Utilize the potential of liquid biopsies through NGS or ddPCR analysis
The blood-based analysis of circulating tumor cells or tumor derived nucleic acids is referred to as “liquid biopsy”. The main target of this analysis is cell-free DNA (cfDNA), which is released into the blood stream by necrotic and apoptotic cells. Elevated levels of cfDNA are found in patients with cancer and other types of diseases.
Since only a small fraction of the circulating DNA is derived from the tumor (ctDNA), highly sensitive detection methods, as for example digital droplet PCR (ddPCR), or next generation sequencing (NGS), are advantageous.
The applications of liquid biopsy are manifold, Therefore, our liquid biopsy product portfolio covers the targeted analysis of single variants, a selected panel of cancer associated genes, as well as large, explorative approaches.
CeGaT’s sequencing and digital PCR services offer reliable and accurate insights into liquid biopsies, from nucleic acid extraction to tailored data analysis.
Your project will benefit from our long-standing expertise in the diagnostic field and thus, strict quality standards, as well as practical knowledge.
Application areas of Liquid Biopsies:
- Monitoring a tumor disease
- Monitoring treatment response
- Patient stratification, treatment selection
- Detection of minimal residual disease
- Early detection and profiling of resistance to therapy
Turnaround time
Sequencing data and digital PCR data are delivered within 20 – 30 working days.
A fast track option is available upon request.
The turnaround time (TAT) may be longer for custom digital PCR assays, and custom bioinformatic analyses.
Delivery
Your sequencing data will be available for download from our server.
Upon request, as well as for large sample batches, data can also be delivered via external hard drive, or upload to your own server.
Storage
The original samples and, if applicable, the isolated nucleic acids will be stored at CeGaT for a period of 3 months after data delivery.
Your data will be stored for 5 months.
Explore our Liquid Biopsy product portfolio
LB Target
Starting material
Whole blood (e.g. Streck® tubes), plasma, other body fluids, isolated nucleic acids
Technology
ddPCR analysis (commercially available assays or custom design)
Duplex UMIs
n.a.
Analytical Sensitivity
Assay dependent, ≥ 0.5% VAF
Variant type
SNVs
Deliverables
Project report, DDPCR, GLP
LB Focus
Starting material
Whole blood (e.g. Streck® tubes), plasma, other body fluids, isolated nucleic acids
Technology
NGS analysis
Panel (CeGaT)
Duplex UMIs
Yes
Analytical Sensitivity
≥ 0.25% VAF
Variant type
SNVs and InDels
Deliverables
Project report, FASTQ, BAM, VCF, TSV
LB Exploratory
Starting material
Whole blood (e.g. Streck® tubes), plasma, other body fluids, isolated nucleic acids
Technology
NGS analysis
TSO500 ctDNA (Illumina)
Duplex UMIs
Yes
Analytical Sensitivity
≥ 0.5% VAF
Variant type
SNVs and InDels, DNA fusions, CNVs, MSI, TMB
Deliverables
Project report, FASTQ, BAM, VCF, TSV, TMB/MSI report
LB Flex
Starting material
Whole blood (e.g. Streck® tubes), plasma, other body fluids, isolated nucleic acids
Technology
NGS analysis
Panel (CeGaT)
Duplex UMIs
No
Analytical Sensitivity
≥ 2% VAF
Variant type
SNVs and InDels, CNVs
Deliverables
Project report, FASTQ
Bioinformatics
LB Target, digital PCR results are available as raw data (.ddpcr, .glp files) and processed .xlsx files (copies/µl, droplet counts, etc).
Raw sequencing data are automatically processed in order to facilitate immediate genetic evaluation. Included in delivery are demultiplexed, and adapter trimmed FastQ files.
LB Focus data analysis includes the alignment of trimmed sequencing data, calling and annotation of SNVs and InDels.
LB Exploratory data are processed using the DRAGEN TruSight Oncology 500 ctDNA Analysis Software (Illumina). The analysis includes the alignment of trimmed sequencing data, calling and annotation of SNVs and InDels, as well as fusions. Furthermore, CNVs and the MSI/TMB status are evaluated.
LB Flex
Further options for bioinformatic analyses are available:
- Alignment of trimmed sequencing data (BAM format)
- Calling of SNVs and InDels (VCF format)
- Annotation of SNVs and InDels (variant frequency and consequence, population frequency, dbSNP ID, position in protein, GNOMAD)
- Loss of heterozygocity calling
- CNV calling
- Variant comparisons in multiple samples
Technical Information
At CeGaT, paired-end sequencing (2 x 100 bp) is performed using state-of-the-art Illumina NovaSeq 6000 Sequencing Systems. Digital PCR is performed using the QX200 Droplet Digital PCR System (Bio-Rad).
Please get in touch for specific liquid biopsy requests, other than those presented in our product portfolio. We can provide further solutions.
Contact Us
Start Your Project Now
We are happy to discuss sequencing options and to find a solution specifically tailored to your clinical study or research project.
When getting in contact, please specify sample information including starting material, number of samples, preferred library prep option, preferred sequencing depth and required bioinformatics, if possible.
Further Reading
Webinar: Liquid Biopsy
