Comprehensive Tumor Profiling
Our CAP/CLIA laboratory-developed wet lab assays enable simultaneous analysis of hundreds of clinically actionable, cancer-associated variants across a broad range of clinical and research applications.
What is Comprehensive Tumor Profiling?
Comprehensive tumor profiling analyzes hundreds of cancer-related genes in a single test, building a detailed molecular picture of each tumor to help guide targeted treatment decisions.
Why DNA and RNA?
DNA sequencing reveals the mutations and copy number changes that drive a tumor. RNA sequencing adds what DNA alone can miss. Gene fusions often have breakpoints in large or repetitive intronic regions that DNA-based methods struggle to detect, and RNA captures them directly while confirming the fusion is actually expressed. Together, they give a more complete view of every sample.
This Comprehensive Genomic Profiling (CGP) panel includes 560 genes covering mutations across all major tumor types and enables the detection of SNVs, CNVs, TMB, MSI, and select fusions. The breadth of this single assay allows for a robust understanding of a tumor profile, alleviating the need to use multiple tumor-specific panels or different modalities of testing.
DNA Panel Key Features
- 2.4 Mb panel size
- Covers SNVs, indels, CNVs, fusions, TMB, MSI
- 560 genes targeted
- Biomarkers from ESCO, ASCO, and NCCN guidelines
This panel includes 160 fusion genes associated with approximately 30 cancer types. The fusion genes were selected by CeGaT, a leading genetic diagnostic and sequencing company located in Europe. The design is not only for the detection of known gene fusions but is also used to identify novel gene fusions.
RNA Panel Key Features
- 3 Mb panel size
- 160 fusion associated genes with 66 genes
- Exon-aware probe design for novel fusion detection
- FFPE and low-input compatible
Related Poster
Development and Validation of a High-Throughput CAP/CLIA-Compliant Laboratory-Developed Test for Comprehensive Genomic Profiling
Why Use Sampled’s Tumor Profiling Service?
Sampled gives biopharma, CROs, and translational research labs fast, flexible access to clinically validated comprehensive tumor profiling.
By pairing broad DNA variant detection with deep RNA fusion analysis, we support patient care, drug development, and translational research.
Powered by Twist Bioscience DNA CGP & RNA Fusion Panels
Broad Coverage, Competitive Price
Rather than relying on whole-exome or whole-transcriptome sequencing, the panels focus sequencing on the 560 genes and 160 fusion targets most relevant to oncology, achieving high on-target depth with far less sequencing per sample.
Sampled’s tumor profiling service powered by the Twist CGP and RNA fusion panels delivers broad genomic and transcriptomic insight at a lower cost than alternative commercial options. Co-extracting DNA and RNA from a single FFPE sample and pooling both libraries on the NovaSeq X Plus further reduces input, handling, and per-sample sequencing costs.
One Partner, Sample to Data
Our team handles every step, from sample intake and QC of challenging inputs like FFPE tissue through sequencing, analysis, and bioinformatics, with results delivered in your preferred format.
Built on Twist panels and Illumina sequencing platforms in our CAP/CLIA laboratory, our workflows are designed for reproducibility across studies of any size, from pilot cohorts to large translational programs. And because our scientists work alongside you from study design through data interpretation, you spend less time managing logistics and more time turning data into discoveries.
DNA & RNA in One Place
Pair DNA/RNA extraction and tumor profiling from the same sample.
Expertise with Challenging Samples
Our team routinely handles real-world oncology material like FFPE, fresh frozen, and low-input samples.
Transparent Project Tracking
Dedicated project manager who provides status updates, tracks timeline, and optimizes client resources.
Scale with Confidence
From pilots to large cohorts, our standardized, HTP workflows deliver consistent, comparable data across every batch.
Go Deeper
Extend the same samples into transcriptome sequencing, single cell, spatial, proteomics, or epigenomics, all with one provider.
Tumor Profiling Applications
Oncology profiling supports many applications across research and clinical care. Common examples for our profiling service are listed below.
Clinical Trial and Precision Medicine Support
- Profiling FFPE samples from Phase I–III clinical trials
- Patient stratification
- Responder/non-responder analysis
- Clinical biomarker assessment
- Companion diagnostic development support
- Generation of data to support IND/BLA packages
Biomarker Discovery and Translational Research
- Biomarker discovery
- Resistance mechanism studies
- Translational oncology research
- Multiomic studies
- Cohort characterization
- Publication-driven research
- Grant-funded research programs
Cohort and Biobank Characterization
- Characterization of archived FFPE collections
- Large-scale cohort profiling
- Cohort building and stratification
- Data-generation initiatives
Potential new applications
At Sampled, we are always happy to discuss potential new applications, so if your application of interest is not listed, please don’t hesitate to get in touch to discuss it further.
Comprehensive Tumor Profiling Workflow
DNA and RNA Tumor Profiling
DNA and RNA are co-extracted from FFPE tumor curls using the AllPrep method. In the DNA arm, UMI-adapted TrueAmp libraries are enriched with a 560-gene (2.4 Mb) Oncology CGP panel; in the RNA arm, FFPE-repaired cDNA libraries are enriched with the 160-gene (~3 Mb) CeGaT RNA Fusion panel. Both are sequenced on the NovaSeq X Plus (2×150 bp).
FFPE tumor curls
TrueAmp library prep
Oncology DNA CGP Panel
RNA library prep
CeGaT RNA Fusion Panel
NovaSeq X Plus, 2×150 bp
Delivery of FASTQ and FastQC files
Sample Input Requirements
We work with a diverse range of sample types and have the technical expertise and infrastructure to process them efficiently and generate high-quality analytes for downstream analysis.
If pre-extracted nucleic acids are provided, we perform QC to ensure they are suitable for analysis.
| Item | Type |
|---|---|
| Sample Types | FFPE Tissue DNA and RNA extracted from FFPE tissue |
| Storage/Transport Conditions | FFPE Sample can be transported at ambient temperature. Pre-extracted DNA should be transported at 4°C (or as close to the previous storage conditions as possible). |
Find out more about our Comprehensive Tumor Profiling Services
Are you interested in learning more about the whole-genome sequencing services we offer here at Sampled? Do you have a project you’d like to discuss with one of our sequencing experts? Get in touch today to find out more and receive a custom quote for your project!
