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Mutation Screening with qRT-PCR

A Powerful Technique Used to Measure Gene Expression Levels

Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) is a widely used technique in molecular biology and biomedical research for detecting and quantifying mRNA and has firmly established itself as a valuable tool for mutation screening in human biosamples. Its high sensitivity and specificity, rapid turnaround time, real-time quantification, broad dynamic range, multiplexing capability, flexibility, and cost-effectiveness make it an attractive choice for various applications in both research and clinical settings.

"qRT-PCR has contributed significantly to our understanding of gene function, regulation, and the molecular mechanisms underlying various biological processes and diseases."

qRT-PCR is a two-step process that involves reverse transcription of RNA into cDNA followed by quantitative PCR amplification of the cDNA. The reverse transcription process is catalyzed by the enzyme reverse transcriptase, which synthesizes cDNA from RNA templates. The cDNA is then amplified using PCR, which generates many copies of the target gene.

The amplified cDNA is quantified by measuring the fluorescence of a reporter dye, such as SYBR Green, during the PCR amplification process. SYBR Green binds to the double-stranded DNA generated during the PCR amplification process and emits fluorescence when excited by light. The fluorescence intensity is proportional to the amount of DNA generated during the amplification process. 

This powerful method has a high degree of sensitivity and specificity, enabling researchers to study gene expression and analyze biological processes at the molecular level. Some typical applications of qRT-PCR in research include: 

Gene expression analysis

By measuring the levels of specific mRNA molecules, researchers can determine how genes are expressed under various experimental conditions or across different tissues, cell types, or developmental stages, which helps in understanding the function and regulation of genes.

Validation of RNA-seq data

High-throughput RNA sequencing (RNA-seq) can provide genome-wide gene expression profiles. qRT-PCR is often used to validate RNA-seq results, as it can accurately quantify the expression levels of selected genes of interest.


Another vital application of qRT-PCR is in the diagnosis of diseases. qRT-PCR can be used to detect and quantify the levels of viral RNA in patient samples, such as blood or saliva, to diagnose viral infections. Similarly, qRT-PCR can be used to detect the presence of cancer cells in patient samples by measuring the expression levels of specific cancer-related genes.

Pathogen detection

Researchers can use qRT-PCR to detect and quantify the presence of viral, bacterial, or fungal pathogens in clinical or environmental samples, enabling rapid and accurate diagnosis of infections.

Functional genomics

By manipulating gene expression using techniques such as RNA interference (RNAi) or CRISPR-Cas9, researchers can use qRT-PCR to measure the resulting changes in gene expression and uncover the functions of specific genes.

MicroRNA (miRNA) analysis

miRNAs are small non-coding RNAs that are crucial in regulating gene expression. qRT-PCR quantifies miRNA levels, enabling researchers to study their role in various biological processes and diseases.

Biomarker discovery is the process of identifying and validating specific biological molecules that can serve as indicators for various biological states, such as normal physiological processes, disease progression, or response to therapeutic interventions. qRT-PCR is a powerful tool for biomarker discovery as it enables the quantification of gene expression levels in biological samples. 

Researchers can identify potential biomarkers for disease diagnosis, prognosis, or treatment response by comparing the expression patterns of specific genes between different conditions or populations. Here's how biomarker discovery is performed using qRT-PCR:

Sample collection

Biological samples, such as blood, tissue, or cells, are collected from subjects (e.g., patients or healthy controls). These samples should be carefully handled to prevent RNA degradation.

RNA extraction

RNA is extracted from the samples using specialized extraction kits or methods. This process usually involves lysing the cells, separating the RNA from other cellular components, and purifying the RNA.

Reverse transcription

The extracted RNA is reverse-transcribed into cDNA using a reverse transcriptase enzyme and specific primers. This step converts the RNA molecules into a more stable DNA form that is amplified in the subsequent PCR step.

PCR amplification and quantification

The cDNA is mixed with specific primers, a DNA polymerase, and a fluorescent dye or probe, allowing the real-time detection of amplified DNA. The PCR machine amplifies the target cDNA sequences exponentially and monitors the accumulation of the fluorescent signal. The increase in fluorescence is proportional to the amount of amplified DNA, which reflects the initial amount of target mRNA in the sample.

Data analysis

The expression levels of the target genes are compared between different samples or groups (e.g., diseased vs healthy individuals) to identify potential biomarkers. Statistical analyses and validation experiments may be performed to ensure the reliability of the identified biomarkers.

The field of drug discovery is perpetually evolving, with new methods and techniques constantly being developed to expedite the process of finding life-saving medications. One such technique that has revolutionized the drug discovery process is qRT-PCR. This powerful tool has become indispensable in biomedical research because it can rapidly and accurately quantify gene expression levels.

qRT-PCR applications in Drug Discovery:

Target Identification and Validation

In the early stages of drug discovery, researchers aim to identify and validate potential targets, such as proteins or genes, that play a crucial role in disease progression. qRT-PCR is widely used to study gene expression patterns in different tissues and under various conditions, enabling researchers to pinpoint disease-associated genes and their potential as therapeutic targets.

High-Throughput Screening

Once a target has been identified and validated, researchers must screen large libraries of chemical compounds to find those that interact with the target and show potential as drug candidates. qRT-PCR is employed in high-throughput screening (HTS) assays to evaluate the effects of these compounds on gene expression levels, helping to identify lead compounds that can modulate the target gene. 

Mechanism of action studies

Understanding the mechanism of action of a drug candidate is essential for further optimization and development. qRT-PCR can provide insights into the molecular events that occur upon drug treatment, such as changes in gene expression or signalling pathways, helping to elucidate the drug's mode of action.

qRT-PCR has significantly impacted the drug discovery process, providing researchers with a powerful tool to accurately and efficiently quantify gene expression levels and specific mutations in human biosamples. Its versatility and high sensitivity make it invaluable in target identification, HTS, mechanism of action studies, and biomarker development. By expediting these crucial steps in drug discovery, qRT-PCR continues to pave the way for developing novel therapeutics and a better understanding of disease mechanisms.

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