PCR-based Diagnostics for Infectious Diseases, Genetic Disorders, and Cancer

The field of diagnostics has been transformed by Polymerase Chain Reaction (PCR), a widely used molecular biology technique. By exponentially amplifying a small amount of DNA, PCR enables analysis to be conducted much more easily. Developed in 1983 by Kary Mullis, the technique has become a common and important tool in medical and biological research labs, with a variety of applications. These include DNA cloning for sequencing, DNA-based phylogeny, or functional analysis of genes, as well as the diagnosis of hereditary diseases, the identification of genetic fingerprints, and the detection of infectious diseases.

PCR has also facilitated the prompt diagnosis of malignant diseases, including leukemia and lymphomas, which are presently at the forefront of cancer research. PCR assays can be conducted directly on genomic DNA samples to identify translocation-specific malignant cells with a sensitivity that is at least 10,000 times greater than other methods. By enabling rapid and precise diagnoses, PCR helps in initiating appropriate treatments and avoiding unnecessary or invasive investigations.

PCR-Based Diagnostics for Infectious Disease Detection and Point-of-Care Testing

Annually, hospitals in the USA report well over 5 million cases of infectious-disease-related illnesses. However, a significantly greater number of cases remain undetected in both inpatient and community settings, leading to substantial morbidity and mortality. Prompt and effective intervention for infectious diseases relies on the swift and precise identification of the pathogen in both acute care and other settings. However, conventional laboratories face several limitations, such as prolonged assay, additional testing to characterize detected pathogens, and the inability to culture certain pathogens associated with microbial infection.

In developing countries with a high burden of infectious diseases, diagnostic challenges due to poor clinical laboratory infrastructure and cost constraints exacerbate the situation. Therefore, the potential for point-of-care (POC) testing is even greater in these regions. One of the major priorities among the ‘Grand Challenges for Global Health’ identified by the Bill and Melinda Gates Foundation and the NIH is the development of POC technologies for diagnosing infectious diseases.

PCR-based diagnostics have proven effective for a broad range of microbes, particularly for identifying organisms that cannot be grown in vitro or in cases where existing culture techniques are insensitive and require prolonged incubation periods. However, implementation in the clinical setting has had mixed success thus far, with only a limited number of assays approved by the US Food and Drug Administration (FDA) and fewer still gaining universal acceptance in clinical practice.

Quantitative real-time PCR represents a notable improvement in PCR technology, as it combines the amplification and detection of products in a single reaction vessel. This process represents a breakthrough in terms of clinical applicability since it eliminates the need for time-consuming post-amplification processing.

The real-time PCR-based platform holds great promise in replacing conventional laboratory-based testing for future point-of-care testing. With advancements in automation, integration of specimen preparation with target identification, and miniaturization, it will become much easier to bring analyses near the bedside to be done by less-trained personnel.

  • Broad-Range PCR

Broad-ranged PCR, also known as multiplex PCR, is a powerful diagnostic tool for the detection of infectious diseases that present with similar clinical symptoms or that are caused by multiple pathogens. The broad-ranged PCR method involves the use of multiple primers that amplify conserved regions of the pathogen’s genome. These conserved regions are present in a wide range of pathogen strains and allow for the detection of multiple pathogen species in a single reaction. This approach is more sensitive and specific than traditional diagnostic methods, such as culture-based techniques or antigen detection assays.

One example of the application of broad-ranged PCR is in the diagnosis of respiratory tract infections. These infections can be caused by a variety of pathogens, including viruses, bacteria, and fungi. Traditional diagnostic methods, such as culture-based techniques, can take several days to yield results and may not identify all potential pathogens. In contrast, broad-ranged PCR can simultaneously detect a range of respiratory pathogens in a single sample, allowing for rapid and accurate diagnosis.

Another application of broad-ranged PCR is in the diagnosis of sexually transmitted infections (STIs). STIs can be caused by a variety of pathogens, including bacteria, viruses, and parasites. Broad-ranged PCR can detect multiple STI pathogens simultaneously, allowing for more accurate and comprehensive diagnosis.

In conclusion, the use of broad-ranged PCR is a promising diagnostic tool for the detection of infectious diseases. However, careful consideration should be given to its limitations, and its use should be validated through comparison with other diagnostic methods.

  • Antimicrobial Resistance Profiling

Antimicrobial resistance profiling refers to the process of determining the susceptibility of bacteria to different antibiotics. This is typically done by exposing the bacteria to a range of antibiotics and observing which ones are effective in inhibiting or killing the bacteria. The results of these tests can be used to guide the selection of appropriate antibiotics for the treatment of bacterial infections.

PCR can be used in combination with antimicrobial resistance profiling to identify specific genes or mutations that are associated with resistance to certain antibiotics. For example, PCR can be used to detect the presence of the mecA gene, which is associated with methicillin resistance in Staphylococcus aureus. PCR can also be used to detect specific mutations in genes that are associated with resistance to other antibiotics, such as fluoroquinolones or macrolides.

Role of PCR and Genetic Disorders

Genetic disorders are typically classified into three primary categories: single-gene disorders, chromosomal disorders, and multifactorial disorders. Single-gene disorders, also known as Mendelian disorders, arise from mutations in the DNA sequence of a gene and encompass autosomal dominant (AD), autosomal recessive(AR), X-linked recessive (XR), X-linked dominant, and Y-linked (holandric) disorders. Chromosomal disorders result from aberrations in the structure or number of chromosomes.

PCR can be used to detect specific DNA mutations that are associated with different genetic disorders. By designing primers that amplify the mutant DNA sequence, PCR can accurately identify the presence of genetic mutations in a patient sample. PCR can also be used in combination with other techniques such as restriction fragment length polymorphism (RFLP) analysis, allele-specific PCR (AS-PCR), and sequencing to diagnose genetic disorders. These techniques can help to identify specific mutations in genes that are associated with genetic disorders such as cystic fibrosis, sickle cell anemia, and Huntington’s disease.

PCR can also be used in pre-implantation genetic diagnosis (PGD) to screen embryos for genetic disorders before they are implanted in the uterus. In this procedure, a single cell is extracted from an embryo and amplified using PCR. The DNA is then analyzed for specific mutations associated with genetic disorders.

  • PCR for Non-Invasive Diagnosis of Genetic Disorders

PCR can detect genetic mutations in various sample types that are easy to obtain from patients, such as blood, saliva, urine, and stool. This eliminates the need for invasive procedures, such as biopsies, which can be uncomfortable and carry risks.

According to research, approximately 10% of the cell-free DNA present in maternal plasma is composed of Cell-free fetal DNA, which can be used as a dependable source of fetal genetic material for noninvasive prenatal diagnosis (NIPD) during early pregnancy. However, detecting paternally inherited point mutations can be challenging due to the relatively high levels of maternal background. This challenge is further exacerbated when diagnosing the inheritance of autosomal recessive disorders using quantitative real-time PCR (qPCR). Digital PCR is a modified and highly sensitive method of qPCR that permits absolute quantification and rare allele detection without requiring standards or normalization.

PCR’s ability to detect genetic mutations in non-invasive sample types, coupled with its speed and sensitivity, makes it a valuable tool for non-invasive diagnostics in genetic disorders. The importance of PCR in genetic disorders cannot be overstated, and it will undoubtedly continue to play a significant role in advancing our understanding of genetic diseases in the years to come.

PCR Applications in Cancer Detection and Monitoring

PCR’s capacity to amplify nucleic acids makes it an ideal method for cancer detection because cancer cells undergo numerous genetic changes to acquire metastatic potential. As tumors are clonal, the modifications in nucleic acid markers are typically permanent and present uniformly in all cancer cells. Experimental evidence shows that the PCR test can identify a single cancer cell in up to 100 million background cells in vitro. Additionally, tissue-specific gene expression enables the application of RT-PCR to identify limited mRNA species in secondary sites, which is consistent with metastatic propagation.

Additionally, PCR can screen for viral infections in cancer samples, such as HPV and HBV, which are known to be associated with certain cancers. Quantifying cancer-specific RNA transcripts can be achieved using PCR, providing valuable information about the severity and extent of cancer and potential targets for therapy. PCR can also monitor the presence of residual cancer cells after treatment by detecting specific cancer DNA sequences in blood or bone marrow samples that may not be visible by other means. Finally, PCR can identify microsatellite instability, which is a hallmark of certain cancers, such as colorectal cancer, by amplifying and analyzing specific microsatellite sequences in patient samples, which can aid in cancer diagnosis and treatment.

Why is PCR considered to be important in Cancer Diagnosis?

PCR-based diagnostics are used to detect cancer in approximately 70% of all cancer cases. It can detect cancer at a very early stage, often before clinical symptoms are evident. This can be particularly important in the case of aggressive or fast-growing cancers, where early detection is critical for effective treatment. It can detect cancer-specific mutations with high sensitivity and specificity, making it a valuable tool for diagnosing cancer and distinguishing it from other diseases or conditions that may have similar symptoms. Also, PCR can help identify specific genetic abnormalities or mutations that are driving the growth of particular cancer. This information can be used to develop personalized treatment plans that target these specific abnormalities, potentially improving treatment outcomes. It is also a valuable tool used to monitor a patient’s response to treatment by tracking changes in the levels of cancer-specific DNA or RNA over time. This can help clinicians determine whether a particular treatment is effective or whether adjustments need to be made.

Future Directions of PCR-based Diagnostics

PCR-based diagnostics hold great promise, as new technologies and advancements in the field continue to emerge. Here are some future directions of PCR-based diagnostics:

Digital PCR (dPCR): Digital PCR is a newer technology that enables the detection and quantification of low-abundance nucleic acid targets with higher precision than conventional PCR. dPCR offers greater sensitivity and reproducibility, making it an attractive alternative to traditional PCR.

High-throughput PCR: High-throughput PCR enables the simultaneous analysis of multiple targets in a single reaction, allowing for the rapid and cost-effective screening of large sample sets.

Point-of-care PCR: It allows for rapid and on-site diagnosis, which is particularly useful for remote or resource-limited areas. Advances in microfluidics and miniaturization technology have enabled the development of portable PCR devices that can be used in field settings.

Next-generation sequencing (NGS) coupled with PCR: It can be used as a pre-amplification step for NGS, which can provide more comprehensive genomic information than PCR alone. This approach can be particularly useful for detecting complex genetic mutations, identifying drug resistance, and monitoring disease progression.

Integration with other diagnostic techniques: PCR can be integrated with other diagnostic techniques, such as immunoassays or biosensors, to provide more comprehensive and accurate results. Combining different techniques can increase the sensitivity and specificity of diagnostics, leading to more accurate diagnosis and treatment.

Overall, the future of PCR-based diagnostics is promising, with ongoing developments in technology and the potential for integration with other diagnostic techniques. These advancements will likely lead to improved accuracy, sensitivity, and cost-effectiveness of PCR-based diagnostics. Additionally, the integration of artificial intelligence and machine learning algorithms can improve the accuracy and efficiency of PCR-based diagnostics. These advancements have the potential to expand the application of PCR-based diagnostics in areas such as infectious disease detection, cancer diagnosis and monitoring, and personalized medicine.

References:

  1. (PDF) Polymerase Chain Reaction (PCR): A Short Review (researchgate.net)
  2. Park, S., Zhang, Y., Lin, S., Wang, T.-H., & Yang, S. (2011). Advances in microfluidic PCR for point-of-care infectious disease diagnostics. Biotechnology Advances, 29(6), 830–839. doi:10.1016/j.biotechadv.2011.06.017
  3. https://www.sciencedirect.com/science/article/pii/S1473309904010448
  4. Barrett, A.N., Chitty, L.S. (2014). Developing Noninvasive Diagnosis for Single-Gene Disorders: The Role of Digital PCR. In: Biassoni, R., Raso, A. (eds) Quantitative Real-Time PCR. Methods in Molecular Biology, vol 1160. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0733-5_17
  5. Yang S, Rothman RE. PCR-based diagnostics for infectious diseases: uses, limitations, and future applications in acute-care settings. Lancet Infect Dis. 2004 Jun;4(6):337-48. doi: 10.1016/S1473-3099(04)01044-8. PMID: 15172342; PMCID: PMC7106425.
  6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3883366/
  7. Boehm CD. Use of polymerase chain reaction for diagnosis of inherited disorders. Clin Chem. 1989 Sep;35(9):1843-8. PMID: 2570652.
  8. Raj GV, Moreno JG, Gomella LG. Utilization of polymerase chain reaction technology in the detection of solid tumors. Cancer. 1998 Apr 15;82(8):1419-42. doi: 10.1002/(sici)1097-0142(19980415)82:8<1419::aid-cncr1>3.0.co;2-4. PMID: 9554517.
  9. DeBiasi RL, Tyler KL. Polymerase Chain Reaction in the Diagnosis and Management of Central Nervous System Infections. Arch Neurol. 1999;56(10):1215–1219. doi:10.1001/archneur.56.10.1215