ability of two or more systems or components to exchange information and to use the information that has been exchanged (NCI Best Practices working definition). Label. Any written, printed, or graphic material on or affixed to a specimen container or package (ISBER 2005).
section_name: Intellectual property (IP).

section_content: Longitudinal data. Data derived from the assessment over a period of time of variables relating to an individual or group of individuals (NCI Best Practices working definition).
section_name: Intramural

section_content: A binding, legal agreement between the institution providing research materials (usually for unpatented biological materials) and the institution receiving materials that sets forth conditions of transfer and use, protects proprietary interests, and restricts distribution of the material (NCI Best Practices working definition).
section_name: Material transfer agreement (MTA).

section_content: A system of words used in a particular discipline (NCI Thesaurus). 

Package. A labeled carton, receptacle, or wrapper containing one or more containers and accompanying labeling material (ISBER 2005). 

Paraffin-embedded. Chemically or otherwise fixed and then embedded in paraffin wax (NCI Best Practices working definition). 

Patent. The right to exclude others from making, using, marketing, selling, offering for sale, or importing an invention for a specified period of time (20 years from the date of filing), granted by the Federal Government or other national government to the inventor if the invention is novel, useful, and nonobvious (NCI Best Practices working definition adapted from Black's Law Dictionary). 

Patient. 1. One who is sick with, or being treated for, an illness or injury. 2. An individual receiving medical care (Taber's Cyclopedic Medical Dictionary). 

Preservation. 1. Use of chemical agents, alterations in environmental conditions, or other means during processing to prevent or retard biological or physical deterioration of a specimen (ISBER 2005). 2. To preserve or maintain (Merriam-Webster Dictionary). 

Prevalence. The total number of cases of a given disease in a specified population at a designated time. It is differentiated from "incidence," which refers to the number of new cases in the population at a given time (NCI Thesaurus). 

Privacy. 1. The condition or state of being free from public attention to intrusion into or interference with one's acts or decisions (Black's Law Dictionary). 2. The quality of being secluded from the presence or view of others; the condition of being concealed or hidden; the ability of a person to control the availability of information about and exposure of him-or herself (NCI Thesaurus). 

Private information. Includes information about behavior that occurs in a context in which an individual can reasonably expect that no observation or recording is taking place, and information which has been provided for specific purposes by an individual and which the individual can reasonably expect will not be made public (for example, a medical record) (45 CFR § 46. 102(f)). 

Procedure. A series of steps designed to result in a specific outcome when followed in order (ISBER 2005). 

Process validation studies. The process of demonstrating that a specific procedure will consistently produce expected results within predetermined specifications (ISBER 2005). 

Processing. Any procedure employed after specimen collection but prior to its distribution, including preparation, testing, and releasing the specimen to inventory and labeling (ISBER 2005).
section_name: Nomenclature.

section_content: Individually identifiable health information transmitted by electronic media, maintained in electronic media, or transmitted or maintained in any other form or medium. Protected health information excludes education records covered by the Family Educational Rights and Privacy Act, as amended, 20 U. S. C. 1232g, records described at 20 U. S. C. 1232g(a) (4) (B) (iv), and employment records held by a covered entity in its role as employer (45 CFR § 160. 103). 

Proteomics. The study of the full set of proteins encoded by a genome; the study of the identities, quantities, structures, and biochemical and cellular functions of all proteins in an organism, organ, or organelle and how these properties vary in space, time, and physiological state (Eiseman et al. 2003). 

Quality. 1. Conformance of a specimen or process with pre-established specifications or standards (ISBER 2005). 2. Having a high degree of excellence or worth (NCI Best Practices working definition). 

Quality assurance (QA). An integrated system of management activities involving planning, implementation, documentation, assessment, and improvement to ensure that a process or item is of the type and quality needed for the project. Same as quality management system (QMS) (ISBER 2005). 

Quality control (QC). Specific tests defined by the QA or QMS Program to be performed to monitor procurement, processing, preservation and storage, specimen quality, and test accuracy. These may include but are not limited to performance evaluations, testing, and controls used to determine accuracy and reliability of the biospecimen resource's equipment and operational procedures as well as monitoring of the supplies, reagents, equipment, and facilities (ISBER 2005). 

Quality management system (QMS). See Quality assurance (QA). 

Reach-through rights. Rights claimed by the provider of materials to the recipient's discoveries where the discoveries are not covered by the provider's patent on the original material. Examples of reachthrough rights required by providers in exchange for use of their material by the recipient might include ownership of recipient's discoveries, license exclusivity, or payments upon the sale of the discovery. Reach-through rights allow the provider to obtain rights in subject matter to which the provider would not otherwise have rights through its ownership or patent coverage of the material alone. Reach-through rights may give the provider an unfairly high level of compensation for the research use of the material by the recipient (NCI Best Practices working definition).
section_name: Protected health information (PHI).

section_name: Remnant human specimen

section_name: _________________________________________ Scientist Receiving Material

section_content: Acknowledgement of Recipient Scientist: I have read and understood the conditions outlined in this Agreement, and I agree to abide by them in the receipt and use of the MATERIAL.

section_content: Date
section_name: _________________________________________ Scientist Receiving Material

section_name: WEB RESOURCES 10

section_content: Government Printing Office Access http://www. gpoaccess. gov/cfr/index. html
section_name: Code of Federal Regulations

section_name: Standard operating procedures (SOPs).

section_content: Simple Letter Agreement (SLA). Streamlined form of material transfer agreement (MTA) approved for use at the NIH. The NIH encourages the use of the SLA to facilitate exchanges between academic institutions (NCI Technology Transfer Branch glossary, http://ttb. nci. nih. gov/glossary. php). 

Specimen. See Biospecimen. 

Stakeholder. One that has a stake or an interest. In the context of the NCI Best Practices, the term stakeholder embraces research participant advocates in addition to scientists (NCI Best Practices working definition).

section_content: Established or prescribed methods to be followed routinely for the performance of designated operations or in designated situations (Merriam-Webster Dictionary). 

Standard operating procedures (SOPs) manual. Written document describing in detail practices, procedures, and policies of a biospecimen resource (NCI Best Practices working definition). 

Storage. 1. Maintenance of specimens for future use (ISBER 2005). 2. Space or a place for storing (Merriam-Webster Dictionary). 

Tissue. An aggregate of cells with different specialized characteristics that are organized anatomically, usually in the fixed framework of an organic matrix. The architectural organization that is maintained contributes to the performance of a specific collective function. Tissues are parts of organs. The term tissue is most often referred to in the context of solid tissue, as originating from a solid organ; however, tissue also can be defined broadly to include collections of cells and the extracellular matrix and/or intercellular substances from bodily fluids such as blood (NCI Best Practices working definition).
section_name: Standard operating procedures (SOPs).

section_content: A Master Agreement among the NIH, universities, and other nonprofit research facilities used to expedite transfer of research materials among non-commercial entities (NCI Technology Transfer Branch glossary, http://ttb. nci. nih. gov/glossary. php). More information about the terms of the UBMTA and its signatories is available at the Association of University Technology Managers Web site (http://www. autm. net/aboutTT/aboutTT_umbta. cfm). 

Unidentifiable. Tissue for which identifiable information was not collected or, if collected, was not maintained and cannot be retrieved by the repository (Eiseman et al. 2003). 

Unique identifier. A code used to identify an object that is unique within a given context (NCI Best Practices working definition). 

Universal precautions. The CDC publication entitled "Recommendations for Prevention of HIV Transmission in Health-Care Settings" is also known as "Universal Blood and Body Fluid Precautions" or "Universal Precautions. " Under universal precautions, blood and certain body fluids of all patients are considered potentially infectious for human immunodeficiency virus (HIV), hepatitis B virus (HBV), and other bloodborne pathogens. Universal precautions are intended to prevent parenteral, mucous membrane, and nonintact skin exposures of health-care workers to bloodborne pathogens. In addition, immunization with HBV vaccine is recommended as an important adjunct to universal precautions for health-care workers who have exposures to blood ("Perspectives in Disease Prevention and Health Promotion Update: Universal Precautions for Prevention of Transmission of Human Immunodeficiency Virus, Hepatitis B Virus, and Other Bloodborne Pathogens in Health-Care Settings," http://www. cdc. gov/mmwR/preview/mmwrhtml/00000039. htm).
section_name: Uniform Biological Material Transfer Agreement (UBMTA).

section_content: A detailed description of the manner in which an end user would use a system to accomplish a task they would consider important and what the system does to satisfy those needs (NCI Best Practices working definition).
section_name: Use case.

section_content: The NCI has identified the ability to share research data electronically as key to achieving its goal of eliminating death and suffering due to cancer. To this end, the NCI established the caBIG™, an infrastructure designed to facilitate the exchange of data and programs across the cancer research enterprise (see https://cabig. nci. nih. gov/). Biospecimen resources are encouraged to draw on caBIG™ to implement the informatics recommendations outlined in Section B. 5 of the NCI Best Practices. Of particular relevance to biospecimen resources is the Tissue Banks and Pathology Tools Workspace (TBPTW) dedicated to the integration, development, and implementation of biospecimen resource and pathology tools. As part of the TBPTW, the NCI is developing the following components:

• caTISSUE Core. An intranet/Internet-based application for managing a biospecimen resource. 

The caTISSUE Core also provides an object model through which existing biospecimen resource systems may be used as a standard to share biospecimen data. • caTISSUE Clinical Annotation. An application for handling the annotation of biospecimens with clinical data.
section_name: APPENDIX 1 NCI INFRASTRUCTURE TO SUPPORT INFORMATICS BEST PRACTICES

section_content: A system for extracting concepts from free-text pathology reports into a structured data model.
section_name: • cancer Text Information Extraction System (caTIES).

section_content: The NCI supports caBIG™ compatibility of the informatics systems used by biospecimen resources as a step toward integrating biospecimen resource systems with other sources and types of data from clinical research and genomic and proteomic laboratory studies. 

All caBIG™ applications are open source and free of charge. While applications like caTISSUE Core and cancer Text Information Extraction System (caTIES) are developed within caBIG's™ TBPTW, use of these tools is not expected to be the only way of achieving caBIG™ compatibility. Biospecimen resources should work with the developers of their software on making these systems interoperable with others through caBIG™ compatibility.
section_name: Interoperability Using caBIG™

section_content: The caBIG™ Compatibility Guidelines provide a high-level description of requirements for interoperability (see https://cabig. nci. nih. gov/guidelines_documentation). The caBIG™ Compatibility Guidelines are organized into four levels of maturity based on degrees of interoperability: Legacy, Bronze, Silver, and Gold. Biospecimen resources are encouraged to establish new informatics systems that are caBIG™ compatible at the silver level and to place systems that are being replaced or upgraded on a path to silver-level compliance. 

Silver-level compatibility requires that systems utilize data elements defined in a common metadata repository, such as the caDSR (see http://ncicbsupport. nci. nih. gov/sw/content/caDSR. html). The caDSR and its associated services provide the infrastructure to handle standardized terminologies addressed in the caBIG™ Compatibility Guidelines. For questions or comments on the caDSR, please contact the NCICB Application Support Group via e-mail at ncicb@pop. nci. nih. gov.
section_name: caBIG™ Compatibility Guidelines

section_content: This material transfer agreement (MTA) is suggested for use when unidentifiable or coded human biospecimens are transferred. Transfer of human biospecimens with associated identifiable private information may require additional terms to this MTA or other documents. 3-6, 12, and 13 apply to Recipients serving as a biospecimen resource. )
section_name: APPENDIX 2 MATERIAL TRANSFER AGREEMENT FOR HUMAN SPECIMENS

section_name: Provider

section_content: If the MATERIAL is being provided by the Provider under this Agreement for the purpose of the Recipient distributing the MATERIAL to the research community, the Provider hereby grants the Recipient explicit permission to further distribute the MATERIAL to the research community as a biospecimen resource. Provider approval (initial here) _________
section_name: 3.

section_content: If the Recipient is designated as a biospecimen resource in Article 2, the Recipient is the custodian of the MATERIAL and therefore does not by virtue of this Agreement acquire any intellectual property rights in the MATERIAL nor in any research conducted by third parties using the MATERIAL.
section_name: 4.

section_content: The Recipient will distribute the MATERIAL in compliance with all applicable Federal, State and local statutes and regulations which include the Common Rule (45 CFR Part 46, Subpart A) and the Health Insurance Portability and Accountability Act (HIPAA).
section_name: 5.

section_content: The above MATERIAL is being distributed as a service to the research community. It is acknowledged that the MATERIAL is a resource in limited quantity and that further distribution for research purposes may be determined by scientific merit of the proposed research project. Accordingly, the MATERIAL will be made available to other scientists under a separate MTA for scientifically approved projects and to the extent supplies are available.
section_name: 6.

section_name: Recipient conducting an independent Research Project