Optimizing Your Sample Handling and Management
Optimizing Your Sample Handling and Management
Sample management in the laboratory can be complicated. Procedures for such management vary significantly depending on the identity of the samples, which can include:
I. Biological samples, referring to samples that have been collected from biological sources, both human (e.g. blood, urine, saliva) and non-human (fungal, bacterial, mammalian, etc.).
II. Environmental samples, referring to samples that have been collected from the environment such as rainwater, soil, or snow.
III. Chemical samples, referring to samples consisting of chemicals, which can be air-sensitive, moisture-sensitive, light-sensitive, or any combination of the above.
IV. Radioactive samples, referring to samples that are known - or suspected - to contain radioactivity.
V. Samples that fit into more than one of the categories listed above, or samples that do not fit into any of the above categories, such as chemical samples that are radioactive, environmental samples that contain biological sources, and nanomaterial-containing samples.
The first step in understanding how to manage these samples is to identify what categories they fall into, which in turn dictates particular areas of concern for managing and working with such samples. As such, this guide for sample management will be divided based on sample type. For samples that fit into more than one category, one must consider and follow the procedures for all the relevant categories.
I. Biological Samples
(a) Safety clearance at the institution for working with biological samples. Individuals working with biological samples can potentially be exposed to a broad range of toxicants from this work, especially in cases where the biological samples are contaminated or can be contaminated with pathogens. As a result, most institutions have developed required training for individuals working with biological samples, to limit their potential exposure to such biological pathogens. This training is in addition to standard training required to work with chemical samples, and includes instruction in how to decontaminate surfaces before and after usage, properly dispose of biological samples, and handle them in a way that minimizes risk.
(b) Institutional review board procedures for collecting biological samples following ethical, approved guidelines. Collection of biological samples, especially from human sources, often requires pre-approval from an Institutional Review Board, or IRB, prior to collection. The procedure of obtaining IRB approval is designed to prevent research misconduct and is a crucial step any time biological samples are being collected. IRB approval is also often required to work with pre-collected samples.
(c) Collection of samples using sterile equipment. Collection of biological samples must be done in a way that does not introduce exogenous contamination. Even handling the samples with ungloved hands can be sufficient to introduce undesired contamination, so every individual who collects and/or handles such samples should take all precautions to avoid such contamination. Moreover, the equipment used for collection (urine collection cups, plasma collection bags, etc.) must also be sterilized prior to use to ensure that biological contamination is not present in any measurable quantities.
(d) Storage of samples under proper conditions. Once the samples are collected, it is critical to ensure that they are properly stored so that they do not degrade prematurely, and are not contaminated by processing or by storage conditions. This generally means storing them at cold temperatures, in sealed containers, and with protection from air, light, and moisture. This also means clear labeling of the samples, with enough information to identify the contents, so as to ensure that other people do not mistakenly open the sample and contaminate it. Proper labeling also limits the number of times that the sample needs to be opened in general, and provides guidance for other laboratory members in the event that the original sample collector is unavailable or incapacitated.
(e) Careful disposal procedures for biological sample waste. These disposal procedures are generally developed in consultation with institutional safety protocols, and need to be approved as part of biological sample-specific safety training and/or IRB procedures. Waste disposal procedures are designed to ensure that all individuals who will handle the waste stream are aware of the biological contents of the waste stream and of the potential for biological pathogens to exist in the stream. This also ensures that biological samples are not kept longer than needed for study protocols, so that confidentiality of data and of participant-identifiable data is preserved. Such procedures also usually include the need to decontaminate all areas of the laboratory with a bleach solution after working with biological samples, which helps other members of the laboratory from being inadvertently exposed to pathogens.
II. Environmental Samples
(a) Safety clearance at the institution for working with environmental samples. Environmental samples, or those that have been collected from a variety of environmental sites, have the potential to include significant concentrations of toxic chemicals, biological pathogens, and other harmful substances. In order to handle such samples, all individuals need to obtain institution-specific safety training. This training is generally administered by an Office of Environmental Health and Safety, but can also be administered through a general public safety office at the institution. Topics covered in this training include the use of personal protective equipment for individuals handling environmental samples, and can also include information about engineering controls (fume hoods, safety cabinets, separate air flow systems) that help to ensure that individuals are protected from harm in their handling of environmental samples.
(b) Collection of samples using equipment and procedures that will not introduce exogenous contamination. Much like the improper handling of biological samples has the potential to introduce undesired contamination from exogenous sources, improper handling of environmental samples can introduce analogous contamination. For example, an individual handling biological samples who is not properly trained may use dirty hands to handle samples; subsequent analysis of the samples that reveals such dirt may wrongly conclude that the dirt originated from the original collection site rather than from improper sample handling.
(c) Storage of samples under proper conditions. Many compounds that are present in environmental samples are known to have significant light, temperature, and humidity sensitivity. The ability to control exposure of the samples to such parameters will have critical import in ensuring that sample analysis is accurate and that the samples remain stable for the duration of analysis. As such, in the absence of explicit knowledge that samples ARE NOT sensitive, one should assume sensitivity to all of the above parameters and should store samples under inert atmosphere (i.e. nitrogen gas-filled vials), in cold environments (i.e. laboratory refrigerator or freezer), and protected from light (i.e. by covering vials with foil to avoid unnecessary light exposure).
(d) Analysis of samples in a way that does not introduce contamination from sample handling. Samples should be removed from their protective environment only for the time necessary to conduct such analysis, and should then be properly returned. This ensures minimal exposure to light, air, elevated temperatures, and humidity, and will help ensure that the samples are stable for the duration of time necessary to conduct such analysis. Moreover, individual handling of such samples should be done using proper protective equipment, including laboratory safety gloves, laboratory goggles, use of a laboratory coat, and handling of all samples only in a functioning fume hood. These precautions will protect both user and sample.
(e) Proper disposal procedures of environmental samples. Disposal procedures may be individualized to the particular environmental samples and the composition of such samples. For example, dirt contaminated with toxic waste from an illegal industrial disposal site will likely require more stringent disposal procedures than river water collected to analyze the contents and assess overall marine health. The more information that is known about sample composition, the more accurate and personalized disposal procedures can be. In the absence of such knowledge, extreme care must be taken, as individuals may be handling samples with significant amounts of highly toxic substances.
III. Chemical Samples
(a) Safety clearance at the institution for working with chemical samples. Chemical samples can contain compounds that are carcinogenic, or known to cause cancer, through handling, touching, or inhalation. Certain compounds are also known or suspected teratogens, or compounds that cause birth defects in infants born to people exposed to the compounds; mutagens, or compounds that are known to cause significant mutations; or have other toxic effects not specified above. As a result, these samples require significant training from the institution prior to usage, so that individuals understand how to handle compounds in a way that minimizes their exposure risk.
(b) Engineering and personal controls to minimize safety risk to the sample handler. Individuals who are handling chemical samples can be exposed to the chemicals through inadvertent skin contact with the chemicals, through inhalation of chemical powders and/or vapors, through puncture wounds from syringes and needles that are contaminated with the chemicals, or through other mechanisms not specified above. Although many chemicals are generally recognized as safe and display no significant health risks from such exposure, there are chemicals with significant associated toxicities that are used in the laboratory for a variety of reasons.
To minimize the safety risks associated with handling such samples, a variety of personal controls and engineering controls have been implemented. Personal measures include the fact that individuals are usually advised to wear laboratory gloves and an approved laboratory coat, which minimizes the risk of inadvertent skin contact with the chemicals. Safety goggles are often recommended as well, to minimize the risk of inadvertent splashing of a liquid sample in the eyes of the individual working with the samples. Of note, these goggles come in many forms, including over-ear glasses and full goggles. They can also include prescription-strength goggles that enable vision-impaired individuals to receive significant eye protection. Importantly, regular eyeglasses do not provide sufficient protection for chemical sample handling as liquid samples can easily go under the eyeglasses and into the individual’s eyes.
Engineering controls for handling of chemical samples include the use of fume hoods, which provide air flow away from the user that minimizes exposure to chemical vapors. Note that fume hoods generally need to be checked on a regular basis, to ensure that the air flow is sufficient to eliminate vapor exposure risks, and that excess clutter in the fume hood can partially block the air flow and reduce the efficacy of this important engineering control. Other engineering controls include using automatic locking of rooms, to prevent individuals from inadvertently walking into a contaminated area, as well as clear signage that indicates the areas in which chemical samples are being handled.
(c) Specialized procedures for air- and moisture-sensitive samples. Chemical samples that are sensitive to air and moisture require significant additional precautions, so that such chemicals are not exposed to these elements which can harm the samples, destroy their efficacy, and/or cause adverse reactions such as fires or explosions. Fire from the inadvertent exposure of air-sensitive chemicals to air has been reported multiple times, and can lead to significant injury or even death to the handler of the samples.
(d) Special procedures for chemical samples that are explosion hazards. Samples that are explosion hazards include perchlorate salts, aromatic nitro compounds such as 2,4,6-trinitrotoluene (TNT) and 2,4-dinitrotoluene (DNT), ammonium nitrate, and other organic and inorganic chemicals. Specialized procedures for the handling of explosion hazards includes use of blast shields to protect researchers from possible explosions, strong limits on the quantities of chemicals that can be handled at any one time, to minimize the scale of any potential explosion, and methods to ensure that all researchers are aware that a chemical is a potential explosion hazard, such as through the use of proper labeling and prominent symbols.
(e) Proper disposal procedures for all chemical samples. All chemical samples need to be disposed of after use in a way that minimizes risk to people who handle the chemical waste further downstream, minimizes risk to researchers through ensuring that incompatible chemicals are not inadvertently mixed, and minimizes the exposure of populations to toxic chemicals, through ensuring that these samples are not poured down the drain, dumped in a river, or otherwise released into a common site. This includes clear labeling of all waste containers, including the use of full chemical names rather than chemical abbreviations. All incompatible chemicals are to be stored in separate waste containers, with clear labeling indicating the contents of the waste containers. Moreover, secondary waste containers are commonly used, which generally consists of a separate bucket or basin that can hold the volume of liquid waste in the event that the first container leaks or spills. Chemical sample waste should be placed in properly marked containers, and handled only by properly trained professionals.
IV. Radioactive Samples
(a) Safety clearance. Radioactive samples are those that contain substances that emit, or give off, radioactivity. Some examples of such substances include heavy metals like uranium, which emits radioactivity as it degrades. Other heavy atoms such as cesium and iodine also emit radioactivity. Handling of radioactive samples requires particular training to minimize the risk of inadvertent harm to the individual handling such samples, and includes behavior controls such as the need to wear significant personal protective equipment while handling such samples. All individuals, even if they have been trained in the general handling of chemical samples, need to be particularly trained in handling radioactive samples.
(b) Engineering and personal controls. Personal controls limit the inadvertent exposure to radioactivity of the user who is handling radioactive samples. Such controls include wearing specialized safety equipment, such as a safety suit, safety goggles, and safety gloves at all times while handling such samples. Engineering controls include only working with radioactive materials in a certain room, with certain ventilation and with prominent labeling of the room, so that other individuals are not inadvertently exposed to such radioactivity.
(c) Mechanisms for limiting spread of radioactivity. Mechanisms for limiting the spread of radioactivity include only working with radioactive materials in a specially designed room, which contains ventilation that removes the risk of inhaling radioactive materials, and contains walls and doors made of materials that are designed to deter the spread of radioactivity.
(d) Reporting structure for inadvertent radioactive spread. Despite all the mechanisms for limiting the spread of radioactivity detailed above, there is still the possibility of an inadvertent spread of radioactivity that can put tens, hundreds, or even thousands of people at risk of inadvertent exposure to harmful radioactivity derived from radioactive samples. Reporting inadvertent radiation spreads promptly allows other researchers as well as the general population to evacuate contaminated areas, and enables first responders to develop effective responses for radiation disaster mitigation.
(e) Mechanisms for proper disposal. Proper disposal of radioactive materials is critical, as many materials continue to emit radioactivity for a long period of time after they have been used, and as such can present serious risks to individuals who handle radioactive-containing waste. Disposal of such materials requires a number of precautions, including clearly labeling waste streams that contain radioactive materials, using special containers that minimize the spread of radioactivity to people who are handling such containers, and including mechanisms to accelerate the release of radioactivity so that remaining radioactivity is minimal. Training in how to properly dispose of radioactive samples once an individual is done using them for scientific purposes is a crucial part of the training necessary to obtain safety clearance (see part a, above).
V. Samples with Multiple Categorizations and Samples Not Otherwise Specified
Samples that fit into multiple categories, such as environmental contamination that contains chemical samples, or biological samples with radioactive components, must be treated by using all the safety precautions of all of the sample categories to which they belong. This means that before one works with biological samples that contain radioactivity, they must be properly trained in the handling of both biological samples and of radioactive samples.
Disposal procedures for such samples must also follow all precautions of all the relevant categories, such as labeling samples with both “biological hazard” and “radioactive hazard” labels, and using containers designed to contain such components.
An example of samples that do not fit neatly into the categories listed above includes nanomaterial-containing samples. Nanomaterials are relatively newly developed materials, and much of their toxicity, especially over the long-term, has not been established. Regulations around the use and handling of nanomaterial samples have been developing and evolving towards more rigorous regulations. In particular, in addition to the standard handling procedures for regular chemical samples, nanomaterial-containing samples need to be stored and disposed of in separate, clearly labeled containers. The use of fume hoods in sample handling is also strongly encouraged, so that aerosolized nanoparticles are not inadvertently inhaled by the sample handler. Other regulations around best practices for waste disposal of nanomaterials have been developed as well.
VI. General Information about Sample Inventories and Sample Management
Regardless of what category of samples you are managing, the ability to manage sample inventory is critical. This inventory, however it is designed, should allow a user to easily find a particular chemical, biological, environmental, or radioactive sample. It should be designed in a way that is easily understood by a new user and is easily shared with and transferrable to multiple users. To do so, the use of proper chemical names is generally recommended, rather than abbreviations which may not be easily understood. Specific details in sample labeling, including the site of collection (for environmental samples), a coded patient identification number (for biological samples), time and date of collection (for multiple times of samples) will help all users access the samples at a later date and understand all necessary information.
Many institutions use barcoding of samples to help maintain inventory, especially across research groups and across departments. Putting such barcoded inventories online provides a straightforward way to search for chemicals, and to track when chemicals are used and when they are disposed of. It is of interest for every research group, department, and institution to devote the time to developing and maintaining an online inventory, which may be a daunting task to contemplate but will save significant time and resources in the long run.
VII. Notes about Storing Samples at Cold Temperatures
Often samples need to be stored at low temperatures in order to ensure long-term stability of the samples and the integrity of the material that is contained in such samples. Laboratory freezers and refrigerators provide the option for achieving such temperature-controlled storage, with laboratory freezers generally maintained between -20°C and 0°C, and laboratory refrigerators maintained between 0°C and 10°C. Care has to be taken when samples are shipped and delivered to ensure continuous temperature control, with the packaging often requiring dry ice during shipments and/or significant labels on the exterior of the packaging to ensure that good temperature control is maintained.
General Summary and Conclusions
Handling of samples of various types is an inevitable part of working in a research laboratory, and is true across a broad variety of disciplines for an even broader variety of research projects. Handling such samples requires: knowledge, of the nature of the samples; training, in order to adequately handle the samples and conduct the experiments of interest; knowledge, in how to properly dispose of chemicals and minimize risks resulting from the waste stream; and care, in order to execute all tasks thoroughly and accurately. Even with the best training, accidents can occur, and proper management and reporting of such accidents makes it more likely that such accidents can be avoided in the future. When in doubt as to the appropriate behaviors/procedures at any point in sample handling and sample management, do research, talk with colleagues, and consult with and report to a superior.
There are a number of useful references available online about proper sample handling. What follows is a non-exhaustive list of some of those references.
Topic 1: Accidents that can result from improper sample handling, especially of chemicals:
Topic 2: Regulations around the handling of biological samples
Topic 3: Regulations around the handling of environmental samples
Topic 4: Regulations around the handling of chemical samples
Topic 5: Regulations around the handling of radioactive chemicals
Topic 6: Accidents that result from poorly controlled spread of radioactive samples
- Hirose, K. Fukushima Daiichi Nuclear Plant Accident: Atmospheric and Oceanic Impacts Over the Five Years. J. Environ. Radioactivity 2016, 157, 113-130.
- Bomanji, J. B.; Novruzov, F.; Vinjamuri, S. Radiation Accidents and their Management: Emphasis on the Role of Nuclear Medicine Professionals. Nuclear Medicine Commun. 2014, 35, 995-1002.
- Steinhauser, G.; Brandl, A.; Johnson, T. E. Comparison of the Chernobyl and Fukushima nuclear accidents: A review of the environmental impacts. Sci. Total Environ. 2014, 470-471, 800-817.
Topic 7: Cases of environmental contamination that would necessitate the collection of environmental samples
- McNutt, M. K.; Chu, S.; Lubchenco, J.; Hunter, T.; Dreyfus, G.; Murawski, S. A.; Kennedy, D. M. Applications of Science and Engineering to Quantify and Control the Deepwater Horizon Oil Spill. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 20222-20228.
- Horzmann, K. A.; de Perre, C.; Lee, L. S.; Whelton, A. J.; Freeman, J. L. Comparative Analytical and Toxicological Assessment of Methylcyclohexanemethanol (MCHM) Mixtures Associated with the Elk River Chemical Spill. Chemosphere 2017, 188, 599-607.
- Kielb, C. L.; Pantea, C. I.; Gensburg, L. J.; Jansing, R. L.; Hwang, S.-A.; Stark, A. D.; Fitzgerald, E. F. Concentrations of Selected Organochlorines and Chlorobenzenes in the Serum of Former Love Canal Residents, Niagara Falls, New York. Environ. Res. 2010, 110, 220-225.
Topic 8: Regulations around the handling of nanomaterials
Topic 9: Accidents that result from improper waste stream handling