SOP’s of a Biorepository

Introduction to Standard Operating Procedures

Biobanks and biorepositories needs to develop and adopt standard operating procedures (SOPs) that describe the policies and processes of the biorepository in detail.
SOPs should be detailed, well structured, and should undergo a strict approval process. SOP’s need to be reviewed periodically to assess the necessity of updates. Once implemented, SOPs should be routinely followed. Copies of SOPs should always also be stored in designated locations accessible to all personnel at any given time. Biorepository and biobank personnel should review SOPs prior to implementation.

Contents of the SOP

The SOP manual can be very dense and detailed, but should at the very least contain the following points:

Informed Consent

All biorepositories need to keep all records and related documents of the informed consent status for every biospecimen. Additionally, the procedures or protocols followed to obtain informed consent must be specified. Along with this the protection of privacy for all participants and data confidentiality should also be described.

Equipment

This section of the SOP should include the monitoring and calibration of all of the equipment. SOPs regarding the maintenance and repair of equipment is also crucial. All biorepositories should have their own procedures that routinely monitor all the equipment that is involved in the preparation and storage of biospecimens. The accurate calibration of equipment is vital to avoid affecting the quality of biospecimens and their data. The operational settings of the equipment should always be recorded along with all of the repairs that have been performed.

Collection Supplies

All biorepositories should have high standards for their reagents and consumable supplies that are used in the collection, processing, and storage of biospecimens. This means that the supplies should be acquired from certified and approved vendors and should meet the material specifications. Personnel should ensure that these supplies are in good condition prior to their utilization.

Identification and Labeling

All biorepositories will need to have their own guidelines and protocols for the labeling and identification of biospecimens. This should be coupled with the linking of biospecimens to their records regarding donor information and informed consent, so that when required it will be readily available.

Collection and Processing Methods

In this section details are extremely important to allow for the accurate replication of collection and processing procedures. This means that detailed descriptions of the supplies and equipment used are necessary. Along with the methods and processes used in the division of biospecimens into respective aliquots. The collection and processing of biospecimens must include records of staff names, dates, and specific times so potential pre-analytical variables are all recorded.

Storage and Retrieval

All procedures for the storage and retrieval of biospecimens from the biobank should be well described. This should include the guidelines for the addition and withdrawal of biospecimens, response to requests, fulfilling requests, and the disposition of biospecimens.

Transport and Distribution

All biorepositories should have designated policies and protocols for the transport and distribution of biospecimens that ensures their integrity, quality, and safety. This means guidelines should include packaging specifications addressing temperature conditions, temperature monitoring, regulations for the transport of hazardous materials, shipment logs, notifications for delivery, delivery confirmation, and agreements that cover transfers.

Quality Control

All biobanks should have their own testing procedures that document the results which are then kept in the records. This should comprise of tests that assess and control the quality of biospecimens, confirmation of histopathology diagnosis, assessment of nucleic acid integrity, biomarker expression, and more.

Informatics

Policies and guidelines for the management of records and procedures that define data collection methods, access to data, reporting, and quality control of data should be available for all biobanks.

Biosafety

It would be best for all biorepositories to have policies and procedures that address biosafety issues such as the reporting of staff injuries, precautions that the staff should have for bloodborne pathogens, the use of personal protective equipment, handling of hazardous material, and the disposal of biohazardous material and medical waste.

Training

All centers should have their own policies and procedures when it comes to the training of their personnel. These training should be documented, corrective actions that are taken, steps taken to resolve discrepancies for inventory or shipment, manage power outages, monitor samples, and the handling of emergencies and natural disasters.

Security

Procedures for security concerning administration and information systems should be available for all biobanks and biorepositories. These SOPs should address the different points of contact and personnel that are involved in backup. Names and contact numbers for the designated personnel should also be available.

Conclusion

It is important for all biorepositories and/or biobanks to have detail-rich standard operating procedures as it helps personnel get organized and offers guidelines in times of emergency. SOPs can also help to provide detailed information about the processes and preservation methods that ensure biospecimens retain their integrity and are of the highest quality.

References:

Quality management: Technical and operational best practices. National Cancer Institute. Accessed 10/18/2018.https://biospecimens.cancer.gov/bestpractices/to/qac.asp#b-3-3

Pre-analytical Variables Affecting the Integrity of Human Biospecimens

Introduction

Biorepositories or biobanks function to collect, process, transport, and store biospecimens. The integrity of these biospecimens is crucial for the success of clinical trials and research. There are many factors that can influence the results within research such as:

• Pre-analytical environmental or biological variables

• Pre-analytical technical variables

• Analytical variables

• Post-analytical variables

Pre-analytical variables are defined as factors that can have an impact before the start of the analytical phase. It not only affects the integrity of the tissue samples, but also the results of the analysis. Pre-analytical variables are critical as the analytical integrity of the research can be jeopardized. Seeing as most errors in the laboratory can be attributed to pre-analytical errors this stage is of upmost importance.

Pre-analytical Factors in the Collection of Biospecimens

It is important to adhere to guidelines for general laboratory safety. The collection of biospecimens require a balance of:

• Accrual rate

• Types of biospecimens

• Sample size

• Costs

• Location

• Storage requirements

• Transport logistics

The biospecimens collected can be either invasive or noninvasive. Biospecimens that are collected through non-invasive methods may lead to an increase in sample size due to easiness of collection, reduced costs, and willingness of donor to participate. This method is especially important when dealing with pediatric biobanking. It is important that biological and environmental factors are standardized and documented when interpreting results as it can affect the downstream analysis. It is also vital to take measurements to observe the effects of intervention and the changes over time.

Pre-Analytical Factors That Affect the Collection of Blood Samples and Its Derivatives

The collection of blood samples should be performed by trained staff. Those that are involved in collecting samples from children should specialize in pediatric phlebotomy. The staff needs to be highly trained as this ensures the highest quality of specimens and prevents the donors from experiencing any kind of discomfort. Depending on the research requirements different additives may be required. Different types of additives are coded using different colored collection tubes. Some of the important pre-analytical factors to take note of include:

1. Using the same tube brand and the same lot number throughout the study. This would be ideal as different brands can have different anticoagulants, additives, and may introduce bias.

2. Another important factor is the expiration dates on the tubes as the vacuum in these tubes can decrease with age and negatively impact the blood draw and filling of the tube.

3. Using the same posture such as supine, standing, or supine as these can cause plasma volume changes that may lead to increased analyte levels.

4. Using the recommended needle gauge as a needle that is too thin can lead to hemolysis that distorts the potassium concentrations and hematological cell counts.

5. Using the recommended and same duration of tourniquet use as prolonged use can cause changes in analyte concentrations and hemoconcentration.

6. Avoid inadequate filling as this can result in inaccurate results due to the decrease in blood and additive ratio.

A general rule for common analyses is to use ethylenediaminetetraacetic acid for hematology, DNA, hemoglobin A1C, and a range of proteins. For plasma glucose, it is recommended to use sodium-fluoride tubes while lithium heparin plasma can be used for assays such as kidney function, iron parameters, liver enzymes, thyroid hormones, C-reactive protein, and more.

In remote sites that are resource-poor, capillary dry blood spot (DBS) are easy biospecimens that can be collected. Small volumes of capillary blood from the peripheries can be deposited onto specific paper cards and dried at room temperature for three to four hours. DBS can be used in many analyses. However, some of the pre-analytical variables to note are:

·         Type of collection paper used

·         Type of chemical used in the manufacturing of the paper

·         Thickness of paper

·         The volume of blood deposited

·         Environmental factors such as heat, humidity, sunlight, and moisture

In DNA and RNA collection, there are also biological factors that can affect the biospecimens. These include the donor’s:

·         Gender

·         Age

·         Body mass index

·         Tobacco consumption

Since RNA is more vulnerable to degradation, some of the preanalytical collection factors that can affect the integrity are:

• Tube additive

• Tube type

• Tube sterility

• Type of biospecimen

• The volume of blood collected

• Short-term storage temperature

• Lag time until extraction

In microRNA’s, the pre-analytical variables include:

• Diet

• Age

• Race

• Exercise

• Drugs

• Altitude

• Tobacco use

• Chemicals

• Hemolysis

• Coagulation times

• Temperature

Pre-analytical Factors That Affect the Collection of Urine and Saliva

Urine can be collected in many different ways as it can be used for measurements of many analytes. In urine biospecimens, the preanalytical requirements can be conflicting.  This may result in the requirement of multiple biospecimens. Some of the preanalytical variables for urine collection include:

• Collection method

• Environmental exposure

• Urine dilution

• Dipstick components

• Preservatives or additives used

For saliva, these biospecimens have many advantages as they are easy to collect and can be used in many situations especially if donors are afraid of needles. The preanalytical variables for this biospecimen include:

• The time of collection

• The temperature the specimen is stored

• The collection method

Conclusion

The factors mentioned are pre-analytical variables that affect the biospecimens during the collection phase. However, it is important to note that there are many more pre-analytical variables that can affect the integrity of the biospecimens during the processing, transport, and storage phase.

Human Blood Samples in Biobanks

What are Blood Samples?

Blood samples are most commonly obtained from the antecubital fossa where the veins are closest to the surface. The blood sample can be taken by anyone from a doctor to a phlebotomist or a nurse. Most blood sample collections will occur at a clinic, hospital, or at a pathology collection center. A tourniquet is first wrapped around the upper arm to slow down the blood flow while the area where the insertion area for the needle is cleaned with an antiseptic cloth. The needle is inserted, and the blood sample is transferred into containers or tubes. Proper dressing of the wound is then administered to prevent infection and to keep it clean. These tubes are then labeled with a unique identification number along with other important information. These samples are then transported to their respective destinations, such as laboratories or biorepositories.

An Introduction to Biorepositories

Biobanks and biorepositories assist in providing the materials required in clinical trials and research. There is a growing number of biobanks that help to collect data and samples from the population as a response to the increased demand of these services. The services provided by various biobanks also mean that acquiring biological materials can be guaranteed. The existence of biobanks has allowed the accumulation of biological samples from various resources. 

Biospecimens in Biobanks

Some of the examples of human biospecimens available through biorepositories include both normal and diseased states such as:

• Purified DNA

• Hair tissue

• Nail

• Whole blood

• Plasma

• Serum

• Red blood cells

• Platelet concentrates

• Platelet-rich plasma

• Saliva

• Semen

• Breast milk

• Organ tissue

• Etcetera

All specimens should be collected and processed according to the proper guidelines and procedures. 

Functions of Biorepositories

While collecting biospecimens, biorepositories also collect demographic data such as medical history, lifestyle habits, medications, and family history to create an accurate scientific database. These samples are only labeled with a unique code for identification purposes. These specimens are then maintained in the proper environment and equipment to ensure the highest quality. Another crucial point in the management of any biobank is the privacy and rights of the donors. This means biobank managers need to train their staff regarding the policies and standard operating procedures (SOPs) of the biobank.

Whole Blood and Blood Cells 

In human biospecimens, the buffy coat and whole blood are essential for biorepositories. Whole blood refers to a sample that consists of red blood cells, white blood cells, platelets, and plasma. The buffy coat describes the white blood cells and platelets that form the anti-coagulated blood sample. Both these samples are essential as they are the main source for cellular nucleic acids, construction of a DNA biobank, and achieving the maximum quality and quantity of germline DNA. 

Storage for Human Blood Cells

Blood is one of the most common biospecimens collected in human biobanks as it is a source for DNA and RNA. This is why anti-coagulated blood is a prerequisite for plasma-derived cell-free circulating nucleic acid molecules and genomic or mitochondrial DNA and RNA. One of the most commonly used anticoagulants is ethylenediaminetetraacetic acid (EDTA) for various protein assays and DNA based studies. However, citrate is more appropriate for white blood cell cultures. Storage conditions and quality of biospecimens are of vital importance as it determines the yield of extracted DNA and RNA from buffy coat or whole blood samples. 

Since RNA is easily degradable, the World Health Organization – International Agency for Research on Cancer (WHO-IARC) has suggested that it be stored in nitrogen storage below -130⁰C. Samples stored at -140⁰C by liquid nitrogen have been observed to keep the RNA in a functional state and intact for more than 50 months. To maintain the biospecimen’s reliability and preventing the possibility of multiple freeze-thaw cycles, DNA protection and stabilization can be done at room temperature which eliminates the costs for freezer storage and lowering maintenance costs for biobanks. While purified DNA can be stored at -20⁰C for months, both purified DNA and RNA are much more stable at -80⁰C in nuclease-free water or aqueous buffers for long-term storage. 

For plasma, anticoagulants such as lithium-heparin and EDTA can be used. Storage of both serum and plasma at -80⁰C have shown that there is adequate stability in the different biomolecules. The cycle of freezing and thawing should be avoided as it leads to the degradation of nucleic acids and proteins. 

Conclusion

Due to the increasing scientific developments in the past few years, it has increased the need for biological material in clinical trials and research. Biorepositories play a crucial role in supporting the researcher’s access to samples that meet their scientific criteria. It is important for biobanks to play their role in the management of data, collection, processing, and storage of biospecimens.  

References:

Mohamadkhani A, Poustchi H. Repository of Human Blood Derivative Biospecimens in Biobank: Technical Implications. Middle East J Dig Dis 2015;7:61-8.

Custom Collection Services

What is a Biorepository?

A biorepository is an organization that collects, processes, stores, and distributes tissue samples for clinical research or other scientific investigations. They assist in maintaining and managing specimens such as tissue samples from humans, animals and other living organisms. A biorepository functions to maintain biospecimens, collect relevant information and assure the quality of the samples in their collection. They follow standard operating procedures (SOPs) that reduce anomalies in samples and which also provide guidelines for storage and maintenance. SOPs also ensure that biospecimens collected closely resemble that of their natural state. It helps biorepositories maintain a standardized framework for conducting operations and allows for the seamless implementation of processes.

What is Custom Procurement?

Some biorepositories, like Geneticist Inc., provide custom tissue procurement. This means that they are able to provide custom collection of biofluids, tissue samples, and blood samples in various specialties such as gastroenterology, oncology, rheumatology, neurology, and dermatology. Biorepositories that offer custom collection services have the ability to collect from a vast range of medical procedures such as elective skin biopsies, resections, autopsies, endoscopies, blood draws, and more. Due to the nature of the collection processes and procedures, biorepositories need to have a skilled logistics team and an expert medical courier network. The custom procurement of biospecimens is important especially if:

• Fresh collections are required

• There is a necessity for matched tissue pairs

• Rare indications or specific specimens

• The need for specific procedures during the collection and processing of samples

• Active cases and autopsies are needed

• The study or research is complicated

Examples of Biospecimens

• Biofluids – Examples of biofluids include stool, urine, whole blood, serum, plasma, cerebrospinal fluid, saliva, sputum, and swabbed material. Biofluids can be available frozen or fresh. Depending on client preference, it can be with or without additives.

• Tissue – Some examples of human tissue include fresh tissue, fixed tissue, frozen tissue, formalin-fixed paraffin-embedded (FFPE) blocks, whole tissue samples, stained slides, unstained slides, tissue microarrays, and more. These samples can be annotated with the proper genetic and molecular characterizations, outcomes data, pathology reports, and patient characteristics.

• Cells – Some research may require frozen or fresh cells that are still viable. These cells can be isolated from peripheral blood, cord blood, and bone marrow of normal donors and those with disease. Some examples include myeloid cells, pluripotent stem cells, mononuclear cells, and lymphoid cells.

What to Look For?

There are several factors that help decide which biorepository to go with when custom collection services are needed. Some of the factors that can help decide are:

a)       Procurement format options

Since prospective collection enable clients to decide which elements fit their needs, a custom procurement format can be designed with the help of our experienced team of scientists. Depending on the need of clients, custom procurement of biofluids, fresh tissue, frozen tissue, and more are available. Clients can also set the exclusion and inclusion criteria for specimens and donors.

b)      Partnerships

It is important to look for a biorepository that has a vast network of clinical partners to help ensure the highest quality of required biospecimen collection. It would also increase the access to more human tissue samples in various formats.

c)       Team members

A biorepository with experienced and certified team members would be the best choice as they would be well-trained with the ability to better understand the needs of researchers and to help find better solutions if necessary. With a great team on hand, specimens are more likely to be of the highest quality and fulfill the requirements of clients.

d)      Quality assurance

It is important for the biorepository to perform quality control checks to ensure that specimens are of the highest quality. This means that the staff should understand the appropriate storage or procurement procedures and ensure that the SOPs are adhered to strictly.

e)      Consent and privacy

Biorepositories should follow the procedures and guidelines during the procurement of human tissue samples. Informed consent and privacy of the donors should be of the highest priority to protect their interests.

Why Geneticist?

For custom collection services, the staff at Geneticist can design custom collections of a wide variety of biospecimens. Our staff are certified, experienced, and highly trained. Geneticist is a biorepository that is compliant with the Institutional Review Board (IRB) standards and provides the highest quality of collections. All our biospecimens and material adheres to the official protocols and is approved by the IRB and Independent Ethical Committee (IEC). Geneticist operates in accordance with current Federal Regulations, Health Insurance Privacy and Portability Act (HIPAA) and International Conference on Harmonisation – Good Clinical Practice (ICH-GCP) guidelines. With the proper inventory management process and extensive procurement formats, Geneticist strives to fulfill client requirements and satisfaction.

Specimen Extraction and Collection Process

Introduction to Specimen Extraction

The number of research and clinical studies being conducted to help improve screening procedures, diagnostic tests, therapies, and prognosis is rapidly increasing. This means tissue samples or biospecimens such as fresh frozen tissue and formalin-fixed paraffin-embedded (FFPE) blocks are of great value researchers. Obtaining high-quality samples is the first step towards credible data and testbale results. This is why suppliers of biospecimens should aim to collect, maintain, and disseminate the best biospecimens possible. High-quality samples are those that resemble the biology of the donor before its removal from the host. Once removed, the specimen may change based on the environment. Such things as exposure to different chemicals or environmental factors during the collection or storage procedure are all things that can negatively affect the sample.

Pre-Analytic Variables

Pre-analytic variables are factors that affect the collection, processing, and storage conditions that impact the integrity of the biospecimen before their removal from the host. Examples include, but are not limited to:

a)       Donor Physiology

This includes things such as the health of the donor, consumption of food, beverages or medications before the collection of the specimen, time of day the specimen was collected, and the type of anesthesia used. In female donors, even the time of their menstrual cycle can affect the downstream analysis. This stresses the importance of collecting this information from donors to decrease variability between samples.

b)      Collection Practices

It is important to maintain uniformity during the removal and collection of specimens from donors as different methods can affect the quality of the biospecimens. These specimens should also be preserved very quickly after removal from the donor. Newer preservation methods should be considered as they can allow for better and more accurate preservation of the biospecimen. Some of the factors that should be considered during biospecimen collection include, inter alia:

• The site of collection

• Type of anesthesia used

• Warm ischemia time

• Use of stabilizing agents

• Types of fixatives used

• Exposure time to fixatives

• The temperature for maintaining biospecimens.

All the above factors can affect the stability and degradation of molecules in the samples. Annotation of the biospecimens should include the donor’s information. This data should be recorded and maintained in a database. Handling of biospecimens should also be optimized to reduce molecular changes that may occur due to processing activities.

Analytic Variables

Analytic variables are factors that affect the performance of a testing procedure. To reduce errors, some of the following factors should be considered:

• Always use validated assays whenever possible.

• Train technical staff regarding the standard operating procedure.

• Use uniformed reagents.

• Use the proper type and number of control samples.

• If possible, randomization should be applied.

• Use standardized methods during the documentation and interpretation of results.

Biospecimen Collection and Reference Ranges

The specimens collected has to be appropriate for the clinical study and downstream applications that will be used in the research. Biospecimens should be examined by a qualified histopathologist to ensure quality and accuracy. Reference ranges should be used to ensure that any deviation from the reference range can be accurately detected. This is due to the reason where disease can be defined as a deviation from normal variation. This means the diagnosis of the disease depends on the scope of normal variation. All reagents should be quality controlled, so it is fit to be used in the assay. The standard operating procedures (SOPs) should be reproducible with control biospecimens that have a range of anticipated assay values. Poorly handled biospecimens tend to produce erroneous test results due to molecular changes.

Biospecimen Storage

The following practices should be applied to all types of biospecimens:

• Follow standard protocols when storing biospecimens to maintain quality. Personnel should record the conditions for storage, deviations from SOPs, temperature, equipment failures, and thaw / refreeze episodes. It is essential to validate storage equipment, maintain back up equipment, and identify “hot spots” in the freezer.

• Store specimens in a stabilized state.

• Avoid unnecessary thawing and refreezing.

• Follow protocols if thawing and refreezing are necessary.

• Inventory tracking is desirable as it helps reduce the disruption of the environment during retrieval of samples.

• Consider the length of storage, type of biospecimen, biomolecules of interest, and study goals when selecting storage temperature for samples.

• Use appropriate storage vessels and ensure stability under storage conditions. The proper storage vessel can prevent sample loss and reduce costs of storage and retrieval of biospecimens.

• Choice of labels and printing should include the consideration of long-term storage conditions.

• Protection for personnel such as face shields and gloves should be worn.

• Each specimen should have a unique identifier that is clear, affixed, and able to endure the storage conditions.

• Automated alarms that monitors the storage equipment with the capability to warn personnel when equipment failure occurs should be in place.

• An alternative power source and other backup equipment should activate automatically if there is equipment failure.

• SOPs to routinely test equipment failure, backup equipment, and other emergency situations should be available.

• Specimens should only be available to authorized personnel.

• Ensure appropriate shipping conditions and documentation.

References

Biospecimen collection, processing, storage, retrieval, and dissemination. National Cancer Institute. Accessed 9/18/2018.https://biospecimens.cancer.gov/bestpractices/to/bcpsrd.asp

CTM Logistics

Introduction to CTM Logistics

Clinical trial materials (CTM) logistics is an important business that manages the transport and delivery of biospecimens and tissue samples. The business of tissue preservation, meeting demands, and shipping these specimens from places like a biorepository to their destinations does not come without challenges.

Challenges facing CTM Logistics

Besides the conventional logistics and supply-chain challenges, those involved in CTM logistics also face:

1)      Standards

Many countries do not have standard protocols for the entry of trial supplies. Due to the demands of clinical materials worldwide, the challenge of shipping CTMs include the extraordinary constraints of import and export.

2)      Notice

Those involved in CTM logistics have very little to no notice when it comes to knowing when the materials need to be shipped out. The issue of material suppliers being disconnected can also cause delays at trial sites due to a supply chain issue.

3)      Product Standards

There are many trials that need both comparator or placebo drugs along with the trial drug. However, these trials are usually “randomized” throughout the course of the trial. This means that different labels will be needed for different trial protocols or different locations.

4)      Handling and Transport

Since the quality of these materials can be affected during handling and transport, companies involved in CTM logistics need to have the equipment and manpower that are suited to deal with the supplies.

5)      End Users

There is also the issue where some end users (such as researchers and physicians who conduct trials at investigator sites) who are not trained supply chain managers.

6)      Cost

Companies providing CTM logistics services also have a high risk of overrunning their cost due to difficulty addressing all cost drivers, inefficiencies in the system, and potential expenses when corrective actions need to be taken.

7)      Communication

Just like any other field, poor communication and coordination of the supply chain can result in action gaps, duplication of efforts, and delays. Frequent plan revisions are required if there are errors.

8)      Circumstances

Many studies often face the risk of delays and the need to lengthen their timeline in situations where there is the unexpected expiration of products or out of stock situations.

The industry has adapted to some of the challenges and constraints over the years. Although the clinical trials can be affected by issues in the supply chain, the successful completion of these researches has led to the better diagnosis, therapy, and prevention of diseases.

Supply Chain Stages

The following are critical supply chain stages:

• Planning: Those that are responsible forecast and come up with a strategy.

• Sourcing: This is done to acquire the necessary materials such as ancillary supplies, drugs, and lab materials.

• Manufacturing: Once ready, the necessary packaging and labels that are needed are manufactured.

• Storage: The CTMs are stored in the appropriate condition using the proper equipment (if needed).

• Distribution: The CTMs are imported or exported according to local authority regulations.

• Site: The CTMs are stored, samples managed, and data processed.

• Return: The company manages the shipment along with final CTM reconciliation.

• Destruction: The CTMs are recycled or destroyed accordingly.

• Analytics: All accumulated data are processed and analyzed.

Training

Individuals who are interested in positions such as clinical supply chain managers or supervisors and those interested or new to the CTM industry. Employees that go through special training pertaining to CTMs are more efficient in their duties in the company and industry. They learn about:

• The overview of the supply chain from beginning to end

• The appropriate packaging and labeling that suits the needs of a specific study design

• Having a plan of action to prepare the materials

• Implementing their plan and troubleshooting

• The logistics involved for distribution of CTM to trial sites that are located worldwide

• How to outsource vendors for the labeling and packaging purposes

• Interactive Response Technology

• The different roles of their team members and their expectations for the CTM group

• Current Good Manufacturing Practices (cGMP)

• The implementation of cGMP in the packaging process

Services

The company that is in charge of CTM logistics generally provides services for:

• The receiving, storage, and distribution of the materials

• Obtaining the necessary import and export licenses from the authorities

• Acquiring custom clearance for the CTM

• Data management (verification, validation, query, tracking, coding for diseases or medications, result presentation)

• Biostatistics (Statistical analysis, writing, result presentation, and more)

• Importing and exporting CTMs

• Short or long-term storage of specimens

Conclusion

More clinical trials are conducted globally. This creates a significant logistical challenge as the management of CTMs and the supply chain require tactical knowledge and a vast commitment of resources to avoid delays. There are many who would find that it is much more efficient to hire CTM service providers to manage the logistics as there are many challenges in this industry.

References:

1)      Basta N. Clinical trial logistics capabilities are expanding. Pharmaceutical Commerce. Accessed 9/5/2018. http://pharmaceuticalcommerce.com/clinical-operations/clinical-trial-logistics-capabilities-are-expanding/

2)      CTM logistics. Geneticist. Accessed 9/5/2018. https://www.geneticistinc.com/ctm-logistics/

3)      Clinical research services: clinical logistics. Parexel. Accessed 9/5/2018. https://www.parexel.com/files/6714/1155/2827/CLS_Supply_Chain_Poster_Sept14.pdf

4)      Clinical trial materials training course. ISPE. Accessed 9/5/2018. https://ispe.org/training/classroom/clinical-trial-materials

The Incredible MicroRNA's

What is microRNA?

MicroRNAs (miRNAs) are a group of small non-coding RNAs that are found in tissue samples of animals, plants, and some viruses. Since the discovery of circulating and extracellular miRNAs, there has been a rapid expansion of studies on miRNAs in biofluids like cerebrospinal fluid, plasma, serum, and urine. miRNAs are similar to small interfering RNAs (siRNAs). However, miRNAs originate from RNA transcripts forming short hairpins while siRNAs are from longer parts of double-stranded RNA. miRNAs are plentiful in mammalian cells and seem to target approximately 60% of these genes. miRNAs are thought to have important biological functions as they are evolutionary conserved. A good example is where there is conservation of 90 families of miRNAs as seen in the common ancestor of fish and mammals. The majority of these conserved miRNAs have been shown to play important roles.

Roles of miRNA

miRNA plays a role in RNA silencing and gene expression as post-transcriptional regulators. Within mRNAs, miRNAs function by base-pairing with the complementary molecules causing mRNA molecules to be silenced through cleavage of mRNA strand, destabilization of mRNA, or reduced efficiency of mRNA translation by ribosomes. Despite the low numbers of miRNA, it is estimated that the miRNAs regulate approximately more than 33% of the cellular transcriptome. Therefore, it should be no surprise that the miRNAs have crucial functions in the developmental and cellular processes that have been thought to be involved in many human diseases.

Since miRNAs are relatively stable in biofluids and have a wide range of biological potential, these molecules are suited to be used as non-invasive biomarkers in diagnosis, drug safety, and pre-clinical toxicity. Many studies have proven that secreted miRNAs are involved in conditions such as organ damage, cancers, and coronary heart disease. While the exact role of circulating miRNAs is mostly unknown, they have been observed to be protected from RNAse degradation through the inclusion in membranous particles or protein complexes.

Disease

Since miRNA plays a role in the normal functioning of eukaryotic cells, miRNA dysregulation is therefore linked to disease. For example:

a)       Hereditary Diseases

• It has been found that a mutation in the region of miR-96 results in progressive hearing loss.

• Hereditary keratoconus with anterior polar cataract is seen in mutation in the region of miR-184.

• Growth and skeletal defects can be seen in those with deletion of miR-17 to 92 cluster.

b)      Cancer

• Chronic lymphocytic leukemia was one of the first human diseases that has been associated with miRNA dysregulation. Other miRNAs that have also been linked to cancer are called “oncomirs”. miRNAs are involved in pathways that are crucial in B-cell development such as B-cell receptor signaling, cell-cell interaction, B-cell migration or adhesion, and production or class-switching of immunoglobulins. They also influence the generation of marginal zone, follicular, plasma, B1, and memory B cells.

• Another clinical trial is using miRNA as a screening assay for the detection of colorectal cancer in the early stages.

• miRNAs can also be used to determine prognosis in cancers based on their expression level. For example, a study on non-small-cell lung carcinoma determined that a low level of miR-324a levels is an indication of poor prognosis. In colorectal cancer, a low level of miR-133b and high level of miR-185 is linked with metastasis resulting in poor prognosis.

c)       Heart Disease

• Studies have found that there are specific changes in the expression levels of miRNAs in diseased hearts which points to the involvement of miRNAs in cardiomyopathies.

• miRNAs can also be used to determine the prognosis and risk stratification of cardiovascular diseases.

• In animal models, miRNAs have been associated with the regulation and metabolism of cholesterol.

d)      Nervous System

• miRNAs are thought to be involved in the function and development of the nervous system.

• Neural miRNAs such as miR-124, miR-132 and miR-134 are involved in dendritogenesis.

• Other neural miRNAs are involved in the formation of the synapses. miR-134 and miR-138 are thought to be included in the process of synapse maturation.

• Studies have found that conditions such as bipolar disorder, schizophrenia, anxiety disorders, and major depression have altered miRNA expression.

e)      Obesity

• miRNAs have a vital role in the differentiation of stem cell progenitors into adipocytes. Studies have found that the expression of miRNAs 155, 221, and 222 can inhibit adipogenesis paving a possible genetic treatment for obesity.

• miRNAs of the let-7 family was found to accumulate in tissues as aging occurs. Based on animal models, the excessive expression of let-7 class miRNAs resulted in accelerated aging, insulin resistance, and therefore increases the risk of obesity and diabetes. When let-7 was inhibited, it resulted in an increase in insulin sensitivity and resistance to high-fat-diet-induced obesity. This means the inhibition of let-7 may prevent, reverse, and cure obesity and diabetes.

Conclusion

Although miRNAs have great promise in the screening, diagnosis, treatment, and prevention of various pathological conditions, more research, and clinical trials will be needed in the study of miRNAs to further explore and discover the potential of miRNAs.

References:

1. microRNA. Wikipedia. Accessed 8/22/2018. https://en.wikipedia.org/wiki/MicroRNA#Disease

2. Blondal T, Nielsen SJ, Baker A, et al. Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods. 2013; 59(1): S1-S6.

Newborn Genetic Screening Program

What actually happens to newborn DNA samples once its been tested for genetic disorders?

In the last five decades, most babies born in the United States have unknowingly participated in a test called the Newborn Genetic Screening program. The test has been established to identify treatable genetic disorders in newborn infants. Early identification of these disorders is crucial in addressing symptoms and preventing a lifetime of disability. The test is a simple one: one small prick to the heel to collect a blood sample. With this sample doctors and nurses test for a variety of hereditary and congenital disorders. The controversy surrounding this program doesn't start until after the completion of the testing, whereby the samples are often stored in state-run biobanks.

Your or your child's DNA may have been stored and shared without your consent. Given that this has been going on since the 1960’s it is more likely than not that your samples are out there without your knowledge. Most people don't even know what the Newborn Genetic Screening test is or that they were a part of it. It’s importance and significance in identifying preventable disorders is not under question, but what happens to residual samples should be brought to light. State-run biobanks (or data repositories as the Association of Public Health Laboratories calls them) are established to store these samples and are shared with departments such as law enforcement for analysis and research. 

What is the Newborn Genetic Screening Test?

The Newborn Genetic Screening test began in the 1960’s. Back then it served to simply detect one genetic disorder, phenylketonuria. A condition that causes brain damage but, if caught early enough can be treated. Since then our knowledge of genetic disorders has improved immensely, largely due to the NGS Program. Collection of the blood sample must be completed within 12 to 48 hours after birth and can now detect between 30 and 50 genetic disorders. It is without a doubt an important and lifesaving program, and an estimated 12,500 newborns are diagnosed and saved annually. Participation in the NGS Program is a legal requirement. and therefore, parental consent is not required. However most states allow parents to “opt out” if there are religious or philosophical reasons. However hospitals do not usually inform the parents that the test will be conducted, making it challenging to opt out.

Duration and Location of DNA Storage

Your blood sample storage is different depending on state of birth. The most common practice is for it to be stored in state-run biobanks. Parental consent laws also differ for storage, in some states parental consent is necessary before storage of samples. In California for example, once tested the state retains the rights to store the samples. other states destroy the samples after six to twelve months whilst other store it much longer, ranging from 21 years to indefinitely.

How are These Samples Used?

Even though states might not use the samples, other researchers and government agencies still have access to them. It might be necessary for parents to find out what their or their children residual blood spots are used for. Residual blood spots storage can be used in the following.

a. Research purposes such as:

• Retesting the samples to confirm the screening results

• Developing new screening tests

• Developing new techniques for forensic studies

• Identification of new diseases

• Quality control purposes

• Access for those who are not biorepository lab technicians (such as those people in law enforcement)

b. Law enforcement purposes such as:

• According to a Columbia Broadcasting System (CBS) report, they discovered that a minimum of four court orders and fie search warrants were obtained for identified blood spots. One of these cases involved a request to test the residual blood spot for drugs at birth. There are also cases where coroners use these samples to help in the identification of bodies or parents who request it to prove paternity.

Most famously the issue of storing these samples was brought to light during the trial of the Golden State Killer. The DNA from the crime scene was matched by law enforcement officials with DNA from a California state-run biobank. They used an open-source genetic database, called GEDmatch to identify the killer.

Controversies

As you can imagine the NGS Program presents several opportunities for abuse. These residual blood spots are easily accessed and many issues can be raised, including: 

a)     Consent

Parents of the children are not usually informed or asked for consent to the screening. Given the nature of the information collected during this test many people are concerned with the number of loopholes that exist. In the Genetic Information Nondiscrimination Act of 2008 that exists to prevent genetic discrimination from health insurance companies. Since the screening is paid for through health insurance companies. Many fear that a positive test could very well taint a child's record and that insurance companies could use it against people in the future.

b)      Ethics

There are ethical concerns surrounding residual bloodspots. Some are concerned that residual blood spot research is a way for the government to further control its citizens and have access to not only their records but also their genetic material.

c)       De-identification

While some believe that de-identification of DNA is possible by not storing the identifying information together with the blood samples, many argue that the DNA itself is an individual’s unique code and can always be used to identify individuals.

Conclusion

The laws for residual blood spots vary depending on the state one is born in. Those concerned should read up on the state’s procedures and policies. It is also important to note that policies and laws can change with time. This means individuals concerned with what happens to DNA samples should stay up-to-date with the new policies.

Types of Biorepositories

Introduction

A biorepository is a center that functions to collect, process, store, and distribute tissue samples or specimens to support future research. These tissue samples can be sourced from humans or animals. The biorepository is responsible for maintaining the quality, accessibility, and distribution of these tissue samples.

Operations

• Upon delivery the tissue samples are recorded all information regarding the sample details are keyed into the laboratory information management system.

• Biospecimens are then processed to ensure consistency of the samples. Proper tissue preservation methodology is absolutely crucial to a biorepository.

• These specimens are then stored and held in their appropriate conditions. Sample holding boxes and freezers are sometimes used, however it depends on the storage requirements. For example Formalin-fixed paraffin-embedded tissue blocks can be stored at room temperature.

• Distribution involves retrieving the required samples from the inventory.

Standard Operating Procedures

Standard operating procedures (SOPs) are important for biorepositories as they help in the following:

• Reduce problematic variables within the samples,

• Ensure that biospecimens resemble specimens in their natural state,

• Provide standards on how operations should be conducted.

Types and Uses of Biorepositories

There are many different types of biorepositories that exist. Some help with biomarker validation, and others are integrated with registries. Most biorepositories are focused on collecting biospecimens for specific diseases. Others function to identify genetic clues that can aid in the guidance of therapeutic development. Similair to disease-focused biorepositories there are those  focused on the understanding of practices and habits. Biorepository sponsors can also vary. While some are funded as part of research to aid in the collection of specimens from participants, some are sponsored by organizations or medical centers to collect, process, and store samples from a wide variety of patients. Some biorepositories are organized by patient advocacy organizations to help kick-start research of specific diseases.

Examples

1. The Alzheimer’s Disease Neuroimaging Initiative – is a disease-focused biorepository and biomarker validation program that uses the samples and data collected from Alzheimer’s disease patients and patients with other forms of memory impairment.

2. The Health Outreach Program for the Elderly (HOPE) is a biorepository at Boston University that supports multiple studies. The HOPE registry follows up with their Alzheimer’s patients annually.

3. The United Kingdom Biobank is a biorepository with a broad focus. They aim to improve the diagnosis, treatment, and prevention of various diseases such as cancer, stroke, diabetes, heart disease, eye disorders, depression, dementia, and arthritis. In between 2006 to 2010, they managed to recruit half a million individuals between the ages of 40 to 69. Samples such as blood, saliva, and urine have been donated for analysis. These participants have also provided detailed personal information and consented to future follow up for many years to help researchers discover how various diseases develop.

4. The Autism Research Resource is sponsored by the state of New Jersey to research autism in families where more than one child is affected.

5. The Centers for Disease Control (CDC) Cell and DNA Repository use samples from transformed cell lines available through the Genetic Testing Reference Material Coordination Program. Some of the samples obtained are from diseases such as Cystic Fibrosis, Huntington Disease, Alpha Thalassemia, Fragile X syndrome, and Muenke syndrome.

6. The National Institute of Neurological Disorders and Stroke (NINDS) Human Genetics DNA and Cell Line Repository focuses on the identification of new genes that causes or contributes to conditions such as Parkinson’s disease, Tourettes syndrome, epilepsy, motor neuron disease, and cerebrovascular disease.

7. The National Institute of Aging (NIA) Aging Cell Repository utilizes cellular and molecular research to determine the degenerative mechanisms and causes of aging. They have strict diagnostic criteria with cells collected over a span of thirty years. Scientists are using these cultures to study diseases such as Alzheimer’s disease, Parkinson’s disease, Progeria, and Werner Syndrome.

8. The National Human Genome Research Institute (NHGRI) Sample Repository for Human Genetic Research successfully completed the sequencing of the human genome. They now aim to participate in a variety of studies that focuses on the understanding of the structure and function of the genome and the role it plays in disease and health.

9. The National Eye Institute Age-Related Eye Disease Study (NEI-AREDS) Genetic Repository was founded to identify how macular degeneration and cataracts develop and progress. This is important as these two conditions are two main causes of vision loss among older patients.

Conclusion

Biorepositories are crucial in supporting different areas of research such as those focused on a specific diseases, broadly focused population studies, identification of genetic mutations, and many more. These studies may have a specific length and purpose and are ongoing studies that follow up with their participants for many years.

References:

1)      Biorepository. Wikipedia. Accessed 8/9/2018. https://en.wikipedia.org/wiki/Biorepository

2)      Greenberg B, Christian J, Henry LM, et al. Biorepositories: Addendum to Registries for Evaluating Patient Outcomes: A User’s Guide, Third Edition [Internet]. Rockville (MD): Agency for Healthcare Research and Quality (US); 2018 Feb. Types and Uses of Biorepositories and Their Application to Registries. Accessed 8/9/2018. https://www.ncbi.nlm.nih.gov/books/NBK493635/

CRO Services

Introduction

A contract research organization or CRO refers to a company that provides support in the form of research. The research conducted through CRO services can be in one of the following fields:

• Biotechnology

• Pharmaceutical

• Medical device industry

In full a CRO is a company contracted by another organization to help lead and manage their trials, responsibilities, roles, and their function.

Services and Advantages

Some CRO services executed include such things as, but not limited to:

• Biologic assay development

• Biopharmaceutical development

• Commercialization

• Preclinical and clinical research

• Management of clinical trials

• Database design and building

• Data entry and validation

• Medicine and disease coding

• Quality and metric reporting

• Statistical

• Pharmacovigilance (the identification, detection, assessment, observation, and prevention of side effects of pharmaceutical products)

CROs are useful for companies when developing new drugs and medications as they reduce costs. CROs are able to simplify the development of new drugs and entry into drug markets. They also support governmental organizations, foundations, universities, and research institutions. CROs can range from small specialty groups to large international organizations. They aim to provide support for clinical studies and trials. Those that specialize in clinical trials services of a new drug are present from its conception until it is approved by the Food and Drug Administration (FDA) or by the  European Medicines Agency (EMA). Evidently CROs play a crucial role and pharmaceutical companies are continually outsourcing critical functions such as research and manufacturing to CROs.

The number of major corporations that are using CROs in clinical trials and the development of new drugs is increasing. Companies that establish contract with CROs aim to acquire the required expertise without having to hire permanent staff, keeping overhead low. Some CRO trade groups have claimed that contracting with CROs has helped reduce the cost by decreasing the time it takes to conduct a trial. This also means that the company that hires a CRO will not need the required infrastructure, manpower, and office space to conduct these trials. Some CROs can even manage all the aspects in a clinical trial starting from the site and patient selection all the way up until the final regulatory approval.

Regulatory Aspects

The International Council on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human use (ICH) defined CROs as “a person or organization contracted by the sponsor to perform trial-related duties and functions”. Their guidelines highlight the following:

• A sponsor can transfer all their duties and function to a CRO. However, the hiring company will be responsible for the integrity of data acquired from the CRO conducted study. It remains the hiring company’s responsibility to ensure that all the data is factual and backed by science.

• CROs should ensure quality control and quality assurance.

• All duties and functions transferred to a CRO should be in writing. The hiring company should oversee the duties and functions that are carried out on their behalf.

• Duties and functions that are not transferred to a CRO will remain with the sponsor.

Market Size and Growth

The Association of Clinical Research Organizations has estimated that more than half of clinical studies conducted by the pharmaceutical industry have been outsourced to CROs. The most popular field for CROs is therapeutic work including infectious disease, oncology, central nervous system, cardiovascular disease, and metabolic disorders. A further 27% work for within the biotechnology field while the remainder work for governments, foundations, and the medical device industry. The CRO sector is doing extremely well for an industry that just started a decade ago. There is increasing pressure facing medical devices organizations and pharmaceutical companies for the high cost of drugs and they are trying to lower costs without decreasing their profits. One of the best and most common solutions is to outsource clinical trial management as it results in significantly lower overhead costs.

By the year 2013, there were more than 1,100 CROs globally. However, there are many CROs that have gone out of business or that have been acquired. In 2008, it was estimated that the top 10 companies control 56% of the market. A 2007 estimate showed that the market would reach $24 billion in 2010 with a growth rate of 8.5% from 2009 to 2015. In 2016, the research and development spending increased by 15.5% from 2015 to 2020.

Conclusion

CROs are an effective solution as it provides an affordable option for companies to pursue the development and approval of new medication. Before the existence of CROs, this was a hugely expensive endeavor which was only embarked on when the likely hood of regulatory approval was high. With CROs, companies are now able to develop drugs for specific markets.

References:

1. Contract research organization. Wikipedia. Accessed 7/30/2018. https://en.wikipedia.org/wiki/Contract_research_organization

2. Stone K. Contract research organizations (CRO) definition. The Balance. Accessed 7/30/2018. https://www.thebalance.com/contract-research-organizations-cro-2663066

Ethics in Biobanking

Introduction

Biobanking ethics are important and one of the most debated issues in public health and bioethics. Biorepositories carry the potential to advance disease research in unprecedented ways. There are however concerns about donor privacy and not all biorepositories make sure that they follow ethical standards. People’s DNA and tissue sample has been used without respect for their rights. Regardless of peoples differing views and perspectives, one thing can be agreed upon among most experts, that biobanks are revolutionary. Biobanking ethics include issues such as, but not limited to:

• Controversies and key challenges faced in biobanking ethics

• Issues of informed consent

• Withdrawal from participants

• Broad consent

• Ethics of re-contact

• Confidentiality issues

• Ownership, property and commercialization problems

Issues in Brief

1)      Informed Consent

Informed consent is crucial in ensuring that ethical standards are followed in both research and therapy. It ensures that the participant understands “the nature, duration, and purpose of the experiment; the method and means it is to be conducted; all inconveniences and hazards reasonable is to be expected; and the effects upon the individual’s health may be due to the participation in the experiment." (Excerpt from Springer Article) One of the major issues of informed consent in biobanking is that it only applies to the donor and not those who are connected to the donor. Next, since biospecimens can be used in future studies, participants cannot be “informed” at the time their tissue is obtained as the nature of future researches are not yet known.

2)      Broad Consent

There are some experts who believe that broad consent can be a potential solution to the issues of informed consent in biobanking. However, there are some who disagree as it offers minimal protection and minimal guarantees. Broad consent is the permission given by the donor for the biobank, so the biorepository can do what they see fit with the genetic material. While some individuals argue that broad consent is a means of maximizing autonomy, some see it as the opposite where it is an abuse for autonomy. Ethicists worry that broad consent causes donors to relinquish their rights regarding how their genetic material is used in the future.

3)      Confidentiality

One of the main features of genetic information is that it can be used to identify the donor and those related to them. While ethicists argue that identification can be discouraged through various methods of anonymization, there is always the possibility that identification is possible. The risk of identification increases as databases grow.

4)      Property and Profit

There is also the issue that participants or donors do not own their tissue samples. This is based on the traditional understanding that body parts are res nullius which means that they do not belong to anyone once detached. Ethicists have argued that there are valid reasons for following the “no property” rule for biospecimens. Allowing property would restrain studies and research to the point where it would become untenable. Another issue is that commercial companies may look to make very large profits from donated samples.

5)      Feedback to Participants

Another ethical issue is whether or not to tell participants regarding incidental findings from their donated tissue samples. Incidental findings can be defined as “observations of potential clinical significance that have been discovered unexpectedly in a healthy subject unrelated to the purpose and variables of the study.”(Excerpt from Springer Article)

6)      Participation, Representation, Maintenance of Trust

Biorepositories are also worried about the mass withdrawal of participants as it will ultimately result in the loss of set-up costs. The maintaining of trust between the public and biobanks are crucial to prevent participant withdrawal and biobank failure. Currently, there is still no one way that is viewed as the best method of practice in this area.

7)      Re-contact

Re-contact is becoming an increasingly crucial issue as there is very little industry conformity on how re-contact should be managed. There needs to be a balance between what donors are informed and what's included without overburdening them. Biorepositories and research teams should view the ability to re-contact as a limited resource. Currently, there is no standard that biobanks can look to adopt for this issue.

Conclusion

The problems and challenges in biobanking ethics mean that there is a need for alternative models to address the issues. Biobanking presents important and significant ethical challenges. It is important for those involved to be aware of the advancements and developments in the debates surrounding these issues. By raising awareness of these issues, public interest of will increase and as a result biobanking can continue to change the medical research landscape.

References:

Widdows H, Cordell S. The ethics of biobanking: key issues and controversies. Health Care Anal. 2011; 19:207-219.

Tissue Procurement Problems

Introduction

Formalin-fixed paraffin embedded (FFPE) tissue blocks are a valuable resource for many significant research programs as researchers tend to select this type of biospecimen as frozen or fresh tissue blocks may be harder to acquire. There is also the challenge that the number of fresh frozen tissue samples may not be able to fulfill the requirements of the research protocol. The FFPE preservation technique demands a fast and rapid fixation after the process of resection of the target biospecimen in a neutral buffered formalin. Once fixed, the specimen is then embedded in paraffin wax. FFPE is now the commonest tissue preparation method used to archive research biospecimens. Currently, almost all surgeries in this day generate FFPE tissue samples. FFPE tissue blocks are crucial as they offer the potential for the discovery of significant information especially in biomedical research programs and drug discovery. Other research applications that utilize FFPE biospecimens include:

• genetic studies

• biomedical identification or authentication

• visualization of tissue structure

This, therefore, makes FFPE tissue blocks ideal for:

• the study of autoimmune diseases – rheumatoid arthritis, systemic lupus erythematosus

• the study of long-term cancers – colon cancer, lung cancer, breast cancer

Challenges

However, there are several challenges that researchers face when it comes to obtaining FFPE tissue samples. Some of the challenges include:

1)     Oversight of the Pathologist

In some cases, the FFPE samples are not obtained or processed appropriately as the certified pathologist is not on site to supervise and ensure that the proper procedures are followed during the procurement of the specimen. Biorepositories should ensure that they hire enough licensed pathologists to ensure that there is no manpower shortage as it could impact the quality of their tissue specimens.

2)     Difficulty Acquiring Samples

There are certain situations where a research team or company requires access to FFPE tissue samples that are hard to come by. For example, FFPE samples from patients with metastatic melanoma might present a challenge to biorepositories. Research teams should partner with a biorepository that has a vast network for tissue procurement as it can help tremendously in the collection of special samples needed in specific research protocols.

3)     Rapid Turnaround

Studies or research that needs a quick procurement of FFPE tissue blocks may pose a challenge to many biorepositories. These research teams that are looking for a rapid turnaround of samples should ask biorepositories about their accelerated procurement method which may then be able to provide the required biospecimens within the time frame.

4)     Transparency

Research teams looking to procure tissue samples need to keep in mind about transparency as studies rely on well-annotated tissue blocks that go through the proper fixation and preservation technique. Before obtaining samples from the biorepository, be sure to ask regarding their specifics and standard of procedure for the fixation and quality assurance protocols. This can impact the result and credibility of the entire study.

5)     Review of FFPE Biospecimens

Some biorepositories obtain their tissue samples from local sources such as the local hospitals. However, not all providers take the time to ensure that the specimens are of the highest quality. Biorepositories are responsible to ensure that a gross and microscopic examination of the FFPE biospecimens to ensure that the samples obtained are of the highest quality.

6)     Sourcing

With the growing number of organizations and biorepositories, research teams that are looking to source biospecimens should consider companies that follow the best practices and have high standards when it comes to their collection and fixation protocols. Unreliable sources may not be able to provide high-quality FFPE tissue samples. Before procuring the required biospecimens, enquire where the organization obtains their samples and the reliability of it.

7)     Patient Information

The patient information from the samples can be valuable and crucial in a research. The more information you can obtain regarding the patient from their data, it can help with some of the results from the research especially in terms of demographics and risk factors of a disease. Patient information also helps you to find the correct patient cohort as some study designs exclude those below or above a certain age. It is therefore important to procure the biospecimens from a biorepository that can provide the necessary data such as the details or a refractory disease, metastatic diseases, or newly diagnosed disease. A new case of cancer or a relapse can also affect the results of a study greatly.

Conclusion

In conclusion, there are many factors to consider when it comes to selecting a new biorepository or organization to partner with to obtain tissue samples. It is important as these specimens ultimately determine the results and credibility of the study. Choosing a credible company that provides the highest quality FFPE tissue samples is one of the most crucial steps in the early stages of a study. Low-quality biospecimens result in wasted hours of study, effort, and decreases the overall morale of the research team.

References:

Doiron L. Typical problems with FFPE tissue samples – and how to solve them. 2014. Folio Conversant. Accessed 7/11/2018. 

https://www.conversantbio.com/blog/bid/387449/Typical-Problems-with-FFPE-Tissue-Samples-And-How-to-Solve-Them

Tissue Microarray

Introduction

The recent advances that have occurred in the human molecular genetics field have found that there are gene-based disease mechanisms in various areas of medicine. Studies regarding diagnostic and prognostic markers in many clinical specimens is vital in the translation of new findings from basic science to applications in clinical practice. With the increased use and advancements of new molecular biology methods, the research of progression and pathogenesis of diseases such as cancer are now revolutionized. Understanding the basic molecular mechanisms in the progression of normal tissues to cancerous or malignant tumors is crucial in the knowledge of the disease as it can lead to improved treatment, diagnosis, and cures. Some clinical studies have discovered various novel markers at the gene level where validation of these markers is necessary. However, it can be a time consuming, costly, and labor-intensive process especially if tested on several specimens.

Tissue Microarray

Tissue microarray is a method used in the field of pathology to overcome issues where the validation of markers is:

• Time-consuming

• Costly

• Labor-intensive

It can be used to organize small amounts of tissue samples on a solid support. It is a method designed to allow the:

• Simultaneous assessment of gene expression on hundreds on tissue samples

• Parallel molecular profiling of tissue samples at DNA, RNA, and protein level

• Analysis of samples using fluorescence in situ hybridization (FISH), immunohistochemistry, and RNA in situ hybridization at lower costs and less time

Tissue Microarray Construction

Tissue microarrays can be constructed using composite paraffin blocks through the extraction of cylindrical core biopsies from donor blocks which are them embedded into a microarray or recipient block at specific array coordinates. Donor blocks are first retrieved and sectioned to produce the standard slides. These slides are then stained with hematoxylin and eosin. Once ready, the slides are examined by a certified pathologist who then marks the area of interest (usually an area with pathology such as cancer). Next, the samples can be arrayed. A tissue core can be acquired from the donor block using a tissue microarray instrument. This tissue core is then inserted into an empty recipient or paraffin block at a specific coordinate which is recorded on a spreadsheet. The sampling process is then repeated as many times as necessary from various donor blocks until many cores are placed in one recipient block. This results in the final tissue microarray block. A microtome is utilized to cut 5-micrometer sections from the blocks to produce slides necessary for immunohistochemical and molecular analyses.

Applications and Advantages

Tissue microarrays have many advantages over other techniques. Some of it include:

1. Amplification of a scarce resource – After a standard histological section that is approximately 3 to 5 millimeters thick is used in primary diagnosis, the sections can further be cut 50 to 100 times yielding a total of 100 assays. In tissue microarrays, instead of 50 to 100 samples, it can produce material enough for 500,000 assays.

2. Simultaneous analysis – Tissue microarrays allows the simultaneous analysis of many specimens as it provides high throughput data acquisition.

3. Uniformity – In tissue microarrays, every tissue sample is treated uniformly. It can also be used in a variety of techniques such as fluorescent or chromogenic visualization, histochemical stains, tissue microdissection techniques, and more. Tissue microarray enables the analysis of the entire cohort on one slide standardizing the variables such as incubation times, antigen retrieval, washing procedure, reagent concentration, and temperature.

4. Time and cost efficient – The tissue microarray method require small amounts of reagents for analysis. It is a method that is both time and cost efficient.

5. Conservation of tissue samples – Tissue microarray is a technique that does not destroy the original block of the tissue sample.

Tissue Microarrays from Fresh Frozen Tissue

In tissue microarray, the method uses tissue samples from paraffin-embedded tissue donor blocks that are then placed into a recipient block. One of the challenges with paraffin-embedded tissue is the antigenic changes seen in proteins and degradation of mRNA due to the fixation and embedding process. Some researchers have modified the tissue microarray technique by using fresh frozen tissue that is embedded in optimal cutting temperature (OCT) compound. It is then arrayed into a recipient OCT block. Tissue samples are not fixed before the embedding process and the arrayed sections are assessed without fixation. The advantage of tissue microarrays from fresh frozen tissue is that:

• It works well for DNA, RNA, and protein analyses.

• Paraffin-embedded tissue arrays can be challenging for RNA in situ hybridization and immunohistochemistry analyses but tissue microarrays from fresh frozen tissue allow the optimal assessment by each technique.

• It has uniform fixation throughout the whole array panel.

• It is a technique that may have significant advantages in the assessment of certain genes and proteins as it improves both quantitative and qualitative results.

References:

1)      Jawhar NMT. Tissue microarray: a rapidly evolving diagnostic and research tool. Ann Saudi Med. 2009; 29(2): 123-127.

2)      Fezjo MS, Slamon DJ. Tissue microarrays from frozen tissues – OCT technique. Methods Mol Biol. 2010; 664: 73-80.

What are FFPE Samples

What is Formalin Fixed Paraffin Embedded Tissue?

Formalin fixed paraffin embedded or FFPE tissues are valuable for both therapeutic applications and research. FFPE is a specific technique used to prepare and preserve tissue specimens utilized in research, examination, diagnostics, and drug development. Tissues are first collected from both diseased and non-diseased donors. The tissue specimen is first preserved through a process called formalin fixing. This step helps to preserve the vital structures and protein within the tissue. It is then embedded into a paraffin wax block and sliced into the required slices, mounted on a microscopic slide, and examined.

The FFPE Process

The process starts by a specimen being selected and then excised from a donor or patient. Samples can also be obtained from other animals such as snakes, mice, or many others. After excision, the tissue is immersed for approximately eighteen to twenty-four hours in a 10% neutral buffered formalin. The tissue is then dehydrated using increasing concentrates of ethanol. Next, the tissue is embedded into paraffin to become FFPE blocks. The methods utilized are dependent on the requirements of the researcher or physician who is requesting the FFPE samples. Specifications about how the issue is cut, size, and purpose of the tissue are all important. Once the procedure is complete a certified pathologist will  evaluate the quality of the specimen.

Storage of FFPE Tissue

FFPE samples can be stored in hospitals, biobanks, and research centers. Storage facilities often keep records of how the tissue was collected, the preservation procedures, and demographic information (such as, but not limited too: the origin, duration, age, ethnicity, gender, and stage of disease) of the donor. The demographic information is an important factor in research and in clinical trials. FFPE samples that are properly preserved are very valuable and can be stored at room temperature for a long period of time.

Applications

FFPE samples are important as they are often used in:

a)       Immunohistochemistry

The sectioned FFPE specimens are mounted on a slide, bathed in a solution containing antibodies, and then stained so that they can be more clearly seen. This method is important for physicians and researchers looking for pathology in the tissue such as Alzheimer’s or cancer.

b)      Oncology

FFPE samples are vital in the field of oncology as tumor tissues have characteristic morphologies allowing researchers to look for certain proteins. These proteins are then used to help in the assessment of treatment and diagnosis.

c)       Hematology

In the study of blood and its disorders, FFPE samples are important in determining the anomalies and discovery of cures. The specimens can be used in studies related to tissue regeneration, genetics, and toxicology.

d)      Immunology

FFPE samples from a donor with autoimmune disease helps in determining the cause and development of therapy for the condition.

Complications or Limitations

One of the possible limitations of the fixation process using formalin is the potential denaturation of the proteins that are present in the tissue making them undetectable to antibodies. To compensate for this issue, antigen retrieval techniques were developed. The antigen retrieval technique specifically recovers DNA, RNA, and proteins from FFPE samples. For this method to work, the quality of FFPE samples are critical. There is also the issue that there is no standard procedure to be used in the preanalytical processing such as fixation and DNA isolation. This means that minor differences such as the different use of instruments, sample handling, and methodology can result in variation that affects the quality of DNA and study results. Some of the factors that have been found to affect study results from FFPE samples are:

1. Inaccurate logging of fixation protocol

2. Variation in fixation time

3. Temperature during fixation

4. Storage conditions of FFPE samples

Quality Control

To ensure the highest quality of FFPE samples, those who collect and store these samples should:

1. Follow ethical and legal standards.

2. Keep a clear and accurate record of donors.

3. Provide information regarding the sampling and collection process

4. Be supervised by a licensed pathologist during the collection of samples

5. Have a complete chain of custody

6. Work only with a carefully selected network of distributors that consistently provide high quality and accurate samples

Fresh Frozen Tissue

Fresh frozen tissues are specimens that are preserved using liquid nitrogen through a method known as “flash freezing”. These specimens are then stored in a freezer that is set at a temperature of less than -80 degrees Celsius. Fresh frozen tissue has different applications than  FFPE samples as they can be used in native morphology studies or molecular analysis as well.

FFPE Samples Vs. Fresh Frozen Tissue

FFPE and fresh frozen tissue have their pros and cons. They are two different types of samples that have different uses dependent on the requirements of the research or clinical study. 

1. FFPE blocks are very hard and can be easily stored at room temperature for decades without the need of special equipment making the type of tissue sample very cost efficient.

2. There is a large archive of FFPE samples available for researchers due to the easiness associated with it storage.

3. FFPE specimens have been used for decades making it incredibly familiar to pathologists.

4. Fresh frozen tissue is much more suitable for the analysis of native proteins, polymerase chain reaction, and next generation DNA sequencing.

5. Fresh frozen tissue ensures the preservation of DNA, RNA, and native proteins.

6. Fresh frozen tissues require specialized equipment for storage. This means mechanical failure, power outages, and carelessness can affect the quality of the samples.

References:

1)      Ward T. The importance of proper formalin fixation of FFPE samples. Personalis. Accessed 6/19/2018. https://www.personalis.com/importance-proper-formalin-fixation-ffpe-specimens/

2)      Doiron L. 5 quality control rules for cancer tissue banks. Folio Conversant. Accessed 6/19/2018. http://www.conversantbio.com/blog/bid/339034/5-Quality-Control-Rules-for-Cancer-Tissue-Banks

3)      FFPE vs frozen tissue samples. BioChain. Accessed 6/19/2018. https://www.biochain.com/general/ffpe-vs-frozen-tissue-samples/

4)      What is FFPE tissue and what are its uses. BioChain. Accessed 6/19/2018. https://www.biochain.com/general/what-is-ffpe-tissue/

Cancer Therapy

Thanks to extended research from human tissue samples we have been able to make major breakthroughs in cancer research. In the twenty-first century, evidence, both epidemiologically and clinically, have supported that the changes in whole-body metabolism can affect oncogenesis, the progression of tumors, and the response of tumor to therapy. It has been observed that metabolic conditions such as hyperglycemia, obesity, hyperlipidemia, and insulin resistance are associated higher with risk of cancer development, accelerated progression of tumors, and poor clinical outcome. Due to these findings, many clinical studies indicate that statins and metformin may help in decreasing cancer-related mortality and morbidity. Phenformin is another drug used to treat diabetics that can help with anticancer effects. However, phenformin was discontinued in the late 1970s due to a high incidence of lactic acidosis. Metformin is the most commonly used antihyperglycemic agent globally. It has an optimal pharmacokinetic profile with:

·         50 – 60% of absolute oral bioavailability

·         Slow absorption

·         Negligible binding to plasma protein

·         Broad tissue distribution

·         No hepatic metabolism

·         Limited drug interactions

·         Rapid urinary interaction

It also has an exceptional safety profile as there is a low number of individuals who have side effects. Statins also have a great safety profile and is currently used by a large population.

Cancer and Cellular Metabolism

The accumulation of evidence has suggested that malignant transformation is linked to changes that affect several factors of metabolism. Metabolic rearrangements associated with cancer have been linked with the inactivation of tumor suppressor genes and activation of proto-oncogenes. However, the accumulation of metabolites such as fumarate, succinate, and 2-hydroxyglutarate (2-HG) drives oncogenesis through the signal transduction cascades. Conclusively, these observations support the notion that signal transduction and intermediate metabolism are associated.

a)       Oncogenes and Metabolism

The signaling pathways from oncogenic drivers are linked to metabolic alterations due to cancer. For example, the expression of the PKM2 (an M2 isoform of pyruvate kinase) encourages the alteration of glycolytic intermediates in the direction of anabolic metabolism while regulating both transcriptional and post-transcriptional program that leads to the addiction of glutamine.

b)      Oncosuppressors and Metabolism

There are some oncosuppressor proteins that can regulate cellular metabolism. The inactivation of tumor suppressor p53 happens in more than 50% of all neoplasms causes a variety of metabolic consequences that could potentially stimulate the Warburg effect. P53 can possibly suppress the transcription of GLUT4 and GLUT1 and stimulate the expression of apoptosis regulator (TIGAR), TP53 induced glycolysis, SCO2, glutaminase 2 (GLS2) and many other pro-autophagic factors. It also interacts physically with glucose-6-phosphate-dehydrogenase (G6PD) with RB1-inducible coiled-coil 1 (RB1CC1).

c)       Oncometabolites and Oncoenzymes

It was found that metabolites can contribute to oncogenesis when mutations such as fumarate hydratase (FH) and succinate dehydrogenase (SDH) was linked to sporadic and familial types of cancer including pheochromocytoma, leiomyoma, renal cell carcinoma, and paraganglioma. once the enzymatic activity of SDH and FH is disrupted, succinate and fumarate accumulate resulting in oncogenesis.

Targeting Cancer Metabolism

The metabolic targets for cancer therapy rewiring of cancer cells is seen as a promising source for new drug targets. Some different approaches have resulted in the identification of agents that can help with targeting glucose metabolism for cancer therapy. However, the low number of metabolic inhibitors reflect the recent rediscovery of the field. There are also some concerns about the uniformity between malignant cells and non-transformed cells that are undergoing proliferation.

a)       Targeting Bioenergetic Metabolism

Some cancer-associated alterations such as the Krebs cycle, glycolysis, glutaminolysis, mitochondrial respiration, and fatty acid oxidation have been studied as potential sites for drug therapy.

b)      Targeting Anabolic Metabolism

The anabolic metabolism in cancer cells increases the output from nucleotide, protein, and protein biosynthesis pathways to help with the generation of new biomass in rapidly proliferating cells (includes both normal and malignant). A high metabolic flux through the pentose phosphate pathway is vital to cancer cells as it generates ribose-5-phosphate and nicotinamide adenine dinucleotide phosphate (NADPH).

c)       Targeting Other Metabolic Pathways

Other pathways involved in the adaptation to metabolic stress may provide drug targets for cancer therapy. This applies to autophagy, hypoxia-inducible factors 1, and nicotinamide adenine dinucleotide metabolism. A competitor of nicotinamide phosphoribosyltransferase (NAMPT) known as FK866 has been observed to have antineoplastic effects in murine tumor models.

Conclusion

The extensive metabolic rewiring in malignant cells provides a large number of possible drug targets. Many agents that target metabolic enzymes are used for decades while others are being developed. Therefore, the use of metabolic modulators that could be complicated by the similarities of highly proliferating normal cells and metabolism of malignant cells, there might be a chance to harness the antineoplastic activity of these drugs clinically. While many efforts were focused on merging metabolic modulators and targeted anticancer drugs, there may be a common view that metabolism and signal transduction are mostly independent if not separate entities. More research is needed to study the extent of how the metabolic functions of oncosuppressive and oncogenic systems contribute to the biological activity.

References:

Galluzzi L, Kepp O, Vander Heiden MG, Kroemer G. Metabolic targets for cancer therapy. Nature Reviews Drug Discovery. 2013; 12: 829-846.