Alignment of trimmed sequencing data (BAM format)
Information
The blood-based analysis of circulating tumor cells or tumor derived nucleic acids is referred to as “liquid biopsy”. It is a non-invasive way of diagnosing or monitoring a tumor disease, or treatment response. 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. Whereas ddPCR allows detecting a specific mutation with the highest sensitivity possible, NGS based analysis has the potential to provide a more complete genetic signature of the patient’s entire tumor burden.
CeGaT’s sequencing and digital PCR services offer reliable and accurate insights into different types of liquid biopsies, from nucleic acid extraction to tailored data analysis.
With our long-standing expertise in the diagnostic field, our clients benefit from strict quality control standards and, therefore, high quality results.
Start your project now
We are happy to discuss sequencing options and find a solution specifically tailored to your sequencing project.
In order to sequence your libraries as fast as possible and deliver the best sequencing data, please indicate the library preparation kit, number of pooled samples, barcodes / indices that have been used, and information about custom primers.
Turnaround time
Sequencing data and digital PCR data are delivered within 15 – 20 working days. A fast track option is available upon request. The turnaround time (TAT) highly depends on the requested digital PCR assay and bioinformatics level.
Delivery
Up to 70 Gigabyte of data will be available for download from our download portal FTAPI, a secure end-to-end encrypted system. Upon request, as well as for large sample batches, data can also be delivered via external hard drive, or uploaded 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.
Data will be irrevocably deleted after 5 months.
Bioinformatics
Raw sequencing data are automatically processed in order to facilitate immediate genetic evaluation. Included in delivery are demultiplexed, and adapter trimmed FastQ files. Further options for bioinformatic analyses are available:
- Calling and annotation of SNVs (hg19, mm10)
- Calling and annotation InDel
- Large homozygous deletions calling
- Variant comparisons in multiple samples
- Gene comparisons in multiple samples
Digital PCR results are available as raw data (.ddpcr, .glp files) and processed .xlsx files (copies/µl, droplet counts, etc).
Technical Information
At CeGaT, paired-end sequencing (2x100bp) is performed using the state-of-the-art Illumina NovaSeq 6000 Sequencing System. 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.
Explore our Liquid Biopsy product portfolio
LBP Classic
Starting material
Whole blood (e.g. Streck® tubes), plasma, other body fluids, isolated nucleic acids, cells
Technology
ddPCR analysis –
commercially available assays
Data format
DDPCR, GLP
LBP Flex
Starting material
Whole blood (e.g. Streck® tubes), plasma, other body fluids, isolated nucleic acids, cells
Technology
ddPCR analysis –
custom designed assays
Data format
DDPCR, GLP
LBS Flex
Starting material
Whole blood (e.g. Streck® tubes), plasma, other body fluids, isolated nucleic acids, cells
Technology
NGS analysis – whole exome sequencing, or panel enrichment
Data format
FASTQ
LBP: Liquid Biopsy PCR, LBS: Liquid Biopsy Sequencing. All products can be combined with further bioinformatics such as alignment, SNV calling and annotation.
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CeGaT is a provider of genetic diagnostics and NGS services. The company is based in Tübingen, Germany and is accredited according to CAP, CLIA and DIN EN ISO 15189.