Test auf Gebärmutterhalskrebs durch Studie bestätigt

Independent study in cervical cancer screening:

The GynTect test for cervical cancer screening is highly informative regarding whether cervical cancer is present or likely to develop. In addition, GynTect is well suited for sampling by the patient herself (self-sampling). All these points are confirmed by a recently published study from China.

The Chinese diagnostics company GeneoDx, a subsidiary of the Sinopharm Group, markets the GynTect clarification test under exclusive licence in China. GeneoDx supported a study in which scientists examined the predictive power of GynTect in more detail. The study with the short title “Methylation panel for the clarification of HPV-positive women” has now been published.

Subject of the study

9,526 women from rural areas of China took part. These have difficult access to medical services. For this reason, the women performed the smear sampling for the HPV test themselves. Many of them participated in cervical cancer screening for the first time.

Of the 9,526 women, 1,758 tested positive for HPV. The samples of these women were then tested for HPV types 16 and 18. Furthermore, smear samples were taken by the doctor and GynTect was performed on these samples. The women were also examined by colposcopy and, if necessary, biopsy and continued to participate in the study. They were followed up annually with HPV tests. HPV-positive women again received a colposcopy and, if necessary, a biopsy was taken.


If there is an abnormality, women currently are examined every three to six months. This is not feasible for many in poorly accessible regions. This problem does not only exist in China, but in many regions worldwide. With GynTect, all it takes is a smear test and the women have certainty. This way we can save lives,” explains Dr Martina Schmitz, Managing Director of oncgnostics GmbH.

Study shows potential of GynTect

The study demonstrated that GynTect, with which methylation markers are detected, has very good predictive power, especially in combination with HPV typing: women who were initially both HPV16 or HPV18 positive and GynTect positive had the highest risk of developing the disease. Women who were infected with a different HPV type and were GynTect-negative had the lowest risk.

Based on several references, the authors of the study also assume that GynTect is suitable to be used as a self-sampling test. This means that the women take the sample themselves, which is then sent to a laboratory for testing. The intermediate step via medical personnel is eliminated. In addition, the study concludes that GynTect has the potential to be used in primary screening. The referral rate for colposcopy was reduced by 55.6% through the use of GynTect. Thus, the study also shows that overdiagnosis and overtreatment can be avoided through GynTect.


“For us, the study confirms once again that we are on the right track to develop our screening test GynTect into a test that will be an integral part of cervical cancer screening. If we then also develop a reliable self-sampling test, we can revolutionise cervical cancer screening,” summarises Dr Martina Schmitz.

How does cervical cancer develop?

The main cause of cervical cancer is infection with human papillomaviruses (HPV). It takes several years from infection to the development of cancer. Modern screening methods can detect cervical cancer early and treat it well. Deaths are therefore preventable.

Figures for Germany (all figures annually) [1]

  • 6 million women infected with HPV[2], of which several hundred thousand have cytological abnormalities.
  • 4,300 are diagnosed with cervical cancer
  • 1,600 die from cervical cancer

Figures for China (all data annually) [3]

  • Around 110,000 women are diagnosed with cervical cancer
  • around 59,000 die of cervical cancer

How GynTect works

The molecular biological test GynTect, developed by oncgnostics, determines at an early stage whether a patient with an abnormal finding in the cervical cancer screening is developing or already has a cervical carcinoma (cervical cancer) that needs to be treated.

The screening test detects epigenetic changes, so-called DNA methylations. All that is needed to carry out the test is a smear, as is also taken for thin-layer cytology or the HPV test.

Conclusion: GynTect is ideal for clarifying a positive HPV test.

This means that GynTect with its very good predictive power is an optimal clarification option in HPV-based screening. GeneoDx has also recently received approval from the competent Chinese authority NMPA (National Medical Products Administration) for precisely this clarification in an HPV-based screening.


Free image material: www.tower-pr.com/oncgnostics

[1] Robert Koch-Institut (2018): Zentrum für Krebsregisterdaten. Gebärmutterhalskrebs (Zervixkarzinom): www.krebsdaten.de/Krebs/DE/Content/Krebsarten/Gebaermutterhalskrebs/gebaermutterhalskrebs_node.html

[2] https://www.frauenaerzte-im-netz.de/erkrankungen/humane-papillomviren-hpv/uebertragung-verbreitung/

[3] https://hpvcentre.net/statistics/reports/CHN_FS.pdf?t=1653896959645


Photo: Shutterstock.com/Hannamariah

Welttag der sexuellen Gesundheit. Bild: melitas

There are many more aspects to the topic of sexual health than are apparent at first glance. We want to use World Sexual Health Day as an opportunity to draw attention to cervical cancer, which develops from a sexually transmitted HPV infection.

Definition of sexual health

The World Health Organization (WHO) defines sexual health as a state of mental, emotional and spiritual well-being. Thus, it does not only mean the absence of disease or dysfunction. The WHO definition also includes respect for sexual rights of all people to have sexual experiences that are free from coercion, discrimination and violence.

World Health Organization

Sexual health and cervical cancer

When talking about sexual health, cervical cancer also has to be discussed. Because already the development of cervical cancer is related to the sexual activity of the affected woman. An infection with human papilloma viruses (HPV) is responsible for the development of cancer of the uterine cervix. These are usually transmitted during sexual intercourse. The HP viruses are widespread. Thus, almost everyone becomes infected with HPV at least once in his or her life. In most cases, this is not bad at all. Most people do not even notice their infection. But in a few cases, HPV infection can develop into e.g. cervical cancer.

Cervical cancer is curable when detected early

The good thing, however, is that cervical cancer develops slowly, over years and in preliminary stages. For the women affected, the chances are therefore good that the disease will be detected early, and treated in good time. For this reason, every woman should take advantage of the cancer screening measures offered by her gynecologist.
HPV is also associated with other cancers, including cancer of the mouth and throat, anus, penis, vagina and vulva.

HPV-positive or Pap smear is abnormal

Depending on the age of the woman, screening for cervical cancer includes a Pap test and/or a test for HPV. If the tests reveal abnormalities, there is usually only a hint of possible cancer. Sometimes the tests give a false alarm, as the HPV infection heals without any problems or slight abnormalities disappear on their own. For this reason, the gynecologist decides whether further examinations are necessary or whether the affected woman should repeat the tests after a certain period of time, usually three to six months. This procedure is also called watchful waiting.

Unclear findings put a strain on the psyche

Unclear findings place a great deal of psychological strain on affected women. This was made clear in a study published in 2020. This psychological stress can even go so far that the affected women develop signs of post-traumatic stress disorder. For this reason, we are campaigning for more accurate and rapid diagnostics of cervical cancer and for more comprehensive education.

World Sexual Health Day raises awareness

World Sexual Health Day was launched in 2010 by the World Association for sexual health (WAS). It aims to promote sexual health, well-being and rights for all.
We are happy to do our part for sexual health by providing education in our field. Our goal is to fight cervical cancer with accurate and early diagnostics.


Photo: melitas


Symbolbild: Frauengesundheit, Vulva- und Vaginalkrebs

There is still no targeted method for early detection of vulvar and vaginal cancer. This is despite the fact that an estimated 45,240 women worldwide were diagnosed with vulvar cancer in 2020, and more than 17,000 people even died from it. Vaginal cancer occurs slightly less frequently – with around 18,000 new cases and 8,000 deaths in 2020 worldwide. [1] Oncgnostics has done first approaches for molecular diagnostics using epigenetic markers.

Diagnosis of vulvar and vaginal cancer

The diagnosis of vulvar or vaginal cancer is usually an incidental finding made by a gynaecologist during a gynaecological examination. There is no special test for vulvar or vaginal cancer. This can have fatal consequences, because here, too, the earlier the cancer is detected, the better its chances of being cured.

HPV infection as a risk factor

Infection with human papillomaviruses is considered one of the risk factors for vulvar and vaginal cancer, while some vulvar cancers develop from a skin disease of the vulva called lichen sclerosus. The affected women usually do not experience any symptoms. For this reason, women usually only find out about their HPV infection when they attend their regular check-up at the gynaecologist. HP viruses are widespread. Almost all people get infected with HPV at some point in their lives; it is the most common sexually transmitted infection. But the good news is: In most cases, an HPV infection heals on its own and only in rare cases does it actually develop into cancer. This process can take years. For this reason, good diagnostics could give women the chance to detect cancer early, possibly in its preliminary stages.

Protection against vulvar or vaginal cancer

Women have the following options to protect themselves: They get vaccinated against human papilloma viruses and they go for regular check-ups. There, the gynaecologist not only arranges an HPV test, but also examines visual changes in the vulva and vagina. If the test is positive, further examinations are ordered.

Methylation test for vulva and vaginal cancer

oncgnostics GmbH has investigated the possibilities of a methylation test for the diagnosis of vulva and vaginal cancer. The study is based on the biomarkers of GynTect, a proven test for the early detection of cervical cancer. Since all three types of cancer can be caused by HPV, it is reasonable to assume that these markers also occur in malignant vulvovaginal diseases. This assumption was confirmed in initial studies. Swabs from women with vulva or vaginal carcinomas and their precursors were examined: All carcinoma samples that were HPV-positive were also positive in the methylation test. Dr Alfred Hansel sees the results of the study as a promising approach for the development of diagnostics for the early detection of vulvar and vaginal cancer.


The new IVDR

The new IVDR (In-vitro Diagnostic Medical Device Regulation) has been in force since 26 May. As a result, numerous companies have had to adapt their approval processes and internal procedures. The new regulations also present oncgnostics with new challenges. For example, the molecular biological cancer tests now fall into the second highest risk level. This means that significantly more requirements have to be met. 

What is the IVDR?

The In Vitro Diagnostic Medical Device Regulation, IVDR for short, is an EU regulation that replaces the previous directive, the In Vitro Diagnostic Medical Device Directive (IVDD). Thus, the IVDR regulates the general safety and performance requirements of in vitro medical diagnostics devices within the European Union. Although the new regulation has already existed since 25 May 2017, it is now mandatory after a five-year transition period. For many companies, the new requirements mean major changes.

The most important changes (selection)

The introduction of the new IVDR is accompanied by several changes. The aim of the new regulation is to improve patient safety.

  • New classification of products into four classes: There are risk classes, ascending from A to D.
  • Common specifications: The EU Commission defines common specifications.
  • UDI system: With the help of the Unique Device Identification, UDI for short, the traceability of each product from the patient via the doctor back to the laboratory is to be guaranteed.
  • Every manufacturer of an in-vitro diagnostic product must install a QM system.
  • Technical documentation: especially the requirements for technical, analytical and clinical performance data have increased in scope.
  • Software: The IVDR now formulates specific requirements for products that contain software.

What the new IVDR means for oncgnostics GmbH

oncgnostics launched GynTect, the screening test for cervical cancer, back in 2015. At the time, this was possible with a CE IVD approval through a self-declaration of compliance. In addition, GynTect fell into the “other” category under the previously valid directive. In the new IVDR classification system, GynTect now falls into the second highest risk level “C”. As a result, the conformity assessment procedure has to be carried out with the involvement of a Notified Body. For products that have already been approved, this means that this must take place in four years at the latest. The same applies to the ScreenYu Gyn test, which was approved only recently, in May 2022.

Patient and Physician -PCR test detects cervical precancerous lesions

Jena, Germany, May 25th 2022 – May 28 marks the 35th International Day of Action for Women’s Health. One “female” disease that should no longer exist due to the availability of modern cancer-screening methods is cervical cancer. One step in the direction of abolishing this form of cancer has been taken by the German life science company oncgnosticsIt has namely developed a cancer-screening test called “GynTect”, which can predict whether cervical cancer will develop in a female‘s body.

What happens if the standard gynecologist cancer-screening[1] procedure ends in a positive result, indicating the presence of cancer? Since most abnormalities heal on their own, doctors tend to prefer closely monitoring of the patient and her condition following this test result. They repeat the test after a period of time, leaving these affected women with a highly uneasy feeling of uncertainty.

Cancer test provides certainty for HPV-positive women

By providing women with a clear test result based on real cancer markers, GynTect minimizes this psychologically stressful waiting time for affected women. This test reliably detects changes in the DNA present due to cancer-cell development. As with regular cancer screenings up until now, the gynecologist performs a Pap smear on the patient, taking a swab from the cervix. This sample is then sent to a lab where the PCR-based test is performed.

When GynTect cancer markers are found, women patients need proper and timely treatment. If there are no markers present, these patients can wait with far greater confidence as opposed to fear prior to their next gynecological examination.

“Whereas other lab tests detect HPV or use the microscope to see abnormal cells when analyzing the Pap-test sample, we look DIRECTLY into the cells’ DNA at the molecular level to determine whether cancer-typical changes are found”, says Dr. Martina Schmitz, co-founder and CSO at oncgnostics.

How cervical cancer develops

Cervical cancer almost always develops after an infection involving human papillomaviruses (HPV) and is sexually transmitted. By contrast, other factors such as environmental influences and genetic predisposition play more minor roles.

Compared to other cancer types, cervical cancer can fortunately take years or even decades to develop from an HPV infection. This means that if cancer screening is regularly performed, abnormalities will be found on time.

Regular cancer screening saves lives

Every year about 14,000 women develop cervical cancer[2] and over 5,700 women in the U.S. even die from the disease. Although regular screening is recommended[3], too few women take advantage of it. Some only go to the doctor when they have symptoms. By this time however, this disease can already exist. Resulting treatment can then be long, tedious and psychologically as well as physically exhausting, not to mention much more expensive. For further information and recommendations regarding cervical cancer screening, please go to the website at the American Cancer Society.

“We now have excellent possibilities of detecting cervical cancer at an early stage. Many women can be spared a lot of suffering. Therefore, all women should take advantage of regular screening”, concludes Dr. Martina Schmitz.


About oncgnostics GmbH:

oncgnostics GmbH has its headquarters in Jena, Germany and specializes in the early detection of cancer. Their cancer-screening tests reveal changes that are characteristic of cancer-cell DNA. Founded in 2012, the company launched GynTect in 2015. As part of this test‘s ability to detect cervical cancer earlier than other existing tests, it can determine whether cervical cancer or its precursors are present in a woman‘s body. GynTect is officially certified in Europe. oncgnostics GmbH is currently developing diagnostic tests for other types of cancer.

For more information, please visit www.oncgnostics.com/en

For free images, click onto the following weblinks: www.oncgnostics.com/downloads and www.tower-pr.com/oncgnostics


oncgnostics GmbH

Löbstedter Str. 41

07749 Jena – Germany

Phone: +49 3641/5548550



[1] https://www.cancer.gov/types/cervical/patient/cervical-screening-pdq#_20

[2] https://hpvcentre.net/statistics/reports/USA_FS.pdf?t=1651740639439

[3] https://www.cancer.org/cancer/cervical-cancer/detection-diagnosis-staging/cervical-cancer-screening-guidelines.html#:~:text=Cervical%20cancer%20testing%20(screening)%20should,test%20alone%20every%203%20years

WHO empfiehlt einmalige HPV-Impfung (xrender/Shutterstock.com)

The World Health Organisation (WHO) recommends the one-dose HPV vaccination of girls and women up to 21 years of age instead of the current two-time vaccination. The WHO wants to increase the vaccination rate in the fight against cervical cancer. In principle, we welcome this plan, but we also have reservations regarding the new recommendation[1].

The fact is, cervical cancer is caused by human papilloma viruses (HPV). While not every HPV infection develops into cervical cancer, there are certain high-risk HPV types. They favour the malignant changes in the cells. There is an effective vaccination against some of these high-risk HPV types. In Germany, the Standing Committee on Vaccination (STIKO) recommends two doses for girls and boys aged 9-14 for sufficient vaccination protection. Those older than 17 should even be vaccinated three times. HPV is sexually transmitted. Condoms do not provide sufficient protection because the viruses are found throughout the intimate and anal areas. For this reason, immunisation is advisable before the first sexual experience.

HPV causes cancer in men and women

It is also a fact that cervical cancer is not the only cancer that can be caused by HPV. In addition to cervical cancer and cancer of the vulva and vagina, an HPV infection can also lead to malignant cell changes in the mouth and throat area, at the anus and also on the penis. Genital warts are also caused by human papilloma viruses. These are harmless, but very unpleasant. Men can not only transmit HPV, but also suffer from HPV-related cancer themselves. In Germany alone, this affects about 1,600 men a year.[2] HPV vaccination also protects against these cancers.

HPV vaccination: useful for girls and boys

Since HPV can cause cancer in both men and women, it is surprising that the WHO focuses its recommendation on cervical cancer – that is, on women. Especially since it also makes sense in the fight against cervical cancer to get boys on board with the vaccination. After all, they can infect their partners with HPV infection as carriers. Since 2018, the Standing Commission on Vaccination in Germany has recommended vaccination against human papilloma viruses for boys aged nine and older.

Dr Cornelia Hösemann (member of the Saxon vaccination commission) takes a very similar view in an interview with the German TV station MDR[3]. In her eyes, the WHO recommendation is a step backwards, because in her opinion, all sexes should be vaccinated from the age of nine. She would like to see a vaccination rate of 80-90 per cent to achieve collective protection. According to a survey by the Robert Koch Institute, the vaccination rate in Germany in 2015 was only around 45 percent[4] among 17-year-olds. This is the age group in which immunisation should ideally already have been completed.

Making HPV vaccination easier – for everyone

The WHO relies on data that show that a single vaccination against HPV ensures full vaccination protection. A single vaccination would mean lower costs, fewer resources, and it would also be easier to administer the vaccination.[5] Thus, access to HPV vaccination would be more low-threshold.

For the time being, the WHO recommendation is only a recommendation. The implementation must be checked by the individual countries themselves. If the vaccination rate can be increased by a simplified HPV vaccination scheme, this is to be welcomed, but then all sexes should be included.


Literature sources:

[1] WHO

[2] Robert Koch Institute (RKI)

[3] MDR

[4] Robert Koch Institute (RKI)

[5] WHO


The EUROGIN is THE event for our current application areas and most of the experts were in Düsseldorf. So were we! With four presentations oncgnostics participated in the scientific discourse at the International multidisciplinary HPV Congress.

The congress was again a great opportunity for us to make new contacts, maintain existing partnerships and exchange ideas about possible new collaborations.

oncgnostics participates in the scientific discourse

Oncgnostics submitted four presentations in the run-up to EUROGIN 2022 and all four were accepted. After a long period of digital-only events, our team was looking forward to receiving direct feedback and exchanging ideas with international colleagues:


Dr Alfred Hansel, Managing Director:

“After two long years, we are present again, meeting competitors, cooperation partners, clinicians and scientists. We present our data, discuss them at our booth with all interested parties, also have conversations with chance meetings again.’


Dr Martina Schmitz, Managing Director:

“I had the impression that all participants were simply happy to be able to exchange information about the latest studies and results live again after 2 years of the pandemic. GynTect-PRO talk had a good response and our booth enjoyed great interest.”


Anna-Bawany Hums, molecular biologist:

“EUROGIN in Düsseldorf has already been worthwhile, as it is the first face-to-face event for me after two years. It’s fun to come into direct contact with interested people at the booth again, to meet existing cooperation partners and to exchange ideas about new projects.”


Carolin Hoyer, biotechnologist:

“EUROGIN was my first big conference and I had the opportunity to present my Master’s thesis there, listening to interesting talks and make friendly contacts.”

Contributions of oncgnostics GmbH at EUROGIN 2022

If you were not on site or would like to read the contents, you can download the respective short summaries of the presentations:


The business magazine Capital selected Germany’s most innovative companies for the third time. Oncgnostics GmbH made it into the selection. The biotech company scored particularly well in the evaluation criterion of innovation areas.

For the third time, Capital, together with the market research institute Statista, determined Germany’s most innovative companies. For this purpose, they brought around 3,600 innovation experts on board. In a first step, they recommended companies and gave their assessment. In addition, the experts were able to add to their list from 40 innovation competitions of the last three years. The expert assessment covered the areas: “products and services”, “processes” as well as “cultural and social innovations”. Subsequently, 9 categorised reasons for recommendation were assessed. “Regularly delivers innovative products” or “has installed innovation-promoting business processes” are examples of recommendation reasons. The partial results were finally transferred into a 5-star scheme. In total, the experts scrutinised 2061 companies from 20 different sectors. 470 companies received a rating of four or five stars.

Germany’s most innovative companies: oncgnostics gets four stars

oncgnostics received five stars in the innovation category and a proud overall rating of four stars in the “Chemicals, Pharmaceuticals & Biotechnology” sector. In addition, the biotechnology company was identified as a company with a particularly technologically relevant patent portfolio.

List of the most innovative companies

The results of the ranking can be viewed online at Capital.de. We are listed under the 3rd category “Chemistry, Pharmaceuticals & Biotechnology” as one of 8 of the most innovative companies with < 250 employees. You can read all about our innovative product GynTect®, the test for cervical cancer, at www.gyntect.com. You can also find out about our research projects and pipeline products at www.oncgnostics.com.

Cover picture: Shutterstock.com/BB DESIGN STOCK

10 years ago a small, very motivated team founded the oncgnostics GmbH to improve cervical cancer screening. Since then, oncgnostics GmbH has been growing and with it the number of its employees. On the occasion of the anniversary, it is time to share the experiences of the employees of the biotech company.

10 years of oncgnostics – employee from the very beginning

Production manager Dr. Juliane Hippe, head of production, has been with the company from the very beginning. Already as a student she joined the Gynaecological Molecular Biology work group of the Department of Gynaecology and Reproductive Medicine of the Jena University Women‘s Hospital. When oncgnostics GmbH emerged from the working group, the biologist was pleased to receive her first employment contract, a PhD fellowship. In addition, Dr. Juliane Hippe completed her doctorate at the start-up thanks to this fellowship: “I was able to develop steadily at oncgnostics GmbH. In the meantime, I am production manager, but also active in the fields of development as well as quality management.”

Development opportunities at oncgnostics GmbH

Oncgnostics gives its employees room to develop. Dr. Carolin Dippmann was also able to convince through her doctorate at oncgnostics GmbH, also made possible through a PhD fellowship. Nowadays, the Pharma-Biotechnologist is a permanent team member. Now she supervises students herself in their final theses and is responsible for the implementation of new methods in the laboratory. “My greatest motivation is the team, the individuality of each person and how it fits together perfectly to form a whole. I am also motivated by the feeling that our work is making an important contribution within the field of cancer diagnostics,” says Dr. Dippmann, summarizing the motivation behind her daily work as an important member of the Research and Development department.

Likewise, Kristin Knoll completed her master thesis at oncgnostics: “From master’s student to application specialist and head of customer management – I have been able to gain a lot of experience in my almost nine years at oncgnostics. When I look back to the beginning, I am happy to have been involved in product development and also in the growth of the entire company. Constructive criticism and suggestions for improvement are welcome here – that’s how we shape the company together,” says the pharma biotechnologist regarding her career at oncgnostics GmbH.

oncgnostics employees show initiative

Through initiative, the employees of oncgnostics GmbH not only develop further, but most of them joined the team in the first place. Among them Dr. Anne Hennig, who applied on her own initiative: “The role of project manager as well as the management of a research project was awarded to me after a short time.” She draws her motivation from the “fact that you can make a difference with your daily work.”

Master’s student Carolin Hoyer was also successful with her unsolicited application. For her, it is important to “complete my pharma biotechnology studies with practical experience and an exciting project.” These criteria could be met by oncgnostics GmbH.

A varied workplace

The biotech company offers its employees a varied workplace. Anna Bawany Hums, a research assistant, appreciates this: “Even with a lot of office work, I still slip into my lab coat every now and then. There are no rigid structures here. In addition, the working atmosphere is characterized by appreciation.” Technical assistant Kristina Wunsch sees it the same way: “Interpersonal relationships are very important here. There is a considerate way of working together.”

Kristin Knoll, among others, was able to leave her desk behind a few times. As an applications specialist, she has been able to travel to countries such as Portugal, Denmark, Sweden and Azerbaijan. “When time permits, it’s especially nice to catch a few cultural impressions of cultures I’m unfamiliar with,” she says. In addition, the staff members regularly present the current state of their research at various national as well as international congresses.


Dr. Carolin Dippmann and Daria Meyer from our research and development team work, among other things, with the “third-generation sequencing” method. With the help of this technology, they are examining DNA (deoxyribonucleic acid) from tumors much more precisely than was previously possible.

The method has enormous advantages: epigenetic changes in the DNA, specifically DNA methylation in certain regions, tell us when healthy cells develop into cancer. And with “third generation sequencing” we can detect these changes directly.

Our goal at oncgnostics is to detect such epigenetic markers. Especially in the early detection of head and neck tumors, development is still in its infancy. In various research projects, including the OroCa-Graz study, we are working together with clinicians on a standardized screening to detect the associated diseases earlier and more reliably than before.

In the following, the two scientists explain to what extent third-generation sequencing is being used and what exactly is behind it.

How does Third Generation Sequencing work?

Part of our daily work is to screen DNA fragments for epigenetic changes, specifically DNA methylation. DNA methylation at specific base sequences indicates that the cell in question has changed.

Third generation sequencing is a method that makes these analyses faster and more effective. In addition, the method provides the DNA sequence information in very high resolution: namely, individual DNA molecules are analyzed. The biological DNA is transferred into a digital version and can be analyzed on the computer. DNA methylation, which occurs during cancer development, can be analyzed directly. And this is of particular interest to us.

The process is illustrated in a video from “Oxford Nanopore Technologies” on YouTube.

How does the method differ from previous methods?

With previous sequencing methods, we could only determine the base sequence of short DNA fragments (300 DNA bases on average). In addition, the DNA to be examined had to be copied several times in advance, very similar to the so-called PCR method explained here. In addition, the DNA had to be chemically treated to detect DNA methylation.

The Third Generation Sequencing method simplifies this process:

  • We can directly evaluate DNA molecules of up to several million DNA bases in length
  • No copies are necessary for this. Rather, we evaluate the individual DNA sequences directly
  • The speed with which we examine the sequences increases accordingly: We now collect the data in real time

What kind of data do we get?

The bottom line is that the Third Generation Sequencing method captures changes in current and records them digitally. It works like this: The DNA to be examined is placed on a surface that is under a specific voltage. Tiny pores made of proteins are embedded in this surface. During the process, the DNA migrates, always in the same direction, through these so-called nanopores. This is why the method is also called “Oxford Nanopore Technology” (ONT).

When the DNA migrates through a pore, the current intensity on the surface changes. This is due to the spatial arrangement and chemical properties of the DNA segments. Sensors measure these changes at each individual pore and transmit them to the computer connected to each. An algorithm then translates the information into the base sequence of the DNA. In the sequence recorded we also read the DNA methylation.

Are there any other advantages or disadvantages?

Since the method is still very new, it has a fairly high error rate. Currently, it recognizes only 95 percent of all sequences without errors. With other methods, the figure is 99.9 percent. Continuous developments will improve this over time. Daria Meyer’s work is part of this. She is a bioinformatician and, as part of her PhD thesis, she focuses on improving the algorithms that are essential for analyzing DNA methylation. In addition, we are constantly optimizing the process flows in the preparation of diagnostic samples. That is Carolin Dippmann’s focus in the project.

In fact, the advantages outweigh the disadvantages. One of the reasons for this is that the analyzer is barely larger than a USB stick and therefore super handy. Theoretically, sequencing can be carried out anywhere, from the Arctic to the desert.

What is our future benefit from Third Generation Sequencing?

With the help of ONT sequencing, major gaps in our knowledge of the human genome (the entire DNA sequence of a human being) have already been closed. We expect further developments in this area. And we are happy contribute to improving the technology.

The biggest advantage for us is the direct readability of epigenetic changes, i.e. DNA methylation. We can analyze these directly at our facility.

The method is gaining acceptance in more and more areas of application. This is not least due to the fact that the initial equipment for starting sequencing projects is very inexpensive. Sequencing of this quality is thus much more affordable. This means that small companies like oncgnostics can also utilize this technology.