SARS-CoV-2 Genome Sequencing: CeGaT now offers Genome Sequencing for Coronavirus Variant Detection

To better understand the spread and evolution of the Covid-19, it is essential to identify viral variants. CeGaT now offers SARS-CoV-2 genome sequencing and classification of the virus. Next-generation sequencing provides valuable information on changes in the SARS-CoV-2 virus, helping to understand which viral variants have a higher potential to infect humans. Variants that can be detected include B.1.1.7, B.1.351, and P.1.

Although the coronavirus has a lower mutation rate than most RNA viruses, mutations accumulate and result in genomic diversity both between and within infected patients. Since the first entry into the human host, SARS-CoV-2 has acquired several polymorphic nucleotide positions in the genome. Some of these new viral variants are even more infectious than the virus first detected in Wuhan, China. 

Potential applications of CeGaT’s SARS-CoV-2 sequencing:

  • Detection and tracing of novel genetic variants
  • Assessment of the impact of mutations on the performance of diagnostic methods, antiviral drugs, or vaccines
  • Exploration of transmissibility and infectivity of virus variants
  • Investigation of virus transmission dynamics

You will receive:

  • Ready-to-use SARS-CoV-2 sequencing data and a project report

Optional bioinformatics:

  • A report including mapping data, statistics, and variants
  • Consensus sequence of the SARS-CoV-2 genome sequence
  • Classification of SARS-CoV-2 genome sequence according to official Pango lineages

As described, you will receive raw sequencing data or use our bioinformatics data analysis service to classify the SARS-CoV-2 genome sequence data. Bioinformatics is conducted by using CoVpipe, a pipeline recommended and maintained by the Robert Koch Institute (RKI) for the reference-based reconstruction of NGS-based SARS-CoV-2 genomic data.

With SARS-CoV-2 genome sequencing, we aim to contribute to the fight against the pandemic. We offer the highest quality standards for sample analysis. It is crucial for us always to use the most advanced technology and constantly evolve to continuously provide you with the most innovative and best sequencing technology.

More information

New Service: Online Genetic Consultation

CeGaT’s online genetic consultation service offers patients the opportunity to receive consultation from a consultant clinical geneticist. The online genetic consultation is aimed at both patients and their relatives who fear that they themselves are carriers of a hereditary disease. Expectant parents can use the online genetic consultation to determine the probability of passing on a genetic variant.

The purpose of the online genetic consultation is to discuss and clarify diverse human genetic issues. This concerns, in particular, the following areas:

  • Paediatric genetics
  • Oncogenetics
  • Reproductive genetics and
  • Neurogenetics

Of course, we also provide consultation in other familial conditions or diseases as well as in all questions of medical genetics.

Dr. med. Schell-Apacik is consultant clinical geneticist. In addition to various positions at the Children’s Center in Munich, he also worked at the Children’s Hospital in Philadelphia. He also practiced as a consultant clinical geneticist in Berlin and took over the medical management of the Medicover Berlin- Westend MVZ, also in Berlin.

The online genetic consultation includes:

  • A detailed discussion with a consultant clinical geneticist
  • Clarification of the question and the aim of the consultation
  • Evaluation of the submitted medical findings
  • A structured anamnesis of the family and medical history, including the creation of a pedigree over 3 generations as well as the recording of the previous course of the disease
  • An assessment of genetic risks
  • Detailed counseling on the possible significance of this information for life and family planning
  • If necessary, the initiation of genetic laboratory tests

The procedure of the online genetic consultation:

To guarantee the best possible quality of the online genetic consultation, CeGaT recommends submitting important documents in advance.  FTAPI SecuPass technology, which encrypts all data end-to-end, is used for secure data transfer.

CeGaT’s consultant clinical geneticist evaluates the documents and contacts persons seeking advice to make an appointment. An online genetic consultation lasts 1.5 hours, although in exceptional cases, the consultation may take longer. A genetic examination following the online genetic consultation is not obligatory and only takes place upon explicit request. If the person seeking advice is interested in genetic testing after the consultation, the blood required for this can be drawn on-site by the supervising specialist or family doctor and sent to CeGaT.

After completion of the genetic diagnostics, patients receive a medical report that contains all relevant findings as well as the results of the counseling session.

CeGaT determines together with the person seeking advice to determine individually which tests are necessary and supports the person seeking advice in weighing up possible risks and therapy options.

Further information on online genetic consultation.

Update of CeGaT Exome Xtra Increases Solution Rate of Complex Patient Cases

Based on the latest scientific findings, CeGaT has optimized its whole-exome diagnostics, further increasing the solution rate of complex patient cases. Since the update, CeGaT Exome Xtra offers optional pharmacogenetic testing. The medical report will then also provide information on personal drug efficacy, enabling individualized medication.

One year ago, CeGaT launched CeGaT Exome Xtra, the most effective genetic test for patients with complex, non-specific, and rare diseases. CeGaT Exome Xtra combines all genetic diagnostics achievements in one test and solves more patient cases than commercially available whole-exome sequencing (WES) and whole-genome sequencing. Regular updates ensure that CeGaT Exome Xtra is always in line with the latest genetics research to increase the diagnostic yield.

20 percent more intronic variants covered

Unlike standard WES, CeGaT Exome Xtra considers all known disease-causing regions of the complete genome, including relevant intronic variants. In the update, the new relevant variants of the HGMD and ClinVar databases were also added to CeGaT Exome Xtra. The number of intronic variants covered was thus increased to more than 20,000 variants. CeGaT Exome Xtra thus still covers all regions of the genome described as disease-relevant in HGMD and ClinVar.

By including intronic variants, CeGaT Exome Xtra sets itself apart from commercially available exome enrichments. It is not limited to coding regions, but includes all disease-causing non-coding variants and also covers individual transcripts or cryptic exons.

Pharmacogenetic testing helps in drug selection and dosage

Pharmacogenetics takes into account that all people metabolize drugs in different ways: A drug that is beneficial to one person remains ineffective or may even cause harm in another. With this update, CeGaT Exome Xtra offers the option of pharmacogenetic testing. Exome Xtra data is used to classify about 80 active ingredients as to whether they are degraded quickly or slowly in the individual. Based on this information, physicians can select the most suitable drug and administer it in the correct dosage.

Continuous consideration of scientific progress

CeGaT Exome Xtra is designed to generate the most comprehensive sequencing data and provide an unmatched foundation for the best genetic diagnostics on the market. Knowledge of genetic diseases is expanding rapidly; new genomic regions of clinical relevance are identified every year. To reflect this progress, CeGaT continuously reviews and revises its genetic diagnostics. The diagnostic panels underlying CeGaT Exome Xtra are constantly updated in close collaboration with medical experts and using the latest literature.

With CeGaT Exome Xtra, patients and treating physicians benefit from a unique approach that combines the advantages of Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) while avoiding their disadvantages. Thereby, CeGaT Exome Xtra achieves better results than commercially available WES and WGS and dramatically increases diagnostic yield. More information can be found here.

Update and Extension of the Panel for Genetic Eye Diseases

CeGaT has updated and expanded the Diagnostic Panel for Genetic Eye Diseases. As part of the regular updates, the panel was revised according to the current scientific knowledge, thereby increasing its diagnostic sensitivity.

In addition, new gene sets have been added to the panel, which can now also be used for precise diagnoses of the following hereditary eye diseases:

Congenital nystagmus, X-linked

Congenital nystagmus is characterized by congenital, uncontrolled movements of the eyes, which are also described as jerking or trembling. Eye movement disorders vary greatly in frequency, amplitude, and shape (e.g., pendulum nystagmus) and are sometimes accompanied by visual impairment and disturbances. The X-linked nystagmus usually occurs in the first half-year of life and results from changes in the genes FRMD7 and GPR143.

Progressive external ophthalmoplegia

Progressive external ophthalmoplegia manifests in progressive paralysis of the external eye muscles, which severely limits the movement of the eyes. Since eyelid muscles can also be affected, a common sign of the disease is the drooping of one or both eyelids (ptosis). The cause are mitochondriopathies, which are caused by a malfunction or damage to the mitochondria.

Congenital cranial dysinnervation syndromes

Congenital cranial dysinnervation syndromes (CCDDs) are a subgroup of incomitant strabismus. It describes strabismus syndromes in which the degree of strabismus depends on the direction of gaze. It is characterized by a non-progressive disturbance of the eye movement (oculomotor function), in some cases accompanied by upper eyelid ptosis, i.e. the drooping of an eyelid. The syndromes are caused by diseases or maldevelopments of eye muscles or eye cavities (orbital diseases) or cranial nerves (cranial nerve paresis). They cause a defective innervation of the muscles.

All CeGaT panels are examined with CeGaT’s large panel approach. We always sequence all genes of a panel and evaluate the requested gene set. If necessary, we can quickly extend the evaluation to other gene sets. This gives you access to the most flexible and cost-efficient differential diagnostics. In addition, we offer a screening of all differential diagnostic relevant genes of the panel for variants of ACMG classes 4 and 5. CeGaT’s panel diagnostics also include the free of charge regular re-evaluation of variants of uncertain clinical significance (VUS) to increase the diagnostic yield further.

We are convinced that all patients should receive the best possible diagnostics. For this reason, our panels routinely examine single nucleotide variation (SNVs) and copy number variants (CNVs) and check for mosaicism. If necessary, we validate pathogenic deletions or duplications using MLPA or qPCR before reporting. The highest quality is our standard.

For further information on the panels, please contact us at The new panel can be ordered here.

Frequently Asked Questions about the Corona Test Center at Stuttgart Airport

My sample was taken before August 13th, 2020. Can I ask you for more information?
We have only been operating the test center at Stuttgart Airport since August 13, 2020. We cannot provide any information about medical reports that were issued before that date.

Can I get my results by email?
No. For data protection reasons, we are not allowed to send any medical reports by email. You can receive your result via the Corona Warning App or by contacting our hotline under 07071 5654420 (available Monday – Friday  9:00 a.m. – 16:00 p.m.). Each tested person receives the result by mail to the address stated at the airport.

How long will it take to get a result?
Up to 3 days.

Will my result be reported to the public health department?
All positive findings will be reported to the public health department.

Can I have a test carried out at the airport if I am not arriving by plane?
All travelers returning from abroad can be tested. However, we need verification (hotel bill, train ticket etc.) that you have stayed abroad.

When can I get tested?
The test center is open daily from 6:00 a.m. to 11:00 p.m.