NGS FAQ

Which are the currently available NGS panels for mutation detection?

Many NGS panels are available for mutation detection, ranging from small hotspot panels to broad comprehensive genomic profiling assays, liquid-biopsy panels, hereditary cancer panels and custom capture designs. The right choice depends on sample type, variant class, target genes, required sensitivity, instrument compatibility, regulatory context and bioinformatics workflow.

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Quick answer

Current NGS mutation-detection options include broad oncology comprehensive genomic profiling panels, focused hotspot panels, hereditary cancer germline panels, liquid-biopsy panels, exome-style panels, UMI-based low-frequency variant panels and fully custom capture or amplicon panels. Major providers include Illumina, Thermo Fisher Scientific, QIAGEN, Agilent, Roche, IDT, Twist Bioscience, SOPHiA GENETICS and clinical testing providers such as Foundation Medicine, Guardant Health and Invitae/Labcorp.

Important: product status, intended use, CE-IVD/FDA/RUO status, regional availability, gene content and compatible sequencers can change. Before purchasing or ordering any panel, verify the latest product sheet and regulatory status directly with the provider.
            

Main categories of NGS panels for mutation detection

Category	Typical use	Common variant classes
Focused hotspot panels	Fast, high-depth testing of recurrent cancer or disease mutations.	SNVs, small indels; sometimes selected CNVs or fusions.
Comprehensive cancer panels	Broad solid-tumour or hematologic malignancy profiling.	SNVs, indels, CNVs, fusions, rearrangements; sometimes TMB, MSI or HRD-related features.
Liquid-biopsy panels	Mutation detection from circulating tumour DNA or cell-free DNA.	Low-frequency SNVs and indels, selected CNVs and fusions; often UMI/error-suppressed.
Hereditary cancer panels	Germline predisposition testing for inherited cancer risk.	Germline SNVs, indels and deletion/duplication variants in predisposition genes.
Exome and broad disease panels	Variant discovery across coding genes or large gene sets.	Mostly SNVs and indels; CNV calling depends on assay and validation.
Custom panels	Research or industrial projects with specific genes, organisms, regions or assays.	Defined by design: SNVs, indels, CNVs, methylation targets, fusion partners or other target classes.

Examples of currently available panel products and assay families

The table below is not exhaustive. It lists representative, currently marketed panel products or assay families that are commonly considered for mutation-detection or cancer-genomics projects.

Provider / panel	Scope and sample type	Key notes for selection
Illumina TruSight Oncology 500 v2	CGPDNA + RNA Pan-cancer NGS assay for FFPE tissue; targets 523 genes for DNA and RNA variant types.	Designed for broad oncology research profiling including SNVs, indels, CNVs, fusions and large BRCA1/2 rearrangements.
Thermo Fisher Oncomine Comprehensive Assay Plus	CGPIon Torrent Comprehensive genomic profiling assay covering 517 genes.	Detects SNVs, indels, CNVs and fusions; designed for Ion Torrent Genexus and GeneStudio S5 workflows.
Agilent SureSelect Cancer CGP Assay	CGPHybrid capture Pan-cancer panel for comprehensive genomic profiling of solid tumours.	Supports detection of SNVs, indels, CNVs, translocations, gene fusions and immuno-oncology biomarkers such as TMB and MSI.
QIAGEN QIAseq Targeted DNA Panels	Targeted DNAMolecular barcodes Targeted panels using digital DNA sequencing with molecular barcodes.	Useful for low-frequency variant detection where PCR duplicates, false positives and library bias must be controlled.
Roche AVENIO Tumor Tissue CGP Kit V2	CGPFFPE tissue In-house NGS research assay for comprehensive genomic profiling of solid tumours from FFPE tissue-derived DNA.	Useful for laboratories seeking an in-house Roche/Foundation Medicine-aligned CGP research workflow.
IDT xGen Pan-Cancer Hybridization Panel	Pan-cancerHybrid capture Panel capturing 127 significantly mutated genes implicated across 12 tumour types.	Research-focused panel for deeper sequencing coverage of cancer-associated genes.
IDT xGen Oncology & Inherited Diseases Amplicon Panels	AmpliconFFPE / cfDNA compatible Includes the xGen 57G Pan-Cancer Amplicon Panel covering 57 oncology-related genes.	Focused amplicon workflow; useful when turnaround, input compatibility and focused gene content are priorities.
Twist Target Enrichment and Custom NGS Panels	CustomDNA / RNA / methylation Predesigned and custom target-enrichment options for flexible target selection.	Useful when off-the-shelf panels do not match the exact gene list, organism, methylation target set or research endpoint.
SOPHiA DDM for Solid Tumors	Solid tumoursDNA + RNA Targeted IVD and RUO NGS-based applications for DNA and RNA analysis.	Combines panel applications with SOPHiA DDM analytics; evaluate regional regulatory status and available content.
Invitae / Labcorp hereditary cancer panels	GermlineHereditary cancer Clinical hereditary cancer testing panels for inherited predisposition variants.	Different from somatic tumour panels: intended for germline risk assessment rather than tumour mutation profiling.

Clinical send-out tests are not the same as in-house panel kits

Some “panels” are clinical laboratory testing services rather than kits that a laboratory purchases and runs internally. They can be highly relevant for clinical oncology but should be discussed separately from research-use assay kits.

Clinical testing service	General scope	Selection note
FoundationOne CDx / FoundationOne Liquid CDx	FDA-approved broad companion diagnostic and comprehensive genomic profiling testing; FoundationOne CDx detects genetic variations in 324 genes according to FDA documentation.	Useful when a regulated clinical report and companion-diagnostic context are needed, subject to country-specific availability and indications.
Guardant360 CDx and Guardant liquid-biopsy portfolio	Blood-based liquid-biopsy comprehensive genomic profiling tests for advanced cancer. Gene content differs by product and regulatory context.	Useful when tissue is unavailable or serial blood-based profiling is required; liquid biopsy sensitivity depends on tumour shedding and context.
Hereditary cancer testing services	Germline panels for inherited cancer predisposition, such as hereditary breast/ovarian, prostate, gastrointestinal and mixed cancer-risk panels.	Requires appropriate genetic counselling, consent and germline interpretation framework.

How to choose an NGS mutation-detection panel

Variant classes Confirm whether the panel detects SNVs, indels, CNVs, fusions, structural variants, MSI, TMB, HRD-related markers or methylation.

Sample type FFPE tissue, fresh-frozen tissue, blood, cfDNA, bone marrow, germline DNA and RNA each require different assay assumptions.

Target content Check whether the required genes, exons, hotspots, introns, fusion partners and clinically relevant regions are covered.

Sensitivity Low-frequency variants require high depth, error suppression, molecular barcodes and validated thresholds.

Instrumentation Panel chemistry must match sequencers, library-preparation systems, automation and local laboratory capabilities.

Regulatory status RUO, CE-IVD, IVDR, FDA-cleared, FDA-approved and laboratory-developed test status are not interchangeable.

Bioinformatics Variant calling, CNV calling, fusion detection, annotation, reporting and QC may require specific software or custom workflows.

Data ownership For research and industrial projects, clarify whether you need raw FASTQ/BAM/VCF files, scripts, metadata and reproducible reports.

Recommended panel-selection workflow

1. Define question Somatic tumour profiling, hereditary testing, ctDNA monitoring, fusion detection or custom research.

2. Define sample FFPE tissue, blood, cfDNA, fresh-frozen tissue, RNA, germline DNA or mixed material.

3. Define targets Required genes, hotspots, exons, introns, CNVs, fusions, TMB/MSI or methylation regions.

4. Compare panels Check gene content, coverage, input requirements, sequencer compatibility and regulatory status.

5. Check depth Estimate raw depth, usable depth and molecular depth for the required sensitivity.

6. Plan analysis Define variant callers, annotation resources, QC thresholds and reporting structure.

7. Validate Use reference materials, known positives and orthogonal methods where needed.

8. Report clearly Document covered regions, limitations, software, parameters and interpretation categories.

Common pitfalls

Assuming all cancer panels detect fusions Fusion detection requires suitable design. Many DNA hotspot panels do not reliably detect all fusions.

Ignoring covered regions A gene may be listed, but only hotspots or selected exons may be covered.

Confusing germline and somatic panels Hereditary cancer panels and tumour mutation panels have different goals, sample types and interpretation frameworks.

Choosing panel size by gene count alone Uniformity, depth, variant classes, bioinformatics and validation can matter more than the number of genes.

Underestimating FFPE and cfDNA constraints Damaged DNA, low input and short fragments require panel chemistry and QC thresholds adapted to the sample.

Forgetting regulatory status RUO assays are not automatically suitable for clinical diagnostics without appropriate validation and regulatory compliance.

How SciBerg can support panel comparison and data analysis

SciBerg can help research and industrial partners select, evaluate and analyse NGS mutation-detection panels.

Comparison of panel content against project-specific gene lists.
Assessment of whether SNVs, indels, CNVs, fusions, MSI, TMB or methylation are supported.
Sequencing-depth and molecular-depth planning.
FASTQ/BAM/VCF analysis workflows for panel data.
UMI-aware duplicate handling and low-frequency variant analysis.
Variant annotation, driver prioritisation and report preparation.
AI-assisted literature triage and evidence summarisation.
Transparent scripts, software versions, parameters and reproducible documentation.

Frequently asked questions

Are there ready-made NGS panels for mutation detection?

Yes. Ready-made NGS panels are available for cancer mutation profiling, hereditary cancer testing, inherited disease testing, pharmacogenomics, infectious disease, mitochondrial DNA and custom research applications. The best panel depends on whether the project is somatic or germline, tissue or liquid biopsy, DNA or RNA, focused hotspot testing or broad comprehensive genomic profiling.

What is the difference between a panel kit and a clinical test?

A panel kit or assay is purchased and run in a laboratory using compatible instruments and analysis software. A clinical test is usually ordered from a testing provider that performs sequencing and reporting in its own laboratory. Regulatory status, intended use and availability differ by country.

Which NGS panel is best for tumour mutation detection?

There is no single best panel. For broad tumour profiling, comprehensive genomic profiling panels such as Illumina TruSight Oncology 500, Thermo Fisher Oncomine Comprehensive Assay Plus, Agilent SureSelect Cancer CGP, Roche AVENIO Tumor Tissue CGP and similar solutions are commonly considered. For focused projects, smaller hotspot, amplicon or custom panels may be more cost-effective.

Should I use a large comprehensive panel or a small hotspot panel?

Use a large panel when you need broad biomarker coverage, copy number, fusions, TMB, MSI or discovery-oriented interpretation. Use a small panel when the question is limited to known hotspots or a focused set of genes, especially when DNA input is limited and deep coverage is required.

Can NGS panels detect fusions?

Some panels can detect fusions, but not all. Fusion detection often requires RNA-based sequencing or special DNA-based structural-variant design. Always check whether the panel includes RNA content, intronic coverage, known fusion partners or novel-fusion capability.

Can NGS panels detect copy-number variants?

Many comprehensive cancer panels can detect copy-number changes, but performance depends on panel design, target size, tumour purity, coverage uniformity, matched normal availability and the bioinformatics pipeline.

Can NGS panels detect very low-frequency variants?

Low-frequency variant detection usually requires high depth, error suppression, molecular barcodes or UMIs, suitable input material and validated analysis thresholds. Panels using molecular barcodes are often preferred for rare variants, cfDNA and minimal residual disease-style applications.

Can SciBerg help choose a panel?

Yes. SciBerg can help compare panel content, target genes, variant classes, sequencing depth, bioinformatics requirements, compatibility with available instruments, regulatory context and expected deliverables for research or industrial projects.

Selected sources and product pages

These links point to official provider pages or public regulatory documentation. Always confirm the latest version, intended use, regional availability and gene list before ordering a panel.

Illumina TruSight Oncology 500 v2 Thermo Fisher Oncomine Comprehensive Assay Plus Agilent SureSelect Cancer CGP Assay QIAGEN QIAseq Targeted DNA Panels Roche AVENIO Tumor Tissue CGP Kit V2 IDT xGen Pan-Cancer Hybridization Panel IDT xGen Oncology & Inherited Diseases Amplicon Panels Twist Target Enrichment Panels SOPHiA DDM for Solid Tumors FoundationOne CDx FDA: FoundationOne CDx Guardant360 CDx Invitae hereditary cancer panels