Like a needle in a haystack: A genetic test provides certainty

Centogene was founded in 2006. It is headquartered in Rostock, Germany, with additional locations in Boston, Berlin, Belgrade and Rotkreuz, Switzerland. The company, which has a bio-database of more than 800,000 individuals, specializes in rare metabolic and neurodegenerative diseases. Their genetic tests enable patients with genetic and rare diseases to be diagnosed.

Everyone knows the big diseases: diabetes, cancer, and high blood pressure. A Lot of research is carried out on these and the medical progress is impressive. By the end of the decade, for example, there could be a vaccine against the fatal types of cancer. However, hardly anyone talks about “rare” diseases from which comparatively few people suffer and whose names hardly anyone knows. Or have you ever heard of abetalipoproteinemia or Zollinger-Ellison syndrome?

There are more than 6,000 rare diseases in the EU; in the USA, the number is given as over 10,000, depending on what is meant by “rare”. While some of these diseases only affect a few dozen people, others can affect more than 200,000. An estimated 350 million people worldwide are affected by one of these diseases. 80 percent are genetically determined, in 70 percent of those affected, the condition begins in childhood and 30 percent do not live to see their fifth birthday. This makes it all the more tragic that there is only effective medical treatment for 5 to 10% of these diseases.

Centogene is committed to changing this. Centogene relies on data - lots of data. The goal is to help diagnose these diseases accurately, because even that is extremely difficult. Any patient who has to run from doctor to doctor with undefined symptoms can confirm this. Centogene, which was founded in 2006 in Rostock and has its headquarters there, focuses on metabolic diseases and neurodegenerative diseases. The company has built up a bio-database with blood and tissue samples from more than 800,000 patients, as well as information from clinical and genetic research. In this database, biomedical scientists search for the needle in the haystack: symptoms that are typical of a particular rare disease.

Anyone who thinks they might have a rare disease can get a Centogene test from their doctor. It provides patients with certainty and Centogene’s scientists with more information for their database. The tests can be easily ordered via Centogene’s online portal CentoPortal.

They also have an online store system, but it’s not easy to use. The information the doctor provides is transferred from the store to the Customer Relation Management (CRM). The Enterprise Resource Planning (ERP) contains the information to send test kits, and the laboratory works with the Laboratory Inventory Management System (LIMS), i.e., its own software. These four applications used to access different data sources, and there was no central data exchange between them; in the past, information was even typed in manually. This was not a problem when the company was small, and the daily orders could be counted on two hands.

But those days are long gone for Centogene. Around 30,000 doctors worldwide now use the service, and the company processes hundreds of test kits every day - and the trend is rising. Manual processing is no longer an option, and discrepancies could occur within the different systems for the same data. Several years ago, the management realized the situation couldn’t continue. In future, data on customers, products, orders and prices would need to be up-to-date and synchronized in all four applications. The company brought PCG on board for this task.

PCG experts quickly realized that the technical implementation was still the least of the problems. “There wasn’t an integrated project management between Centogene and the external stakeholders,” says the Delivery Manager at PCG. PCG experts were therefore primarily needed as project manager, coach and trainer. Not only were four different teams at Centogene responsible for the four software packages, but the providers of this software - above all Microsoft and Salesforce - also had to be brought together. Together, the task force determined what information needed to be available and where. The software providers for CRM and ERP made binding commitments for standardized interfaces.

Today, when a customer registers and orders online, the information is transferred from CentoPortal to the other systems in a fraction of a second. Amazon EventBridge plays a central role here. It is the link between the systems and communicates changes in a customer object, such as a change of address. PCG delivered an auto-scaling, extensible and flexible serverless solution that enables the integration of additional source and target systems, according to the motto: any source, any target. The architecture is event-based with near real-time synchronization and integrated error handling, as well as orchestration workflows that enable central control and “all-or-nothing” transactions.

Integration tests have shown this works reliably. Nevertheless, nothing is perfect. Sometimes the customer enters invalid data or irregularities occur during data transfer. Dealing with errors was therefore an important aspect of the project. Runbooks define what to do in the event of errors.These runbooks ensure that the quality of the diagnostics is always guaranteed. The system is designed to automatically respond to errors and take appropriate action to ensure data integrity and continuity of operation.

The result is a solution that allows the integration of additional source and target systems and is therefore ideally prepared for Centogene’s further growth. One of the plans is to replace the existing Laboratory Inventory Management System with a new LIMS in such a way that the old system continues to run in parallel until the changeover is complete and there are no gaps in operations.

Here, too, PCG will provide support.

PCG not only provided us with technical support, but also guided us through this change process with prudent project management. The PCG colleagues took a lot of time for detailed documentation and training with the new team.

Stefan Scheller

Vice President IT

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Centogene

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