Research demonstrates an automated next-generation sequencing workflow designed to reduce hands-on time while delivering next-day CGP results.
By Alyx Arnett
Comprehensive genomic profiling (CGP) continues to expand in oncology research, but traditional next-generation sequencing workflows can still be limited by complex preparation steps, long turnaround times, and tissue constraints.
At the 2025 Association for Molecular Pathology (AMP) annual meeting, Thermo Fisher Scientific presented research describing an automated workflow designed to deliver next-day CGP results while reducing hands-on time for laboratories.
The poster, “Accelerating Precision Oncology Research: Automated Comprehensive Genomic Profiling Solution with Next Day Results,” outlined performance data for an automated sample-to-report sequencing approach using a more than 500-gene oncology research panel capable of detecting multiple variant types and genomic signatures. The workflow automates key NGS steps—from sample preparation through analysis—with approximately 20 minutes of hands-on time and next-day turnaround.
In this Q&A, Dinesh Cyanam, staff scientist in bioinformatics at Thermo Fisher Scientific, discusses the motivation behind developing an automated CGP workflow, key performance findings presented at AMP, and how faster, more standardized sequencing approaches could influence the future of precision oncology research.
CLP: What got your team interested in exploring a next-day automated approach to CGP?
Cyanam: Conventional CGP workflows are slow, labor-intensive, waste precious tissue, and leave many samples as quantity not sufficient (QNS). Given these barriers, the team started with the problem statement that CGP is essential for precision oncology but is constrained by labor-intensive workflows and extended turnaround times. The goal for this process was to produce an oncology panel that could be run with minimal hands-on time and deliver next-day results to accelerate research decisions. The outcome was that we developed an automated, end-to-end solution to address those exact pain points for research labs.
Assays for Genexus are explicitly designed as end-to-end, highly automated sample-to-report workflows to produce next-day CGP results and reduce operator burden. The process only requires two touchpoints, needing about 20 minutes of hands-on time, and with the automation and speed of the Ion Torrent Genexus System, laboratories—from large academic centers to smaller regional labs—can unlock genomic insights in as little as 24 hours.
CLP: Why is automation and speed so important in precision oncology research?
Cyanam: Automation and speed are redefining the boundaries of precision oncology research. Newer NGS technologies automate formerly complex and time-consuming workflows, streamlining end-to-end processes from sample testing to data analysis. This modernization alleviates the need for specialized NGS expertise, minimizes handling errors, and dramatically reduces turnaround times.
Ultimately, rapid NGS technology puts researchers in a more optimal position than ever before. By enabling research teams to reach more patients for more comprehensive results, while simultaneously providing superior sensitivity that analyzes samples for trial eligibility faster and simpler, organizations can create a clinical trial workflow that is more effective and can easily be scaled.
For example, a single comprehensive gene research panel—like the OCA Plus on the Genexus platform—can analyze 517 genes across both DNA and RNA, detecting single‑nucleotide variants (SNVs), indels, copy number variants, fusions, and key genomic signatures including tumor mutational burden (TMB), microsatellite instability (MSI), and homologous recombination deficiency (HRD). By enabling one test to address multiple research questions, this approach eliminates the need for separate assays for each endpoint, which is critical for accurately characterizing tumors and efficiently selecting appropriate cohorts or therapeutic strategies in oncology research.
In the future, we can see the potential where users research the ability to combine AI-enhanced analysis that clinicians may use to address a patient’s path.
CLP: You’ve shown this automated NGS workflow can return results very quickly, meaning next-day CGP. What were your key findings on the performance of this assay?
Cyanam: The Genexus system with the OCA Plus research panel demonstrated true next‑day sample‑to‑report capability, combining rapid turnaround with strong analytical performance across all endpoints. Analytical sensitivity and specificity were consistently high for SNVs and indels (>98.6% and >99%, respectively), copy number variation gains and losses (98–99%), fusions (~98% sensitivity in FFPE samples), and MSI (~99% for both metrics). TMB measurements also showed excellent concordance with whole‑exome sequencing and orthogonal assays (Pearson r² = 0.95). Collectively, these data confirm that the assay delivers both speed and analytical depth, supporting its reliability in research study applications.
In addition, the workflow achieved a very high overall success rate with low input requirements (~94%). External and internal studies demonstrated that this amplicon‑based CGP approach yields a substantially higher proportion of reportable samples than certain hybrid‑capture methods, enabling laboratories to successfully profile specimens that might otherwise be classified as QNS.
CLP: What were some of the design decisions that shaped how you built out this panel?
Cyanam: We designed the assay to balance biologic relevance with practical ease of use, focusing first on content and then on workflow. The curated panel includes more than 500 genes that are highly relevant to solid tumors, encompassing biomarkers that are recurrently altered by single- and multi-nucleotide variants, insertions and deletions, and copy number changes, while providing approximately one megabase of exonic coverage to enable accurate and reliable TMB assessment.
In parallel, the workflow was engineered for simplicity and reproducibility, with automated library preparation, templating, and sequencing that require minimal touchpoints, supported by an optimized bioinformatics pipeline that delivers robust, reproducible results. The 500-plus gene set was carefully selected to capture key regions and domains of oncogenes that are frequently altered by somatic mutations, and to provide full coding-sequence coverage of tumor suppressor genes, which can be inactivated by truncating variants throughout their exons.
Beyond panel content, the entire end-to-end process—from nucleic acid extraction and quantification through library preparation, sequencing, analysis, and reporting—was highly automated to minimize hands-on time for the Genexus System and reduce the need for specialized NGS expertise, enabling institutions with varying experience levels to implement research into comprehensive genomic profiling more easily and consistently.
CLP: You included genomic signatures like TMB, MSI, and HRD—all of which are getting a lot of attention in oncology research. How do you see these complex biomarkers influencing the future of cancer research?
Cyanam: These genomic signatures are rapidly moving from single-biomarker roles to components of multi-modal biomarker strategies that may guide future therapy selection, trial design, and mechanistic research. Having them analyzed in a single assay accelerates translational research and provides more insight into personalized medicine strategies.
Tumor-agnostic biomarkers like TMB and MSI are becoming more relevant across cancer types regardless of tumor histology. Making an accurate assessment of TMB and MSI is important as they provide insight into the response to immune checkpoint inhibitors. Additionally, HRD is a common feature in many cancers, including ovarian, breast, pancreatic, and prostate cancers. Cancers with HRD may be sensitive to poly (ADP-ribose) polymerase (PARP) inhibition by way of synthetic lethality. A comprehensive panel that includes both genomic alterations and genomic signatures will help to accelerate translational research efforts to drive the development of more efficacious targeted therapies.
CLP: What do you see as the larger significance of this work?
Cyanam: Automated, next-day CGP democratizes access to comprehensive tumor profiling: It allows more labs to run high-quality CGP in-house, accelerates experimental timelines, conserves tissue samples, and increases the proportion of samples that yield informative data—all of which speed discovery and enable new study designs.
An automated CGP solution with next-day results reframes genomic profiling from being a specialized, bottlenecked send-out service to a more approachable and accessible in-house solution for laboratories with varied levels of NGS experience. By lowering the expertise and operational burden, automation allows smaller laboratories, translational teams, and early-stage programs to apply sophisticated genomic analysis to accelerate innovation and oncology discovery.
The next leap in precision oncology won’t come from a single discovery. It will come from combining speed, automation, and smart analysis to turn data into action—quickly, clearly, and with the urgency that every patient deserves.
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