In connection with emerging questions regarding the project to create the Genomic Map of Poland (GMP), below we briefly present its history, conditions in which it was created, its objectives, and the manner and state of its implementation. We are aware that the GMP is an extremely important project, so it is not surprising that it attracts a lot of media attention. Unfortunately, a large part of the information published about the project is unreliable and unverified. As we are not able to provide individual explanations and interviews to all journalists requesting information from us, we have decided to make the following information public.
Why is the Genomic Map of Poland being created
The application for the creation of the Genomic Map of Poland was submitted to the call for proposals no. 1 under the Smart Growth Operational Programme 2014-2020; Priority Axis IV: Increasing the Scientific Research Potential; Measure 4.2: Development of a Modern Research Infrastructure for the Science Sector (Competition 1/4.2/2015). This call was organized by the National Information Processing Institute – National Research Institute, and its objective was to support activities aimed at further development of ventures entered into the Polish Road Map of Research Infrastructures (PMDIB), in accordance with the decision of the Minister of Science and Higher Education. Therefore, only the entities that were included in the PMDIB as of August 4, 2014, as a result of an earlier procedure could participate in the call. The venture, the development of which we wanted to support under the project, was the European Centre for Bioinformatics and Genomics (ECBiG), established by the Institute of Bioorganic Chemistry of the Polish Academy of Sciences and the Poznań University of Technology, and entered into the PMDIB by the Minister’s decision as key infrastructure for the development of science and economy in Poland.
At the time of submitting the application, we believed that genomic research is and in the coming years will be one of the basic elements determining the development of many new methods and techniques used in modern medicine (in prevention, diagnostics and therapy, including personalized therapy). In our opinion, there was also no doubt that genomics is becoming a strategic area on a global scale, hence Poland’s independence in this area should be ensured. Moreover, our analyses showed that:
Objective of the project
Taking into account the above considerations, we decided that the main objective of the project will be to create bioinformatics tools and resources that will enable Polish scientists to fully and equally participate in international genomic research. An additional effect of creating such infrastructure should be the independence of domestic scientific, research and development and service centres from foreign companies, and the popularization of genomic research in Poland, by significantly reducing its costs. Following extensive discussions, we decided that the project should aim at creating the so-called Genomic Map of Poland, that is national infrastructure encompassing the following advanced bioinformatics tools and resources: 1. Reference genome (a set of bioinformatics tools and databases for assembling and reading the complete genomic sequences of Polish inhabitants); 2. Database (a tool for storing and sharing heterogeneous information on people the DNA donors); 3. Map of genetic variation (a set of bioinformatics tools and databases for studying the genetic variability of the population living in Poland); 4. Fen Gen (bioinformatics tools to analyse the relationships between the phenotype and the genotype); 5. Et Gen (bioinformatics tools for the analysis of genetic variation, within and between small populations, e.g. ethnic minorities or historical populations).
The information presented above clearly shows that the objective of the project is not about conducting basic, medical or commercial research, but about creating national bioinformatics infrastructure, consisting of databases and bioinformatics tools that shall enable genomic research in Poland. The bioinformatics platform created this way is to serve all national entities dealing with genomics. The rules of access to the platform will take into account all bioethical requirements, as well as those related to data security. Only in the future, as part of subsequent projects implemented by specialized medical centres, will specific genomic data be collected, allowing for the analysis of genetic determinants of phenotypic traits of Polish inhabitants, including their susceptibility to specific diseases. A similar scheme of action was adopted also by other countries, though still limited in number, willing to possess their own genomic resources. The United Kingdom is a perfect example thereof. In the first stage of the British strategy (UK10K project), identification of the sequence of 10,000 genomes was planned, in order to create (in cooperation with world leaders in the field of genomics, including BGI, which has one of its branches in London) the appropriate tools and databases. The second stage, which is currently being carried out under the 100,000 Genomes Project, involves identification of the sequence of 100,000 genomes, and creation of an appropriate genomic resource database (only this database is of strategic importance). The British example illustrates the general pattern of work to build a national genomic resource. It consists of two main phases. The first phase is the development of bioinformatics tools and reference databases. These databases describe the genetic background of a given population, and do not link genomic data to specific individuals. The second stage involves the use of the created infrastructure to generate specialized databases, for example, for analysing selected disease entities. Undoubtedly, implementation of the second phase requires precise legal regulations corresponding to ongoing scientific progress. Our project, aimed at creating the GMP, corresponds to the first phase of the project for creating national genomics resources.
Basic conditions for the implementation of the project
As a result of the call, our project entitled “European Centre for Bioinformatics and Genomics – Genomic Map of Poland” was qualified for funding. The project is implemented by a consortium formed by the Institute of Bioorganic Chemistry of the Polish Academy of Sciences (IBCH PAS) in Poznań and the Poznań University of Technology (PUT). The business partner of the project is Centrum Badań DNA Sp. z o.o. (CB DNA). The presence of a business entity in the project stems from the call regulations, according to which participation of a commercial company was a necessary condition for obtaining the grant. At the same time, according to these rules, CB DNA is not a beneficiary of the grant, i.e. it cannot obtain any funds or be the owner of any products resulting from project implementation. The role of the business partner is to represent the needs and points of view of the private sector, so that the created infrastructure meets the requirements of scientists, clinicians and entrepreneurs.
When we began to implement the grant in 2016, we were well aware of various doubts that may arise from the involvement of commercial companies, especially foreign ones, in the process of implementing domestic genomic projects. The idea of creating the Genomic Map of Poland was, and still is, an attempt to counteract the already existing and constantly deepening problems in this area. For years, it has been a common practice to outsource genomic and genetic tests to foreign companies – this applies both to scientific and commercial research, including the studies within the field of medical diagnostics. We are glad that this problem has recently also been noticed by the Committee on Human Genetics and Molecular Pathology of the Polish Academy of Sciences, which estimated its statement from 2021 that, in recent years, about 100,000 DNA samples from Poland have been sent for sequencing to Asian research and service centres.
One of our priorities was to create the GMP on a global level. Achieving this goal required finding a strategic partner with the greatest possible expertise in the latest mass genome sequencing and assembly technologies, ready to perform not only simple sequencing services but also technology transfer. According to the Polish Public Procurement Law, this partner had to be selected via an open tender procedure.
Recognizing the challenges of preserving the security of genomic data, most of the samples used to create the GMP were fully anonymised. All samples submitted for sequencing are labelled with numbers only. The sequencing company does not have access to any data of DNA donors. At this point, it is worth mentioning that analogous genomic reference databases were produced in many previous projects carried out on behalf of various countries (e.g. the United States or Great Britain) and are now available to scientists all around the world. For example, similar data is provided by the American National Institute of Health (https://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml) and often used by scientists also in Poland.
Project implementation status
The first stage of the project was to work out the optimal path for its implementation. We assumed that the sequencing and technology transfer necessary to create the GMP will be carried out by an external business entity. The company – Central Europe Genomics Center Sp. z o.o. (CEGC) based in Białystok, which met high requirements set for contractors in the terms of participation in the procedure, and in the technical specification of the contract, as it started to cooperate with one of the world leaders in the field of genomics, the Chinese company BGI Shenzen Co. Ltd., was selected through an open tender. A similar strategy has been adopted in most similar projects implemented in various parts of the world (Great Britain (2012), Saudi Arabia (2013), Scotland (2014), South Korea and the USA (2015) and Estonia, Iceland, Italy (2017), Denmark (now), also attended by a number of the world’s leading companies, including BGI.
From the very beginning, implementation of the project required overcoming many difficulties. Activities related to the acquisition of samples for sequencing were complicated upon entry into force of the GDPR (Regulation of the European Parliament and of the Council (EU) 2016/679 of 27 April 2016 on the protection of individuals with regard to the processing of personal data and on the free movement of such data, and repealing Directive 95/46/EC (General Data Protection Regulation), and later (since 2020) – by the outbreak of the COVID-19 pandemic. Despite these difficulties, the work on the project progressed. By March 2021, majority of the planned sample pool had been collected. About 3,000 DNA samples were submitted to CEGC and the results of their sequencing were successively collected. All samples were anonymized in accordance with the GDPR, therefore, under its provisions, they could not be treated as personal data.
In the first half of 2021, official statements of foreign agencies and politicians began to appear in the media, expressing doubts related to cooperation with China, also in the field of genetic research. Hence, in March 2021, in consultation with the funding institution, we asked the Contractor to stop using BGI’s resources. CEGC, thereby meeting our expectations, declared its readiness to cooperate in this area. Together, we decided that in this situation, further implementation of the project will only be taking place in our country. The rightness of this decision is demonstrated, among others, by the above-mentioned position of the Committee on Human Genetics and Molecular Pathology of the Polish Academy of Sciences, published several months later, i.e. on July 26, 2021. The committee took note of emerging reports of abuse by Far East biotech companies, providing mass DNA sequencing services, and suggested that it was better to perform genetic testing domestically. For years, we have been supporters of this hypothesis, hence, also to facilitate the idea by creating the GMP. At this point, however, it should be stated that, at the time of commencing works on the GMP, (end of 2016), the Polish biotechnology market was absolutely unprepared to take on this kind of challenge. As mentioned earlier, the cost of purchasing high-throughput sequencing equipment was then very high, amounting to approx. PLN 50 million, and the cost of one genome sequencing service performed by a Polish company amounted to PLN 20 000 (for comparison, this price was several times lower outside Poland).
We are currently applying a new project implementation scheme, based solely on domestic resources. We have no doubts that having our own reference databases and bioinformatics tools will not only facilitate future genomic research of the Polish population, but will also put us in the position of a potential partner of international initiatives, such as Beyond 1 Million Genomes (B1MG) or European 1+ Million Genomes (1+MG) .
Additional information is available at the following websites:
http://gmp.ichb.pl/
http://gmp.ichb.pl/https://portal.ibch.poznan.pl/hrpb7v/Genomiczna%20Mapa%20Polski
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