Choosing Between Custom and Catalog NGS Panels

Next-generation sequencing (NGS) panels provide researchers with the ability to target specific areas within the genome or transcriptome, while offering a more efficient and resource-saving alternative to broader approaches. These panels have become increasingly versatile, with an expanding selection of catalog (pre-designed) panels and custom solutions available. In many cases, selecting a panel type for a research project is relatively straightforward. However, each option offers distinct strengths and requires attention to key factors when determining the most suitable choice.

Key Takeaways

• Custom panels: Designed for specific genes or applications; ideal for novel or niche regions and unique experimental needs.
• Catalog panels: Developed with standardized content; suitable for established applications and quick implementation.
• Cost and time: Catalog panels are often cost-effective for smaller projects, while custom panels can match catalog turnaround times with routine use and are economical for large-scale studies.
• Flexibility: Catalog panels can be adjusted with added content, while custom panels allow inclusion of the latest findings.
• Challenges: Supplier expertise helps overcome any design issues, such as difficult regions.
• Supplier support: Essential for optimizing design and addressing specialized needs like RNA sequencing or long-read capture.
• Choosing the right panel: Base your choice on project scope, budget, timeline, and coverage needs.

Differences between custom and catalog panels

While both aim to address similar needs, custom and catalog panels have several notable differences. As the name suggests, custom panels are sequencing assays customized to target specific genes or regions of interest. “They allow for the targeting of any content, organism, or scientific application,” explained Kathryn Woodfine, Ph.D., NGS Senior Product Manager at Agilent Technologies. This approach helps researchers focus their sequencing efforts on relevant regions and cut down on any unnecessary sequencing and analysis. Woodfine also noted that custom panels can be created from scratch, adapted from catalog designs, or developed from subsets of existing panels.

Conversely, catalog panels are pre-designed and developed by experts for targeted applications such as exome sequencing, detecting disease-causing mutations, pathogen identification, and more. Catalog panels also come with standardized, pre-validated content for immediate implementation, offering reliable performance and quick delivery times. Furthermore, Woodfine shared that they are ideal for applications where the genomics community has established a standard consensus on panel content.

Factors to consider when choosing a panel

Before selecting a panel type, it is important to compare the characteristics of both custom and catalog panels. “Catalog panels can be advantageous for smaller throughput projects, as their overall turnaround time and cost may be lower depending on factors such as panel size and the number of reactions requested,” stated Brittany Niccum, Ph.D., Senior Commercial Product Manager at IDT. Woodfine also noted that catalog panels are often more cost-effective per region of interest due to their predefined content and immediate availability.

Along with those considerations, Niccum highlighted that catalog panels can be customized by spiking in supplementary content to expand the panel or adjust the coverage. This enables researchers to target specific subsets with higher coverage and makes catalog panels a versatile option for researchers who need to balance predefined designs with the ability to alter coverage to experimental priorities.

In contrast, custom panels allow researchers to focus on unique regions that may be missing from catalog options. “The flexibility of a custom panel means content from recent publications and studies that have newfound implications as a driver for a given disease or tumor type can be included in the panel,” added Niccum. While custom panels typically require more time to produce, Woodfine explained that their turnaround time can match that of a catalog panel with routine use. Additionally, they can be more economical for designs focusing on limited regions by eliminating unnecessary workflow costs or for large projects requiring a significant number of reactions.

Overall, the costs and turnaround times for each panel type are influenced by each product and its complexity. Niccum shared that additional pricing considerations include the panel’s size, the volume of reactions, and the quality control options selected.

Challenges and support

Another important consideration involves overcoming any challenges associated with designing custom panels. As Woodfine noted, the design of capture probes can be difficult in regions with repetitive sequences or high GC content. However, supplier tools can adjust bait coverage to mitigate these obstacles effectively. “Partnering with a reputable bait supplier with expertise in targeted enrichment and strong technical support is crucial,” advised Woodfine. She noted that with the right tools and expertise, suppliers can help ensure that custom panels achieve their intended performance.

Niccum similarly emphasized the importance of partnering with a supplier’s support team to discuss experimental needs and give guidance on panel selection. These support teams can also assist with specific design strategies, such as targeted RNA sequencing, long-read capture, or designs to non-standard reference sequences, that may not be available through public design tools.

Final thoughts

The decision of which panel type to use depends on the requirements of the study, the scope of the project, and the desired balance between cost, turnaround time, and customization. Researchers can maximize the potential of either approach by using the expertise and support of supplier teams to ensure that their chosen panel type aligns with their scientific goals.

As Woodfine aptly summarized, “Catalog panels offer high-quality, expertly curated content with known performance statistics, making them a reliable solution and a great starting point for those new to targeted enrichment. Custom panels, on the other hand, allow you to tailor your experiment to your specific vision, whether that involves updating an existing gene list with the latest scientific knowledge or exploring unique research questions.”