Solid Tumor Research

Overview

Solid Tumor Profiling Challenges with NGS

Solid tumor oncology research has greatly benefited from next generation sequencing methods to find relevant cancer-driving biomarkers. NGS’s ability to interrogate hundreds of genes for variants at very low levels has been a boon to molecular labs. The use of NGS for more complicated genomic alterations or assessments, such as structural variants, MSI, and TMB, has fueled comprehensive genomic profiling of solid tumor samples, ultimately providing labs with more information to understand these cancers.

However, traditional NGS methods may not provide all relevant information and can have challenging workflows and analysis. For example, traditional opposing primer assays limit identification of fusions to known partners only, missing potentially relevant novel fusions (Figure 1). Samples with low tumor cellularity, degraded nucleic acids (e.g. FFPE), or low-input (e.g. cfDNA) can all make detection of genomic alterations challenging.

Additionally, NGS library preparation workflows can be cumbersome, allowing many points for manual errors. Bioinformatic pipelines can be expensive and time-consuming to maintain. A pipeline may also lack the QC and statistical tools necessary to reduce errors and guide calling, which can leave it to lab staff to make difficult calls.

Archer NGS assay solutions for solid tumor research resolves these concerns with patented AMP™ chemistry, streamlined parallel workflows, and user-friendly analysis. Additionally, assays are designed to fit your lab’s unique needs from comprehensive profiling and high-throughput workflows, to smaller footprint assays and low-throughput manual workflows.

Detect more with AMP chemistry

Anchored Multiplex PCR (AMP) is a target enrichment method that uses molecular barcoded adapters and single, nested, gene-specific primers for amplification, permitting open-ended capture of DNA, RNA, and cfDNA fragments. This approach enables the detection of novel fusions (Figure 2), allows for flexible primer design, and protects against dropout of primers. MBC adapter ligation prior to PCR combined with Archer Analysis software power the correction of systematic errors and quantitative analysis of the original unamplified template.

High performance even with low input samples

Samples with low tumor cellularity, degraded nucleic acids (e.g. FFPE), or low input (cfDNA) that are typically challenging for traditional amplicon NGS variant detection are reliably amplified with AMP chemistry. In fact, 96% of expected fusions were identified with the FUSIONPlex Core Solid Tumor panel using 50 ng of 10% fusion positive material. (Figure 3) 

Genomic alterations, including fusions and CNVs, are consistently amplified from FFPE tissue with Archer solid tumor research assays. Figure 4 demonstrates one example of reliable variant calls by the VARIANTPlex™ Core Solid Tumor panel, with identification 100% of expected variants in FFPE reference material. 

For solid tumor variant detection in plasma samples, AMP chemistry provides preferential enrichment of cell-free fraction compared to amplicon-based NGS. Additionally, Archer’s unique outlier identification algorithm leverages position-specific noise data to enable confident reporting at low allele frequencies.

Solid tumor panels and reagent formats fit for your lab’s needs

VARIANTPlex Pan Solid Tumor and Complete Solid Tumor panels offer TMB in small and medium NGS panels with simultaneous detection of other relevant alterations, while demonstrating high concordance with WES-based TMB, as shown in a scientific poster presented at AMP 2023.

Additionally, the IMMUNOVerse TCR panel can provide tumor-infiltrating lymphocyte information relevant for solid tumor characterization.

Pair DNA- and RNA- based assays to efficiently generate a complete biomarker profile

Data assumes Archer libraries are prepared using the liquid adapters.

*Sample = 1 VARIANTPlex library + 1 FUSIONPlex library

VARIANTPlex and FUSIONPlex panels can be paired for cost-effective solutions to provide SNVs, indels, ITDs, fusions, and expression alterations from a single sample.

Choice of assay reagent formats are available to suit your lab’s sample volumes.

• For high-throughput labs, liquid reagents are ideal for automated liquid handling workflows. Liquid adapters are available in a 96-well plate format and include an increased number of dual indexes (over 36,000 unique combinations of sequencing indices) to support high-throughput sequencing. 
• For manual workflow labs, single-use, reaction-size lyophilized reagents allow your lab to avoid potential contamination during manual pipetting and provide extended shelf life.

Both reagent formats have demonstrated excellent performance, with identification of 100% of expected variants in reference materials*. Regardless of reagent format, all reagents are color-coded to match protocol steps, making benchwork easy (Figure 5).

Customize your panel content

Relevant oncology biomarkers are emerging rapidly, necessitating labs to modify their assays to meet the pace of discovery. With the foundation of proprietary AMP chemistry and Archer Analysis you can confidently add targets to existing Archer assays or start from scratch without compromising assay performance. To get started, visit Assay Marketplace, the Archer assay design tool.

*Data available upon request

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