Custom Target Sequencing

Are you interested in small, focused panels targeting specific regions of interest in human or non-human species? For comprehensive analyses—such as full genes, exons, or non-coding regions over 10 kb—we offer a hybridization-based approach using Agilent SureSelect technology. This method enables efficient enrichment of large genomic regions and supports the detection of a wide variety of variant types, including SNPs, INDELs, CNVs, and structural rearrangements. Custom-designed synthetic probes ensure precise targeting of your regions of interest, delivering high-quality and reliable results tailored to your study.

For target regions smaller than 10 kb, our proprietary custom amplicon sequencing offers a robust and flexible solution with deep coverage and reliable variant detection. Advanced primer design enables the simultaneous amplification and sequencing of hundreds of specific regions in a single reaction.

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Highlights

Expertly developed custom assays by Ph.D.-level scientists to ensure highly consistent and uniform target coverage
Detection of relevant SNPs and InDels, structural rearrangements and copy number variations (CNV)
Ultra-sensitive detection levels down to 1% allele frequency
Highly cost-effective pre-capture pooling of samples before hybridization
Unique Dual Indexing (UDI) for high data accuracy and minimal cross-contamination
Advanced bioinformatics services with detailed, customizable analysis reports
Optional high-quality DNA isolation service available
Data transfer via secure FTP

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Sample Submission

Specifications

QC of DNA for both quantity and integrity
Illumina-compatible DNA library preparation using Unique Dual Indexing (UDI)
Library indexing offered at pre-capture and stages of the hybridization workflow using Agilent SureSelect technology
Technology: Illumina NovaSeq
Run type: paired-end
Read length: 2 x 150 bp
F, guaranteed read amounts as option available
Depending on your needs we recommend the following coverage:
- Somatic/rare variants: 100x

Starting material

Sample Type: Genomic DNA (RNA-free)
Minimum Amount: 100 ng (gDNA), 200 ng (FFPE DNA), 30 ng (cfDNA)
Volume: 20 to 100 µL (gDNA + FFPE DNA), 20 to 30 µL (cfDNA)
Concentration: >1 ng/µl (gDNA, cfDNA), >2 ng/µl (FFPE DNA)
Purity (OD260/280): 1.8-2.0
Resuspension Buffer: Water, EB, or low TE (<0.1 mM EDTA)
Format: barcode labelled 1.5 ml Eppendorf Safe-Lock tubes; or for > 48 samples in Eppendorf twin.tec PCR Plate 96, full-skirted, leave position G12 & H12 empty 
Shipment Method: room temperature

Deliverables

Raw data as FASTQ files (.fastq.gz)

Additional deliverables for optional bioinformatics, e.g. variant analysis package:

Alignment file (.bam)
SNP and InDel tables including annotated variants and effects (.vcf, .tsv, .bed)
Comprehensive data analysis report (.pdf, .html)
Tables of copy gain and copy loss events (.tsv)
View our demo variant analysis report below

Applications & services

Our Variant Analysis service includes detection and annotation of germline single nucleotide polymorphism (SNPs), insertions and deletions (InDel).
Additionally, we provide optional services such as structural variant analysis, copy number variation detection, tumor vs. normal and tumor-only (somatic) variant analysis to pinpoint genetic mutations in tumor samples, joint-genotyping to analyze multiple samples for shared genetic variations, and population genotyping to understand genetic diversity within specific groups.

CNV analysis should be performed in paired analysis of tumour versus matched normal tissue which is used as reference.
In the case of tumour FFPE samples, we strongly recommend sending a healthy tissue FFPE sample from the same patient. Alternatively, tumour FFPE samples from at least seven other patients can be sent.
For fresh frozen tissue, we strongly advise that blood or healthy tissue from the same patient is sent. Alternatively, fresh frozen tissue from at least seven other patients or controls is recommended.

For optional DNA isolation service from a wide variety of materials, including cell pellets, fresh frozen tissue, blood, and FFPE slides, please refer to our DNA isolation guide.

Frequently Asked Questions

Agilent SureSelect is a hybridization-based target enrichment method that allows selective capture of large genomic regions for deep sequencing.

We can target full genes, exons, and non-coding regions larger than 10 kb, customized to your study’s requirements. Please provide coordinates based on the hg38 reference genome. If you prefer to use gene names, kindly specify the databases you are referencing to ensure accurate targeting.

Our approach detects SNPs, insertions/deletions (InDels), copy number variations (CNVs), and structural rearrangements.

We accept high-quality genomic DNA from various sample types, including blood, fresh-frozen tissue, and FFPE.

Our method ensures highly uniform coverage, reducing bias and enabling reliable variant detection across all targeted regions.

Yes, with high sequencing depth, we can detect variants at low allele frequencies down to 1% allele frequency.

Quality is important for us at Eurofins

Our products and services are produced and performed under strict quality management and quality assurance systems.

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Custom Target Sequencing

Frequently Asked Questions

What is Agilent SureSelect technology?

What regions can be targeted with this service?

What types of variants can be detected?

What sample types are compatible with this service?

How uniform is the coverage across target regions?

Can this method detect rare variants?

Quality is important for us at Eurofins

Our products and services are produced and performed under strict quality management and quality assurance systems.