DNA strand intertwined with a cityscape symbolizing personalized cancer treatment.

Decoding Cancer: How Advanced Tumor Profiling is Revolutionizing Treatment

Theo Raines in Health & Wellness November 2025 • 4 min read.

"A deep dive into TumorNext, a comprehensive approach combining NGS and OncoScan for personalized cancer therapy."

The landscape of cancer treatment is rapidly evolving, driven by the development of targeted therapies that address both germline and somatic DNA mutations. This progress has created a critical need for sophisticated molecular profiling assays capable of precisely determining the mutational status of specific genes. The potential benefits of prescribing targeted therapies based on a tumor’s unique DNA alterations, rather than traditional tissue pathology, are becoming increasingly clear.

Traditional methods for characterizing tumors, such as immunohistochemistry (IHC) and in situ hybridization (ISH), are highly specific but provide limited information. Next-generation sequencing (NGS) offers an unbiased approach, providing extensive genomic data. However, the high costs and complex bioinformatics associated with whole genome sequencing (WGS) make it prohibitive for routine clinical use. Targeted gene panels are emerging as the optimal solution, balancing comprehensive analysis with cost-effectiveness.

This article explores TumorNext, a custom probe-based NGS tumor panel designed to detect single nucleotide variants, small insertions and deletions in 142 genes frequently mutated in somatic and germline cancers. TumorNext also identifies gene fusions and structural variants in 15 frequently disrupted oncogenes and tumor suppressors. Paired with a matched control and a custom bioinformatics pipeline, TumorNext distinguishes between somatic and germline mutations, enabling precise variant classification.

The Power of Combined NGS and OncoScan

DNA strand intertwined with a cityscape symbolizing personalized cancer treatment.

TumorNext’s comprehensive approach combines NGS with OncoScan, an array technology for high-resolution copy number variant detection. This combination allows for the detection of single copy amplifications and hemizygous deletions, offering a complete genomic profile of the tumor. By analyzing both SNVs, indels, SVs, and CNVs, TumorNext provides a multi-faceted view of the tumor's genetic makeup.

One of the key advantages of TumorNext is its ability to differentiate between somatic and germline mutations. This distinction is crucial for accurate variant classification and appropriate treatment recommendations. As highlighted in the study, misclassifying germline mutations as somatic can lead to inappropriate therapy, increased healthcare costs, and lost time for patients. By incorporating a matched blood or normal tissue control, TumorNext enhances the accuracy of NGS-based tumor panels.

Here are some key benefits of using TumorNext’s combined approach:

Enhanced Accuracy: Reduces the risk of misclassifying variants, leading to more appropriate treatment decisions.
Comprehensive Profiling: Provides a complete genomic picture of the tumor, including SNVs, indels, SVs, and CNVs.
Personalized Treatment: Enables the selection of targeted therapies based on the tumor’s unique genetic alterations.
Improved Outcomes: By identifying the "second hit" in hereditary cancer patients, TumorNext can guide more effective treatment strategies.

The analytical validation of TumorNext confirms its high sensitivity and specificity. In silico testing demonstrated the pipeline’s ability to detect SNVs and indels down to a minor allele frequency of 3% with 500x coverage. Real-world testing using previously characterized samples further validated its accuracy and reliability. The integration of OncoScan for CNV detection complements the NGS panel, providing a more complete genomic profile.

Looking Ahead

TumorNext represents a significant advancement in cancer diagnostics, offering a comprehensive and accurate method for tumor profiling. By combining NGS and OncoScan, and by differentiating between somatic and germline mutations, TumorNext empowers clinicians to make more informed treatment decisions, ultimately improving patient outcomes. As personalized medicine continues to evolve, TumorNext exemplifies the potential of advanced genomic technologies to revolutionize cancer care.

About this Article -

This article was crafted using a human-AI hybrid and collaborative approach. AI assisted our team with initial drafting, research insights, identifying key questions, and image generation. Our human editors guided topic selection, defined the angle, structured the content, ensured factual accuracy and relevance, refined the tone, and conducted thorough editing to deliver helpful, high-quality information.See our About page for more information.

This article is based on research published under:

DOI-LINK: 10.18632/oncotarget.11910, Alternate LINK

Title: Tumornext: A Comprehensive Tumor Profiling Assay That Incorporates High Resolution Copy Number Analysis And Germline Status To Improve Testing Accuracy

Subject: Oncology

Journal: Oncotarget

Publisher: Impact Journals, LLC

Authors: Phillip N. Gray, Huy Vuong, Pei Tsai, Hsaio-Mei Lu, Wenbo Mu, Vickie Hsuan, Jayne Hoo, Swati Shah, Lisa Uyeda, Susanne Fox, Harshil Patel, Mike Janicek, Sandra Brown, Lavinia Dobrea, Lawrence Wagman, Elizabeth Plimack, Ranee Mehra, Erica A. Golemis, Marijo Bilusic, Matthew Zibelman, Aaron Elliott

Published: 2016-09-08

Everything You Need To Know

What exactly is TumorNext, and how does it provide personalized insights for cancer therapy?

TumorNext is a comprehensive tumor profiling approach that combines Next-Generation Sequencing (NGS) and OncoScan technology. It analyzes a tumor's genetic makeup to detect single nucleotide variants (SNVs), small insertions and deletions (indels), gene fusions, structural variants (SVs), and copy number variants (CNVs). This combined approach provides a multi-faceted view, helping clinicians make more informed treatment decisions.

How does TumorNext distinguish between somatic and germline mutations, and why is this differentiation important for cancer treatment decisions?

TumorNext differentiates between somatic and germline mutations by incorporating a matched blood or normal tissue control. This is crucial because misclassifying germline mutations as somatic can lead to inappropriate therapy, increased healthcare costs, and wasted time for patients. Traditional methods like immunohistochemistry (IHC) and in situ hybridization (ISH) don't offer this level of differentiation.

What role does OncoScan play in TumorNext, and how does it complement Next-Generation Sequencing (NGS) for comprehensive tumor profiling?

OncoScan enhances TumorNext by adding high-resolution copy number variant (CNV) detection capabilities. While Next-Generation Sequencing (NGS) excels at identifying SNVs, indels, and structural variants, OncoScan identifies single copy amplifications and hemizygous deletions, giving a more complete genomic profile of the tumor. The integration of both ensures that a broader range of genetic alterations are detected which provides a complete genomic picture of the tumor.

What are the key benefits of using TumorNext in cancer treatment, and how does it improve patient outcomes?

The benefits of using TumorNext include enhanced accuracy in variant classification, comprehensive profiling of the tumor's genetic makeup, enabling personalized treatment strategies, and improving outcomes by identifying the 'second hit' in hereditary cancer patients. By providing a complete genomic picture, TumorNext empowers clinicians to select targeted therapies that address the tumor’s unique genetic alterations, ultimately improving patient outcomes.

How accurate and reliable is TumorNext, and what validation processes confirm its effectiveness in detecting genetic mutations?

TumorNext demonstrates high sensitivity and specificity in analytical validation. In silico testing shows it can detect SNVs and indels down to a minor allele frequency of 3% with 500x coverage. Real-world testing with previously characterized samples further validates its accuracy and reliability. The integration of OncoScan for CNV detection complements the Next-Generation Sequencing (NGS) panel, providing a more complete genomic profile and improves the accuracy of the test.