Targeted Sequencing

Focus your sequencing where it matters most

When the answer to your research question lives in specific genes or genomic regions, targeted sequencing lets you concentrate sequencing depth exactly where it's needed. Use it to detect actionable variants in clinical research samples, uncover novel variants in cancer or disease-associated exomes, or genotype samples.

How researchers use targeted sequencing

Clinical and oncology research

Interrogate clinically relevant genes and regions including detecting single nucleotide variants (SNVs), copy number variants (CNVs), and gene fusions from DNA and RNA with hybrid capture panels for solid tumor or hematologic samples. Deep targeted sequencing provides the sensitivity needed for early detection studies, understanding treatment response, and minimal residual disease (MRD) characterization.

Agrigenomics & trait selection

Focus on specific markers or genes relevant to crop yield, disease resistance, or livestock production. And, with optional low-pass whole-genome coverage available in the same workflow, you can capture more markers without additional library preparation.

Genetic Disease  

For rare and Mendelian disorders research, targeted sequencing of focused gene panels, exomes, or non-invasive prenatal testing (NIPT) panels delivers the precision needed to identify pathogenic variants with high confidence, at reduced cost.

What to look for in a targeted sequencing workflow

Not all targeted sequencing workflows are equal, when evaluating approaches, a few factors matter most:

Turnaround time: Long hybridization steps and manual wash procedures can add hours of hands-on time and introduce variability. A streamlined approach with minimal manual intervention is ideal for high-throughput labs.
Sensitivity on difficult samples: Clinical research often requires detecting low variant allele frequency SNVs, CNVs, and gene fusions, even from challenging inputs like FFPE with custom with comprehensive genomic profiling (CGP), or minimal residual disease (MRD) panels.
Panel flexibility: Look for a workflow that can evolve with your research from focused gene panels to whole exomes, with guidance on custom panels sized for oncology, inherited disease, or agrigenomics.
Compatibility with established workflows: Switching to a new sequencing platform shouldn’t mean abandoning your existing workflows. Ensure your sequencing system supports pre-validated, industry-standard content and protocols from your preferred provider.
Downstream analysis options: Variant calling and reporting are important aspects of the workflow. Integration with established bioinformatics platforms helps avoid bottlenecks between sequencing and insights.

Targeted sequencing on the AVITI™ family of systems

Trinity™ target capture kits are designed to address each of these needs on the AVITI family of systems. Trinity shortens hybridization and moves wash steps onto the instrument, eliminating temperature-sensitive manual handling without sacrificing read accuracy or coverage uniformity.

The workflow is built for single day turnaround with an industry-leading 1-hour hybridization and no compromise on data quality, read accuracy or fold-80 base penalty.

targeted-sequencing-workflow

Built with flexibility in mind, Trinity and AVITI24™ offer end-to-end solutions and compatibility with industry-leaders in DNA extraction, library prep, and analysis.

Partner	DNA Extraction, Sample Prep Automation	Library Prep	Target Capture Panel	Sequencing	Secondary Analysis	Reporting
	Beckman Biomek i5 8 and i7 8+96, Hamilton NGS Star, PT Labtech firefly, Agilent Bravo B, Revvity Scicione NGSx, Tecan Fluent / Dreamprep, Opentrons Flex NGS	Twist EF2.0, FlexPrep	Twist CGP, Exome, Bovine, Canine, custom panels; Trinity Freestyle compatible	Element AVITI, AVITI24	QIAGEN CLC Genomic Workbench Curio Genomics	QIAGEN QCI Interpret Curio Genomics
	Agilent Magnis NGS Prep System, Bravo	SureSelect XT HS2	Agilent SureSelect panels, Avida cfDNA panels Trinity compatible		SeqOne	SeqOne
	QIAsymphony SP, QIAcube Systems, EZ1 Advanced XL	QIAseq Multimodel DNA / RNA Lib Kit	Qiagen xHYB CGP, Exome panels Trinity compatible		QIAGEN CLC Genomics Workbench	QIAGEN QCI Interpret
	Hamilton Clinical STARlet, NGS Star	SOPHiA Genetics Universal Library Prep	MSK-ACCESS, MSK IMPACT for CGP, Exome, HRD panels Trinity compatible		SOPHiA DDM