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Biobank Sample Collection

2022-03-25T14:40:54Z

Mcaffet: /* Sample Collection */ I added an extra space since things were cramped together in the samples list

==Sample Collection==

As you are planning your resource, you will to need determine if your collection will include biologic samples now or in the future. Collecting biological samples is important if adequate samples do not currently exist, or if current collections are fragmented and not shared. Advocacy organizations can also leverage their biobank sample collections to direct the research being done on their disease or condition of interest.

Well-characterized biological samples are a very valuable research tool. However, sample collection is not a trivial undertaking, and proper planning is required. Advocacy organizations will need to work with their medical and scientific advisors to determine what is appropriate to collect. There are also technical considerations and resource considerations.

Some basic questions to consider include:

* What types of samples will you collect?
* From whom will you collect samples?
* Where will samples be collected?
* When will samples be collected?
* Who will collect the samples?
* How often will you collect samples?
* Do other similar sample collections exist?

OBBR has developed a [http://biospecimens.cancer.gov/global/pdfs/OBBR_Brochure_102510-508.pdf brochure] on the importance of high quality biospecimens.

==Biological Samples and Derivatives==

It is vital to anticipate how samples will be used prior to collecting them, so they can be collected and processed appropriately. For example, [http://www.bd.com/vacutainer/pdfs/plus_plastic_tubes_wallchart_tubeguide_VS5229.pdf different vacutainer tubes] are used for blood collection, depending on how the blood will be processed in the lab.

Many biobanks collect blood and/or tissue. Blood is a robust source for DNA, as all cells in the body generally have identical DNA signatures. Blood can also be used to isolate PBMCs (peripheral blood mononuclear cells), study biomarkers, or make EBV-transformed cell lines (although this is not as common today since smaller amounts of DNA are needed for experiments). Blood is usually processed (e.g. DNA isolated) prior to being sent to researchers.

Tissue is often used to study changes in gene expression (RNA) and can be a source for cell line generation. Tissue samples can be processed prior to being sent to researchers, or sent to researchers directly as frozen pieces of tissue. Representative pieces of tissue may also be embedded in paraffin, sectioned, and stained to see the characteristics of the tissue (histology and pathology). Generally, tissue is much more complex to collect and process than blood, and the more complex the processing, the higher the cost.

As you are planning your collection, you will need to understand what biological materials and derivatives are needed from the research community. There are many options to consider, and below is a list of biological samples and common derivatives. While not comprehensive, this is a starting place for the discussion.

Blood
* DNA
* RNA
* Protein
* PBMCs
* Cell lines
* Serum
* Plasma
Tissue
* DNA
* RNA
* Protein
* Cell lines
* Cell blocks
* Paraffin sections
* Frozen sections
* Frozen pieces of tissue
* Whole tissue from autopsy

==Mechanisms for Sample Collection==

Once you have decided what biological samples you will collect, you must then determine how you will collect them. Blood and tissue are the most commonly collected sample types. Blood collections are relatively straightforward, and can occur in collaboration with a healthcare provider or by non-traditional mechanisms, such as sending kits directly to participants or at outreach events. Outreach events are an excellent opportunity to bring your community together, educate about the importance of research, and collect samples. Tissue is collected exclusively at point of care with the collaboration of the provider. For all collections, it is important to include materials required for collection and instructions on how samples should be collected, stored, and shipped to the lab.

Below are common ways to collect blood and tissue:

Blood
* Collection at point of care with provider
* Sample donation kit mailed directly to participant
* Collection at outreach events

Tissue
* Collection at point of care with provider
* Collection at autopsy (special arrangements required)

==Sample Processing and Storage==

As we discussed, sample collection is not a trivial undertaking, and proper planning is required. In addition to deciding what to collect, you will need to determine how the samples will be processed and stored. Since most organizations do not have laboratory space, you will likely need to work with a vendor or partner for processing and storage.

Some basic questions to consider include:

* Where will samples be processed?
* How will samples be processed?
* Where will samples be stored?
* How will samples be stored?
* How will samples be accessed?
* For what types of experiments will samples be used?

==Pre-analytical Variation==

Procedures for biospecimen collection, processing and storage can lead to a wide variation in quality of specimens and data. For example, changes in specific transcript levels may be based on the ischemic time and not the disease. Pre-analytical variation includes both pre-acquisition and post-acquisition factors. (Pre-acquisition factors can include presence of antibiotics or other drugs, type and duration of anesthesia, and time of arterial clamp time. Post-acquisition factors include time at room temperature, temperature of the room, type of and time in fixative, and aliquot size to name a few.)

Ideally, every piece of relevant data should be collected to support future users who may have no connections to or understanding of the biospecimen collection protocols. Research is also needed to better understand how these variables affect molecular integrity, as some variables will have great influence on molecular pathways and others will not.

A number of initiatives are underway to better understand pre-analytical variation and biospecimen science:

* The Office of Biospecimen and Biorepositories Research (OBBR) has developed [http://pubs.acs.org/doi/abs/10.1021/pr200021n Biospecimen Reporting for Improved Study Quality] (BRISQ ) to guide researchers to capture information about the source and handling of biospecimens.

* The ISBER Biospecimen Science Working Group has developed the [http://www.isber.org/wg/bs/sprec.cfm Standard PRE-analytical Coding] for biospecimens (SPREC) to improve biospecimen research experimental protocols and to provide information about the biomolecular quality of samples.

* [http://www.spidia.eu/ The Standardisation and Improvement of Generic Pre-Analytical Tools and Procedures for In Vitro Diagnostics consortium], better known as SPIDIA, has developed pan-European quality assurance schemes and guidelines for pre-analytical procedures, including sample collection, handling, transportation, processing, and storage of clinical samples.

==Best Practices==

When working in any area, including registries and biobanks, it’s important to know where to find trusted information. What are the best practices, and who are the key organizations in the field?

In biobanking, best practices are needed to provide state-of-the-science guidance and to harmonize procedures for collection, processing, storage, and distribution of data and samples. While multiple best practices exist, there is not yet uniform adoption of these protocols. Three useful resources are listed below.

* The Department of Health & Human Services' (HHS) Agency for Healthcare Research and Quality (AHRQ) released a handbook, [http://www.effectivehealthcare.ahrq.gov/index.cfm/search-for-guides-reviews-and-reports/?pageaction=displayproduct&productid=12 Registries for Evaluating Patient Outcomes: A User's Guide], that provides guidance for establishing, managing, and analyzing patient registries.

* The International Society for Biologic and Environmental Repositories (ISBER) has developed [http://www.isber.org/ibc.html Best Practices for Repositories], focusing on the collection, storage, retrieval and distribution of biological materials for research.

* The National Cancer Institute (NCI) has developed [http://biospecimens.cancer.gov/practices/default.asp NCI Best Practices] that examine the scientific evidence for collection, annotation, processing, and storage of biospecimens.

==Insuring your biobank samples==

Biobank collections are precious and in many instances not replaceable. The samples are priceless, with immense scientific value. It is possible to insure the facility and equipment, but insurance for loss of samples is almost always cost prohibitive. If you do insure your collection, it is important to assess the cost of obtaining similar samples, including labor and all logistics for acquiring and storing the replacement samples. It is very challenging to assign a value to the collection itself.

Instead of focusing on insurance, a better strategy may be to focus on risk management and preventing loss in the first place. This can be accomplished by:

* Storing samples in multiple freezers and routinely splitting samples from the same case into separate freezers.

* Separating critical batches of samples to different sites. If offsite storage is not possible, store samples in different tanks or freezers in different rooms.

* Utilizing higher floors to decrease flood risk.

* Using internal controls, automated monitoring, routine maintenance and staff training to minimize risk of loss.

==Related Information==

*[[Getting a Biobank or Registry Started]]
*[[Biobank and Registry External Relations]]
*[[Biobank and Registry Financial Management]]
*[[Obtaining and Maintaining Registry Data]]
*[[Registry and Biobank Ethics and Governance]]
*[[Registry and Biobank Weekly Tips]]
*[[Registry Questionnaires]]

Genetic Alliance BioBank

2021-09-15T06:25:17Z

Mcaffet: Fixed typo in HIPAA

==Genetic Alliance BioBank Executive Summary==

[[Image:gabiobank.png]]

The [http://www.biobank.org Genetic Alliance BioBank] was founded in 2003 by leaders in the research advocacy field. It is establishing a centralized biological and data [consent/clinical/environmental] repository to enable translational genomic research on rare genetic diseases. The BioBank works in partnership with academic and industrial collaborators to develop novel diagnostics and therapeutics to better understand and treat these diseases. The BioBank will include a state-of-the-art, web-based informatics core, which is suitable for both research and product development [FDA compliant] studies. The centralized management and infrastructure of the BioBank provides a relatively cost-effective mechanism by which individual advocacy organizations for the first time can pursue sophisticated, novel research collaborations.

In recent decades biorepositories have tended to illustrate science at its worst: insufficient, uninformed patient consent; small, redundant collections that have no power; and legal structures that provide insufficient protection for the rights of both patients and researchers. Too often the result has been orphaned collections, disillusioned, disenfranchised patients, and frustrated scientists lacking the tools necessary for their work. The Genetic Alliance BioBank is built upon the lessons of the past, and has a practiced eye on the technology that will change the future. It presents a new paradigm, one in which the motivations and rights of all players are acknowledged and protected.

Similar to other research organizations, the founding advocacy organizations of the BioBank consistently experience significant challenges in executing rare disease research . These include: limited cohort size, variable disease phenotyping, limited bio-sample & data repositories, fragmentation/lack of scale, ineffective privacy and data security, limited funding resulting in limited research, and poor feedback to participants. The BioBank acknowledges and addresses these issues via the following key functions:

#Recruits donors to the bank, in the context of the advocacy organizations community, using state-of-the art methods that emphasize trust, privacy protections, data security, empowerment of participants and the member advocacy groups, and ongoing education.
#Provides a robust and dynamic method for the informed donor decision-making process, leading to truly informed consent, tailored to specific uses of the samples and related information. The system provides for dynamic re-contacting and reconsenting as the need arises.
#Provides a state of-the-art storage facility and system for collection and archiving of DNA, tissue and cell lines.
#Provides a BioBank informatics core that encodes identifiers in a centralized database. The database, similar to the sample repository, will be owned and maintained by the advocacy organization, and enable re-contact by the researchers to the (anonymous) donors.
#Provides sophisticated study management suitable for regulatory-grade filings and research.
#Raises the resources necessary to develop both the infrastructure and the enrollment of the bank.
#Facilitates collaboration of academic, government and industrial partnerships.

The BioBank is developing these functions in two phases. Phase I included functions 1 through 3. Phase II involves functions 4 through 6. The 7th function is ongoing and is occurring throughout both phases.

Phase I began in January 2002, and resulted in the incorporation of the BioBank in October 2003. At present, seven foundations have banked DNA, tissue and cell lines with the BioBank at this facility. BioBank members are bound by membership agreements and have IRB approval for their protocols. All of the protocols, template documents and procedures have IRB approval.

The BioBank is governed by representatives of the participating advocacy organizations and experienced outside directors from a variety of disciplines:
:''Sharon Terry, President (Genetic Alliance and PXE International) Joan Scott, Treasurer (Genetics and Public Policy Center, Johns Hopkins University) Patrick Terry, Secretary (PXE International, Genomic Health, Personalized Medicine Coalition, International Genetic Alliance), Claire Driscoll (National Human Genome Research Institute) Elizabeth Horn (National Psoriasis Foundation) Owen Johnson (Inflammatory Breast Cancer Research Foundation)''

Through a contract with PreventionGenetics of Marshfield, WI, the BioBank collects, stores and distributes samples in accordance with the procedures and specifications determined by the Genetic Alliance BioBankÂs board of directors and approved by the BioBanks Institutional Review Board, exceeding the requirements of all applicable federal, state and local laws, rules and regulations. The sample facility is managed by pioneers in the art of research advocacy organization banking.

Phase II of the BioBank has begun. Critical to the success of this model is the BioBanking and Research Management IT infrastructure. The Genetic Alliance will be using a clinical data structure to allow:

Swiss Banking Grade privacy and confidentiality protection via a highly secure, validated IT infrastructure [i.e., HIPAA, Regulatory compliant].
#Effective data aggregation via a scalable web-based architecture.
#Integration of all required clinical research management tools to enable online consent, enrollment, clinical and genomic data capture, and sample and genetic data banking.
#The ability to reuse and share patient resources across research networks.
#Integration of molecular datasets, linking the molecular characterization platform and BioBank.
#Utilization of data representation standards for effective data exchange and mining.

==Internal Links==
*[[Barriers to Rare Disease Research]]
*[[Benefits of Collaboration with Advocacy Organization Community]]
*[[Consumers and Researchers: Making It Work|Consumers and Researchers]]
*[[Educating Membership about Research]]
*[[Facilitating Quality Research]]
*[[Funding Research by Others]]
*[[Getting Needs onto the Research Agenda]]
*[[Genetic Privacy]]
*[[Orphan Drug Application]]
*[[Patient's Bill of Rights]]
*[[Promoting Research]]
*[[Registries]]
*[[Research Models]]
**[[Research Model 1: Recessive Disorder]]
**[[Research Model 2: Chromosomal Disorder]]
**[[Research Model 3: Dominant Disorder]]

Registries

2020-10-08T13:50:24Z

Mcaffet: /* What Will You Collect? */

Step by step start-up guide for registries and repositories

This guide asks 53 questions about things to consider when creating a registry or repository. This guide is divided in 3 sections:

*What will you collect?
*How will you collect it?
*What else is needed?

We hope this guide will help you in your registry and repository planning.

==What Will You Collect?==

'''Area of Focus'''

1. Will your registry or repository focus on a specific condition?

*Yes
*No

If yes, describe:

2. Which statement best describes your organization’s priorities?

*Clinical information is more important than physical samples
*Clinical information and physical samples are equally important
*Physical samples are more important than clinical information

3. Will you create a registry to collect medical/clinical information?

*Yes
*No

4. If yes, what information will you collect?

*Medical information
*Participant demographics
*Participant lifestyle information
*Family history
*Genetic information
*Diagnosis/treatment information
*Pedigree information
*Information on physical samples
*Other

5. Will you collect physical samples?

*Yes
*No

6. If yes, what physical samples will you collect?

*Blood for DNA extraction
*Buccal swab for DNA extraction
*Tissue (frozen)
*Tissue (formalin)
*Cell blocks
*Cell Lines
*Other

'''Study Design'''

7. Will you collect data or samples from any of the following?

*Cases
*Controls
*Affected families
*Trios
*Sib-pairs
*Children
*Vulnerable populations
*Other

8. What is the inclusion/exclusion criteria for those described above?

9. What is your collection goal? (This will affect funding and resources.)

10. What do the following advisors/experts in the field recommend for study design?

*Scientific advisory board
*Medical advisory board
*Researchers who will use samples
*Clinicians
*Other advocacy organizations with registries/repositories

11. How will researchers use your samples? (e.g. DNA/genomics analysis, RNA expression, etc).

'''Ownership and Access'''

12. Who will own your data and/or samples?

13. Who will govern/make decisions about your collection?

14. Who will determine access to data and/or collected samples?

15. Who will have access to data and/or collected samples?

16. Do you have material transfer agreements in place?

==How Will You Collect Data and/or Samples?==

'''Regulatory Compliance'''

17. Who are the principal investigators (PIs)?

18. Who will develop the protocol?

19. Who will submit the IRB application? Where will you submit the application?

20. How will you obtain informed consent? Who will obtain the informed consent?

21. How will you protect participants’ information and privacy?

'''Operations and Resources'''

22. How much will your collection cost to build? To maintain?

23. How will your collection be funded?

24. Who will manage day-to-day operations of your collection?

25. Are systems in place to manage the administrative aspects of a research study?

26. How will you recruit participants?

27. How will you retain participants?

28. Who will help you collect data and/or samples?

29. Are protocols in place for data and/or sample collection? Who will help you design protocols?

30. How will you distribute data and/or samples?

31. How will this program impact other parts of your organization?

'''Registry Considerations'''

32. Where will the data be stored?

33. Who will design the questionnaire? What format will the questionnaire be?

34. Is there controlled language/vocabulary?

35. Who will complete the questionnaire? How often will the questionnaire be completed?

36. What steps are in place for quality control?

37. Who is responsible for technology and security? What back-up systems are in place?

'''Repository Considerations'''

38. Where will your samples be physically located?

39. Who will assemble and send kits to donors?

40. Who will receive completed kits?

41. Who is responsible for sample processing? For sample storage?

42. Are appropriate protocols in place for sample processing, storage and distribution?

43. Who is responsible for sample integrity/security? What back-up systems are in place?

==What Else Do You Need?==

'''Public Relations and Materials'''

44. How will you announce your collection to your community?

45. How will you announce your collection to the medical and research community?

46. What materials will you develop?

*Web site
*Brochures
*Features in newsletter/ magazine
*E-newsletters
*Direct mail pieces
*Incentive materials (stickers, pens, note cards, post its)

47. What is your recruitment strategy?

*Web site
*Member communications
*Outreach events
*Medical professionals
*Media (press releases and NAPS release)

48. What is your retention strategy?

*Incentive mailings
*Timely updates (member communications and quarterly updates)
*Event cards (Thank you card, Birthday card, New Year’s card)

'''Making Samples Available to Researchers'''

49. How will you make your collection available to researchers?

50. Do you have a Biobank oversight committee?

51. How will you attract new researchers to your collection?

52. How can you promote collaborative research?

53. How will you drive the research agenda?

==Internal Links==

*[[Barriers to Rare Disease Research]]
*[[Benefits of Collaboration with Advocacy Organization Community]]
*[[Blood and Tissue Banks]]
**[[Genetic Alliance BioBank]]
*[[Consumers and Researchers: Making It Work|Consumers and Researchers]]
*[[Educating Membership about Research]]
*[[Facilitating Quality Research]]
*[[Funding Research by Others]]
*[[Getting Needs onto the Research Agenda]]
*[[Genetic Privacy]]
*[[Orphan Drug Application]]
*[[Patient's Bill of Rights]]
*[[Promoting Research]]
*[[Research Models]]
**[[Research Model 1: Recessive Disorder]]
**[[Research Model 2: Chromosomal Disorder]]
**[[Research Model 3: Dominant Disorder]]