Next-Generation Sequencing (NGS) has transformed how we study genetic material, enabling deep insights into an individual’s unique biological makeup. Among its many applications, the NGS custom panel stands out as an adaptable tool. This technology allows researchers and clinicians to focus precisely on specific genetic regions, providing a highly targeted approach to understanding health and disease.
What is an NGS Custom Panel?
An NGS custom panel represents a targeted approach within Next-Generation Sequencing, concentrating the sequencing effort on a pre-selected set of genes or specific genomic regions. Unlike whole-genome sequencing, which examines an organism’s entire genetic code, or whole-exome sequencing, which focuses on all protein-coding genes, a custom panel is highly selective. It involves designing probes or primers to capture only the DNA or RNA sequences relevant to a particular research question or clinical need. This selective nature allows for deeper coverage of the chosen regions, meaning each selected genetic location is read multiple times, increasing the accuracy of variant detection.
This method is built on the principle of enrichment, where the genetic material of interest is isolated from the larger genome. Various methods are employed for this enrichment, including hybridization-based capture or multiplex PCR amplification. The choice of method often depends on factors like the size of the target regions and the desired sensitivity. This focused approach helps reduce the amount of data generated, streamlining the analysis process and making it more efficient.
Key Applications of Custom Panels
NGS custom panels are applied across various fields, offering precise genetic insights. In cancer research and diagnostics, these panels identify specific mutations within tumors, which can guide personalized treatment strategies. For instance, a panel might target genes involved in a particular type of cancer, helping detect actionable variants for targeted therapies.
The panels also aid in diagnosing inherited diseases by pinpointing genetic variations linked to hereditary conditions. By focusing on genes associated with a suspected inherited disorder, clinicians can efficiently identify causative mutations. This targeted approach is useful when multiple genes are linked to a single condition, allowing for simultaneous analysis.
Pharmacogenomics benefits from custom panels by helping understand how an individual’s genes influence their response to drugs. Identifying genetic markers that predict drug efficacy or adverse reactions can lead to more tailored and safer medication regimens. Custom panels also contribute to infectious disease surveillance by detecting and characterizing pathogens, allowing for rapid identification of specific viral or bacterial strains, aiding in outbreak management and understanding disease transmission.
Advantages and Important Considerations
Custom NGS panels offer several advantages, including efficiency and cost-effectiveness compared to broader sequencing methods. By focusing only on specific genes or regions, they reduce the amount of sequencing data that needs to be generated and analyzed, which translates to lower costs and faster turnaround times. This targeted approach also allows for greater sequencing depth on the chosen regions, improving the detection of rare genetic variants. For example, a small hotspot panel focusing on fewer than 50 genes can provide results more quickly due to being less sequencing-intensive.
However, the focused nature of custom panels comes with a trade-off: they will only provide information about the pre-selected genetic regions. Genetic variations located outside the designed panel’s scope will not be detected. This means if the cause of a condition or relevant genetic information lies in an unselected region, the panel will not identify it. Researchers and clinicians must carefully consider their specific research questions or clinical hypotheses when designing a panel to ensure all relevant genetic areas are included.
The Custom Panel Workflow
The design of an NGS custom panel begins with selecting specific genes or genomic regions of interest. This initial step requires a clear understanding of the research question or clinical objective, as the chosen targets will dictate the panel’s utility. Online design tools allow users to input gene lists or specific genomic coordinates (like BED files), which are then used to create the probe or primer sets. Repetitive or low-complexity regions are often masked during this design phase to ensure efficient and accurate sequencing.
Following the design, library preparation involves transforming DNA samples into a format suitable for sequencing. This includes fragmenting the DNA into smaller pieces and attaching adapter sequences, which are short DNA segments that help the DNA bind to the sequencing platform. These prepared libraries then undergo the sequencing process, where the genetic code of the targeted regions is read multiple times.
Finally, the sequencing data undergoes a thorough analysis. This involves processing the raw reads, aligning them to a reference genome (often GRCh38), and identifying any genetic variants present in the targeted regions. Bioinformatics tools are then used to interpret these variants, determining their potential significance and relevance to the initial research question or clinical diagnosis.