Polish reference genome for genomic diagnostics and personalized medicine

Project title

Name of Beneficiary/Beneficiaries

Beneficiary: POLGENOM consortium:

1. Consortium leader: Genomed S.A., ul. Ponczowa 12, 02-971 Warsaw

2. Co-performer 1: Institute of Experimental and Clinical Medicine of the Polish Academy of Sciences. M. Mossakowski (IMDIK PAN), 02-106 Warszawa, ul. A. Pawińskiego 5

3. Co-performer 2: International Institute of Molecular and Cell Biology in Warsaw (MIBMiK), ul. Fr. Trojdena 4, 02-109 Warsaw

4. Co-performer 3: 24 Hours Limited Liability Company, ul. Garażowa 7, 02-651 Warszawa

Name of programme

National programs

Competition

II Program Competition INNOTECH

Project value

PLN 5,984,717.00

Funding value

PLN 4,648,937.00

Project delivery period

from January 1, 2013 to February 29, 2016

Get to know our team

Genomed S.A.:

The team participating in the project consisted of molecular biologists, bioinformaticians and diagnosticians led by DSc. Anna Boguszewska-Chachulska, president of Genomed S.A., and DSc. Marek Zagulski.

IMDIK MR.:

Clinical and Research Team (ZKB) of Human Epigenetics led by prof. DSc. Monika Puzianowska-Kuźnicka

MIBMiK:

Team led by DSc. Małgorzata Mossakowska

24 Hours Sp. z o. o.:

Przemysław Łyszkiewicz

See the effect of our work

The main goal of the project was to create a reference database of the Polish Caucasian subpopulation for use in diagnostic processes and in research in the field of personalized medicine - collecting and presenting genomic data characterizing a healthy, long-lived Pole. This goal was fully achieved - a tested database was created, based on the complete genomes of 126 healthy, long-lived (90+) Poles, containing a rich set of clinical and biochemical data. Nearly 22 million sequence variants were detected and placed in the genomic database, of which approximately 24% were new variants.

The genomic database (in Polish and English) is available at: https://polgenom.pl.

It has practical use in scientific work and diagnostic processes, and constitutes a control group for population studies. The mitochondrial genome database obtained as part of the project is an excellent complement to the main genomic database as a reference base and a control group for all studies on diseases caused by mitochondrial mutations. The information obtained about structural variants for such a large group of healthy people constitutes a unique source of knowledge about this aspect of natural genome variability, the existence of which was detected only as a result of the development of whole-genome analysis methods. Information about sequence variants detected in the genome of long-lived healthy people, described in publications as potentially pathogenic mutations, allows for the verification of data found in the literature and reference databases, improving the quality and reliability of diagnostic results.

The second, fully implemented goal of the project was to obtain a reference genome sequence for the Polish Caucasian subpopulation, based on the variants occurring with the highest frequency in the genomes of healthy, long-lived Poles.

The project was carried out based on biological material and clinical data of healthy, long-lived people from the POLSTU and POLSENIOR projects and additionally recruited for this study as people with genomes potentially containing the lowest number of pathogenic mutations and constituting the best material for creating a genomic reference base of "healthy Poles". The reference genome sequence is a reference point for genome analyzes of patients carried out at Genomed SA since 2016 for preventive purposes.

The project results were used in the business activities of Genomed S.A. by launching and providing access to the Polish Genome Reference Database (POLGENOM) and selling genetic tests based on NGS technology, for which data analysis is carried out using data from the POLGENOM database. Numerous scientific institutions were users of the database on a paid or free basis.

From the beginning of POLGENOM's operation until the end of 2021, 12,000 queries were made to the database, indicating its active use. The implementation of the project significantly facilitated the analysis of genomic data, enabling shortening the time of genetic tests and lowering their costs, consequently increasing their availability for patients.

What problem does our project solve?

Introduction of a new type of database that collects genetic data (derived from whole-genome sequencing), biochemical data, lifestyle data and psychophysical health status, allowing for correlations between detected sequence variants and data on the health of long-lived people.

Who will benefit from the project results?

The Polish Reference Genome Database is available (after prior registration, on a commercial basis, with a significant discount for scientific and public utility units, taking into account only the costs of maintaining the database) at: https://polgenom.pl or via the Genomed SA website.

The offer of genetic tests, using data from POLGENOM, is addressed to a wide group of patients and people seeking preventive screening tests in the field of oncology and lifestyle diseases. The Genomed SA laboratory has become the main diagnostic center in Poland, performing tests based on NGS technology, including analyzes of the patient's entire genome.

In the years 2017-2023, the following were published: thanks to the use of the POLGENOM database, results for over 5,000 patients with genetically determined diseases and for preventive screening tests, including: assessing the risk of developing cancer.

The company's participation in conferences, training for smaller groups of doctors and patient care in its own genetic clinic also serve the diagnostic and social use of the POLGENOM database. Increasing public awareness of genetic research and project results is carried out through health campaigns and publications popularizing knowledge about our genome.