Liquid biopsies involve measuring cell-free DNA (cfDNA) in a sample of bodily fluids, such as blood. This sample can then be tested for circulating tumor cells (CTCs), DNA fragments shed by tumors (circulating tumor DNA), and other biomarkers that provide information about the cancer’s characteristics and behavior. Liquid biopsies often use non-invasive ways to collect fluid samples. For example, blood samples are drawn from the veins, urine is collected in a sterile cup, or saliva can be swabbed in the mouth. Liquid biopsies are essential for cancer detection, tumor profiling, guiding personalized treatment, monitoring treatment responses through changes in ctDNA levels, assessing tumor heterogeneity, and disease progression tracking. 

Liquid Biopsy: 4 Pros & Cons

Here are the pros and cons of liquid biopsies vs. tissue biopsies:

Pros of Liquid Biopsies:

1. Faster Results: Liquid biopsies can often be processed more quickly than tissue biopsies, resulting in faster decision-making for life-altering treatment. 
2. Minimally Invasive: The main difference between liquid vs. tissue biopsy is the level of invasiveness. Since liquid biopsies involve a simple blood draw or a swab of saliva, they are much less invasive than tissue biopsies. This can lead to enhanced patient comfort and lower risk of complications.
3. Real-Time Monitoring: Liquid biopsies allow for ongoing monitoring of cancer through repeat testing, making it possible to track the effectiveness of treatments, detect potential recurrences, and monitor changes in the tumor’s genetic makeup. 
4. Comprehensive Tumor Profiling: Liquid biopsies have the potential to capture genetic material from multiple tumor sites, providing a more complete view of the cancer’s molecular profile. 

Cons of Liquid Biopsies:

1. Limited Data: While they provide molecular information, liquid biopsies do not offer histological data, which can limit their ability to fully characterize certain cancers.
2. Lower Sensitivity: Liquid biopsies may fail to detect small tumors or low levels of circulating tumor DNA, potentially resulting in false negatives or incomplete and inaccurate information. 
3. Not Always Suitable: Liquid biopsies are not yet a suitable replacement for tissue biopsies in all cases. Certain cancers may not release enough ctDNA to be detected or analyzed accurately.

Cost Considerations: Liquid biopsies can be expensive and may not be covered by all insurance plans, potentially limiting access.

Selecting a suitable method is crucial for recovering high-quality proteins when planning your protein extraction protocol. Here, we break down a common protocol for FFPE samples that can be adapted to your research needs. 

Step 1: Deparaffinization

Deparaffinization removes the paraffin wax embedding the tissue, enabling access to the preserved proteins. To do this, place your FFPE tissue section in a xylene solution to dissolve the paraffin. Typically, two 10-minute xylene washes work well. Once the tissue is deparaffinized, wash it with ethanol to remove any residual xylene, and then rehydrate it with decreasing ethanol concentrations (100%, 90%, 70%, and distilled water). This step ensures that the tissue is ready for protein extraction.

Step 2: Rehydration and Buffer Preparation

After deparaffinization, the tissue should be rehydrated to prevent protein denaturation. Prepare a rehydration buffer, common Tris-HCI, or a PBS buffer, which stabilizes the proteins. Place your sample in a buffer for about 10 minutes to allow complete hydration.

Step 3: Antigen Retrieval

Antigen retrieval is a critical step in the FFPE tissue protein extraction process as it breaks the formalin-induced cross-links, freeing the proteins. Heat-induced epitope retrieval (HIER) is the most commonly used method, where samples are heated in a high-pH or low-pH buffer solution. Depending on your protocol requirements, use a microwave, pressure cooker, or water bath to heat the samples for approximately 20–30 minutes. After antigen retrieval, let the sample cool gradually to room temperature, which will reduce the risk of protein denaturation.

Proper deparaffinization is crucial to obtaining reliable, reproducible results. The incomplete or improper removal of paraffin can hinder the efficiency of downstream processes such as staining, DNA extraction, or protein isolation. Tissue that still contains paraffin can lead to false negatives in assessments or poor visualization to ensure accurate results.

Before starting the deparaffinization process, tissue sections are usually mounted onto glass slides. These tissue sections should be handled with care to ensure they are securely attached and free from any debris. Typically, sections are cut between 4 and 6 microns thick and adhered to the slides using a section adhesive for microscopic examination. 

The main distinction between FFPE vs. fresh frozen tissue is how they’re preserved. Fresh frozen tissue is dipped in liquid nitrogen during “flash freezing.” The biospecimens are stored in an ultra-frigid freezer at less than -80℃. While FFPE tissue samples have been the preferred preservation method for clinical analysis, frozen biospecimens are becoming more popular due to the various advantages they offer researchers. 

The downside of fresh frozen tissue vs. FFPE biospecimens is that they’ll quickly degrade at room temperature and not maintain their quality when stored in a more standard food or household freezing environment. Researchers must freeze tissue as soon as possible and keep it frigid to maintain quality. This can be difficult for biopsy tissue since surgeons don’t always have access to liquid nitrogen to flash-freeze the tumor material. Additionally, fresh frozen tissue samples may not maintain their quality if technicians leave the biospecimens on the counter or neglect to close the freezer door fully. Since frozen tissues require immense care and caution, biobanks generally store a smaller collection of these biospecimens than FFPE samples. 

Biorepositories are used across the scientific research community to gain valuable insights into human biology, disease profession, and potential treatments. Without biobanks, we couldn’t extend our medical research and discoveries as far as we have. Here are 5 reasons why biobanks are essential for research purposes and for enhancing scientific knowledge:

1. Biobanks Facilitate Medical Research

Biobanks are the backbone of medical research. They provide researchers with access to extensive volumes of biospecimens, enabling them to perform research and testing on a previously impossible scale. Whether healthcare professionals need to identify the genetic underpinnings of diseases or better understand how our environment contributes to health illnesses, biobanks serve as a crucial starting point for reliable data. Biobanks have helped accelerate research for decades, leading to the identification of disease markers and the development of enhanced treatments for illnesses like cancer, neurological disorders, and more. 

For example, genomic data collected from biobank samples can help identify genetic mutations associated with cancer subtypes. 

2. Biobanks Personalize Medicine & Treatment Options

Biobanks are extremely important for contemporary research areas like personalized medicine. Instead of a one-size-fits-all approach, customized medicine allows healthcare professionals to personalize treatment plans to an individual’s unique genetic code. With biobank data, scientists and researchers can study individuals’ genetic makeup to better understand how different patients respond to varied treatments. This is essential for areas like oncology, where specified treatments are developed based on the patient’s particular genetic profile. 

When specimens are collected at biobanks, they’re often combined with questionnaires or medical record data from the donor, providing crucial resources for researching diseases and providing proper treatment plans. Biobanks allow researchers and healthcare professionals to create customized and increasingly effective medicine options for patients experiencing cardiovascular diseases, diabetes, cancer, and more. Every year, biorepositories save lives by supplying researchers and scientists with the ability to study and successfully eradicate life-threatening diseases. Imagine what it would be like if polio or malaria became widespread worldwide—biobanks are essential in helping prevent such scenarios. While these diseases have been largely eliminated or reduced in developed nations, third-world countries still grapple with their effects daily. Thanks to the establishment of several biobanks around the globe, researchers can effectively conduct research, advancing personalized medicine, improving quality of life, and decreasing the spread of devastating diseases. 

3. Biobanks Improve Cancer Research

Cancer is the second leading cause of death worldwide, meaning effective medical care and timely diagnosis are crucial for prevention and proper treatment. Although oncology has made extensive strides over the years, there’s still room for growth. Biobanks are important to varying components of cancer research, including proteomics, metabolomics, and epigenomics. Cancer research has come far over the last decade, especially in diagnostic, prognostic, and therapeutic areas. With the help of biobanks, researchers can identify biomarkers and apply proper pharmaceutical treatment. 

Since biobanks carry extensive collections of several types of biological samples, such as malignant tissue samples and blood combined with clinical data, they’re essential for cancer studies. Researchers can investigate cancer at a molecular level, label genetic mutations, and recognize how different cancers respond to medicine or treatment plans. Additionally, biorepositories enhance the development of tailored therapies, making treatment more effective and improving cancer patients’ outcomes. 

4. Biobanks Accelerate Drug Discovery & Development

Biobanks are changing how pharmaceutical organizations develop and test new drugs. By studying biospecimens, scientists and researchers can determine how differing populations respond to several types of drugs, which is important for creating successful and safe treatments. 

The data collected from biological samples helps significantly reduce the time it takes to introduce a new drug to the market, speeding up the approval process. This enables researchers to investigate potential adverse effects earlier in the drug development cycle, improving patient safety. 

5. Biobanks Advance Genomic Research

Genomics, or the study of an organism’s complete set of DNA, is an exciting field in modern science. It makes it possible to predict, diagnose, and heal diseases more accurately and personally than ever before. Biobanks provide the essential material for advanced research in this area. Researchers can comprehend how genes influence health and illness by analyzing the genetic variations across large populations.

These studies are leading to incredible breakthroughs in areas like gene therapy, which is the process of repairing or replacing defective genes. CRISPR technology, a powerful tool for gene editing, can potentially correct genetic disorders at the DNA level.

The paraffin embedding protocol involves several steps, each critical to the success of the process. The end sample is an FFPE (formalin-fixed paraffin-embedded) human tissue sample. Let’s explore a detailed guide to the standard protocol for embedding tissue in paraffin:

Step 1: Fixation

Before embedding, tissue samples must be fixed to preserve their structure and prevent degradation. Formalin is the most commonly used fixative, but other fixatives may be employed depending on the specific requirements of the study. The fixation process typically takes several hours up to a full day, depending on the size and type of tissue.

Step 2: Dehydration

After fixation, the tissue needs to be dehydrated to remove trace water, which is incompatible with paraffin. This is done by passing the tissue through a series of increasing alcohol concentrations, typically starting with 70% ethanol and progressing to 100%. Each step should be timed appropriately to ensure complete dehydration without damaging the tissue.

Step 3: Clearing

Once dehydrated, the tissue is cleared of alcohol and other substances that are incompatible with paraffin. This step involves immersing the tissue in a clearing agent, such as xylene, which prepares it for paraffin infiltration. Clearing is a critical step, as any residual alcohol can prevent proper paraffin embedding. 

Step 4: Paraffin Infiltration

After clearing, the tissue is infiltrated with melted paraffin wax. This step involves placing the tissue in a series of molten paraffin baths. The tissue is left in the wax for several hours to ensure complete infiltration, with the duration varying based on tissue and type. 

Step 5: Embedding

Once the tissue is fully infiltrated with paraffin, it is transferred to an embedding mold filled with liquid paraffin. The tissue is carefully oriented within the mold to ensure proper sectioning later on. The mold is then cooled to solidify the paraffin, encasing the tissue in a stable block that can be easily handled and sectioned.

Step 6: Sectioning

After embedding, the paraffin block is trimmed and mounted on a microtome, where it is sliced into thin sections, typically 3–5 microns thick. These sections are then mounted on slides for staining and microscopic examination. 

This paraffin embedding protocol ensures that the tissue is adequately preserved and ready for analysis. However, successful paraffin embedding requires attention to detail at each step, as errors can lead to issues like poor sectioning quality, tissue distortion, or incomplete infiltration.

1. Misdiagnosis or Delayed Diagnosis

The most harmful consequence of false specimen labeling is the risk of a misdiagnosis or delayed diagnosis. With 70% of treatment options determined by lab results, all specimens must be appropriately labeled with the correct patient identification, ensuring every lab result corresponds to the right patient. 

If a specimen is mislabeled, whether with the wrong patient’s information or incorrect details attached, it can lead to potentially life-threatening consequences such as a misdiagnosis. For example, if a breast tissue sample from Patient A is accidentally labeled as belonging to Patient B, the implications can be severe. If Patient B’s results indicate a condition like cancer, the treatment they receive will be radically inappropriate, potentially harmful, or even fatal. Meanwhile, Patient A, who may need urgent medical attention, would not receive the correct diagnosis and treatment. Misdiagnosis can also lead to unnecessary medication prescriptions, surgeries, or therapies. Correcting a misdiagnosis is incredibly time-consuming, leading to worsening symptoms or disease progression of the patient. 

Once a specimen is mislabeled and the error is identified, healthcare providers often need to repeat the test or analysis to obtain accurate results, leading to a delay in diagnosis. A delayed diagnosis can postpone needed treatments, possibly leading to critical delays in life-saving treatments. It’s crucial to avoid mislabeling specimens and ensure patient health and well-being. 

2. Legal and Ethical Issues

Incorrect labeling of specimens can result in legal and ethical issues. Here are a few legal ramifications you can experience if you fail to label specimens correctly: 

Medical Malpractice: Medical malpractice lawsuits are costly and damaging to your reputation. In malpractice lawsuits, patients often seek compensation for incorrect treatment or delayed diagnosis.

Regulatory Penalties: Healthcare facilities must comply with strict rules regarding specimen labeling. If specimens aren’t labeled correctly, you could be fined, lose your accreditation, or, if you own a facility, it could risk permanent closure.

Ethical concerns are another consequence of not labeling specimens correctly: 

Patient Autonomy: Incorrect labeling erodes informed consent since patients may make decisions based on false information, violating their right to autonomy. 

Non-Maleficence: Healthcare providers, researchers, and laboratories have an ethical duty to avoid causing harm. Failing to label specimens correctly could result in inappropriate or delayed treatment, directly harming patients.

Trust & Integrity: Trust is essential in the health and research industries. Unfortunately, incorrect labeling can quickly erode trust and damage the integrity of healthcare professionals, facilities, scientific researchers, and more.

The consequences of legal and ethical issues caused by incorrect labeling highlight the critical need for accuracy and meticulous attention in specimen handling. Don’t risk a damaged reputation or the ill-treatment of patients by failing to label specimens correctly and thoroughly.

3. Damaged Reputation

Repetitive mistakes in specimen labeling can severely affect the reputation of a healthcare facility, researcher, or professional, resulting in a loss of trust among patients, peers, and the medical community as a whole. If errors recur, they signal to outsiders a systemic failure in quality control and raise concerns about the overall reliability of the institution or practitioner. A damaged reputation can lead to decreased patient confidence and an inability to conduct accurate testing, causing a decline in patient numbers, correct research results, and precise scientific discoveries. 

The long-term impact of a damaged reputation can be profound, affecting not only the ability to attract new patients or conduct conclusive testing but also partnerships and funding for further career growth.

4. Negative Impact on Research

False specimen labeling negatively impacts scientific research, potentially skewing results and leading to inaccurate conclusions. Data integrity is crucial in research, as it forms the basis for scientific findings and subsequent recommendations. If specimens are mislabeled, specific samples are associated with incorrect data, distorting the final analysis. For instance, if a mislabeled tissue sample is assumed to belong to a particular demographic or disease group, every finding derived from that specimen will be inaccurate. This results in flawed conclusions that misrepresent the effectiveness of treatments, the progression of diseases, and the identification of biomarkers. 

Moreover, these errors can lead to the publication of false research, which may then be used by other researchers as the basis for additional studies, only adding to the inaccuracies. This ripple effect can be substantial, potentially causing wasted resources, time, money, and effort in the larger scientific community. If research discoveries influence clinical practices or policy decisions, the consequences of incorrect specimen labeling can extend far beyond the laboratory, impacting patient care and public health. In a worst-case scenario, an entire study may need to be revoked, leading to a loss of credibility and reliability in the research institution or scientists involved. 

For the success of human tissue research, reputable biobanks offer both normal, malignant, and disease-state tissue samples, including breast, cervical, lung, muscle, uterine, and more. To achieve the highest standards in tissue sample collection, 6 key practices should be followed. These practices ensure that the samples remain viable for research and diagnostic purposes, maintaining their integrity from the point of collection to their final use: 

Step 1: Preparation and Planning

Before collecting tissue samples, it’s essential to plan and prepare thoroughly. This includes understanding the specific requirements of the study or diagnostic tests, such as the type of tissue needed, the size of the sample, and the preservation method required. 

Step 2: Sterilization and Hygiene

Proper planning also involves ensuring that all necessary tools and materials are sterilized and ready for use. All instruments used in the collection process must be thoroughly sterilized to prevent contamination. Additionally, the environment in which the samples are collected should be clean and controlled. This is particularly important in surgical settings where tissue samples are often obtained. 

Step 3: Minimizing Handling

Excessive handling of tissue samples can lead to degradation and contamination. To maintain sample integrity, especially in control samples, it’s crucial to handle tissue samples as little as possible. When handling is necessary, it should be done with care and precision, using tools such as forceps to avoid direct contact with the simple. Minimizing handling is a key principle in tissue sample collection, helping to reserve the biological materials for accurate analysis. 

Step 4: Rapid Preservation

Once the tissue sample has been collected, it must be preserved quickly to prevent degradation. Depending on the type of tissue and the intended use, different preservation methods may be used, such as freezing or embedding in paraffin. Rapid preservation is essential for maintaining the molecular structure of the tissue, which is critical for downstream applications like genetic sequencing or protein analysis. FFPE tissue samples are sustained using a rapid preservation method that is widely recognized for its ability to maintain tissue integrity over long periods. 

Step 5: Accurate Labeling and Documentation

Proper labeling and documentation are vital for tracking tissue samples and ensuring their correct use in research or diagnostics. Each sample should be labeled with detailed information, including the date of collection, the type of tissue, and any relevant patient data (in compliance with privacy regulations). Documentation should also include a clear record of the collection process, storage conditions, and any handling procedures. Accurate labeling and documentation are essential for the success of any study or diagnostic procedure involving tissue samples. 

Step 6: Ethical Considerations

Lastly, ethical considerations are paramount in collecting tissue samples. Before collection, patients or donors must provide informed consent, ensuring they understand the purpose of the collection and how their tissue will be used. Additionally, all tissue sample collection processes should comply with local, national, and international regulations governing the use of human biological materials.

At Superior BioDiagnostics, we are committed to upholding the highest ethical standards in our tissue sample collection practices, ensuring that our work contributes positively to scientific advancement and patient care. How tissue samples are collected can make a significant difference in the success of medical research and diagnostics. By adhering to best practices in tissue sample collection, researchers can ensure the integrity of their samples and the accuracy of their results.

1. Increased Throughput and Cost-Effectiveness

One of the most significant advantages of automated DNA extraction is the ability to process many samples simultaneously. Automated systems can handle multiple samples in parallel, significantly increasing throughput compared to manual DNA extraction methods. This capability is particularly beneficial for large-scale studies and high-throughput screening applications, often leading biomedical professionals to search for a trusted biospecimen provider.

Although automated DNA extraction systems may require a significant initial investment, they result in substantial long-term cost savings. Automation reduces labor needs, minimizes errors, and increases overall efficiency, making it a more cost-effective operation than manual DNA extraction over time.

2. Enhanced Reproducibility and Consistency

Automated DNA extraction systems eliminated the variability associated with manual techniques. Manual extraction can be influenced by the technician’s skills and experience, leading to inconsistencies in DNA yield and purity. Automation ensures that each sample is processed under identical conditions, producing highly reproducible and consistent results. 

3. Time and Labor Savings

Manual DNA extraction is a time-consuming and labor-intensive process that requires multiple steps and careful handling of reagents. By contrast, automated DNA extraction systems streamline the workflow, reducing the hands-on time required from technicians. This allows laboratory personnel to focus on other critical tasks, improving overall efficiency and productivity. 

4. Reduced Risk of Contamination

Contamination is a significant concern in DNA extraction, as it can compromise the integrity of the results. Automated DNA extraction systems are designed to minimize the risk of contamination by reducing the number of manual handling steps. Closed systems and automated pipetting further decrease the likelihood of cross-contamination between samples.

5. Improved DNA Yield and Quality

Automated DNA extraction systems are optimized to maximize DNA yield and purity. These systems use precise and controlled conditions for each step of the extraction process. Ensuring the DNA is efficiently isolated and free from contaminants. The result is high-quality DNA that is suitable for a wide range of downstream applications, including PCR, sequencing, and genotyping. 

6. Scalability and Flexibility

Automated systems offer scalability and flexibility, allowing laboratories to adjust their workflows based on sample volume and throughput requirements. Whether processing a few samples or hundreds, automated DNA extraction systems can be tailored to meet the specific needs of the laboratory.

Immunohistochemistry (IHC) research is crucial in the analysis of various FFPE tissue types because it provides for the visualization and localization of specific proteins within the preserved tissue architecture, aiding in accurate disease diagnosis and research into tissue-specific protein expression. It is a powerful tool for:

• Diagnosing diseases, particularly cancers, by identifying specific biomarkers.
• Researching the role of proteins in various biological processes.
• Evaluating the effectiveness of therapeutic inventions by assessing target protein expression.