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‘The Thousand Polish Genomes Project’ - a national database of Polish variant allele frequencies

View ORCID ProfileElżbieta Kaja, Adrian Lejman, View ORCID ProfileDawid Sielski, View ORCID ProfileMateusz Sypniewski, View ORCID ProfileTomasz Gambin, View ORCID ProfileTomasz Suchocki, View ORCID ProfileMateusz Dawidziuk, View ORCID ProfilePaweł Golik, View ORCID ProfileMarzena Wojtaszewska, View ORCID ProfileMaria Stępień, View ORCID ProfileJoanna Szyda, Karolina Lisiak-Teodorczyk, Filip Wolbach, Daria Kołodziejska, Katarzyna Ferdyn, View ORCID ProfileAlicja Woźna, Marcin Żytkiewicz, Anna Bodora-Troińska, Waldemar Elikowski, Zbigniew Król, Artur Zaczyński, View ORCID ProfileAgnieszka Pawlak, Robert Gil, View ORCID ProfileWaldemar Wierzba, View ORCID ProfilePaula Dobosz, View ORCID ProfileKatarzyna Zawadzka, View ORCID ProfilePaweł Zawadzki, View ORCID ProfilePaweł Sztromwasser
doi: https://doi.org/10.1101/2021.07.07.451425
Elżbieta Kaja
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
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  • ORCID record for Elżbieta Kaja
Adrian Lejman
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
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Dawid Sielski
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
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Mateusz Sypniewski
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
10Department of Genetics and Animal Breeding, Poznań University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland
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Tomasz Gambin
3Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland
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Tomasz Suchocki
2Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
13National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
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Mateusz Dawidziuk
9Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
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  • ORCID record for Mateusz Dawidziuk
Paweł Golik
4Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
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Marzena Wojtaszewska
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
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Maria Stępień
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
11Faculty of Medicine, Medical University of Lublin, 20-059 Lublin, Poland
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Joanna Szyda
2Biostatistics Group, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
13National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
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Karolina Lisiak-Teodorczyk
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
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Filip Wolbach
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
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Daria Kołodziejska
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
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Katarzyna Ferdyn
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
12Medical and Science Sp. z o.o., Podebłocie 107B, 08-455, Poland
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Alicja Woźna
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
8Molecular Biophysics Division, Faculty of Physics, A. Mickiewicz University, Poznań, 61-614 Poland
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Marcin Żytkiewicz
7Internal Diseases Department, Józef Struś Multidisciplinary Municipal Hospital, Poznań, 61-285, Poland
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Anna Bodora-Troińska
7Internal Diseases Department, Józef Struś Multidisciplinary Municipal Hospital, Poznań, 61-285, Poland
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Waldemar Elikowski
7Internal Diseases Department, Józef Struś Multidisciplinary Municipal Hospital, Poznań, 61-285, Poland
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Zbigniew Król
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
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Artur Zaczyński
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
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Agnieszka Pawlak
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
14Mossakowski Medical Research Centre, Polish Academy of Science, Pawińskiego 5, 02-106 Warsaw, Poland
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Robert Gil
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
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Waldemar Wierzba
5Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, Warsaw, 02-507, Poland
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  • ORCID record for Waldemar Wierzba
Paula Dobosz
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
6Department of Hematology, Transplantation and Internal Medicine University Clinical Center of the Medical University of Warsaw, 02-091, Warsaw, Poland
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Katarzyna Zawadzka
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
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Paweł Zawadzki
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
8Molecular Biophysics Division, Faculty of Physics, A. Mickiewicz University, Poznań, 61-614 Poland
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Paweł Sztromwasser
1MNM Diagnostics Sp. z o.o., ul. Macieja Rataja 64, Poznań, 61-695, Poland
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  • For correspondence: pawel.sztromwasser@mnm.bio
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Abstract

Although Slavic populations account for over 3.5% of world inhabitants, no centralized, open source reference database of genetic variation of any Slavic population exists to date. Such data are crucial for either biomedical research and genetic counseling and are essential for archeological and historical studies. Polish population, homogenous and sedentary in its nature but influenced by many migrations of the past, is unique and could serve as a good genetic reference for middle European Slavic nations.

The aim of the present study was to describe first results of analyses of a newly created national database of Polish genomic variant allele frequencies. Never before has any study on the whole genomes of Polish population been conducted on such a large number of individuals (1,079).

A wide spectrum of genomic variation was identified and genotyped, such as small and structural variants, runs of homozygosity, mitochondrial haplogroups and Mendelian inconsistencies. The allele frequencies were calculated for 943 unrelated individuals and released publicly as The Thousand Polish Genomes database. A precise detection and characterisation of rare variants enriched in the Polish population allowed to confirm the allele frequencies for known pathogenic variants in diseases, such as Smith-Lemli-Opitz syndrome (SLOS) or Nijmegen breakage syndrome (NBS). Additionally, the analysis of OMIM AR genes led to the identification of 22 genes with significantly different cumulative allele frequencies in the Polish (POL) vs European NFE population. We hope that The Thousand Polish Genomes database will contribute to the worldwide genomic data resources for researchers and clinicians.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/MNMdiagnostics/1000PolishGenomes

  • 1 https://github.com/MNMdiagnostics/1000PolishGenomes

  • 2 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

  • 3 https://github.com/brentp/smoove

  • 4 https://github.com/brentp/smoove

  • 5 https://github.com/MNMdiagnostics/1000PolishGenomes

  • 6 https://www.omim.org/, accession date 26-04-2021

  • 7 https://panelapp.genomicsengland.co.uk/panels/, accession date 27-06-2021

  • 8 https://github.com/MNMdiagnostics/1000PolishGenomes

  • 9 https://www.omim.org/, accession date 26-04-2021

  • 10 https://polgenom.pl

  • 11 https://www.genompolski.pl

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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‘The Thousand Polish Genomes Project’ - a national database of Polish variant allele frequencies
Elżbieta Kaja, Adrian Lejman, Dawid Sielski, Mateusz Sypniewski, Tomasz Gambin, Tomasz Suchocki, Mateusz Dawidziuk, Paweł Golik, Marzena Wojtaszewska, Maria Stępień, Joanna Szyda, Karolina Lisiak-Teodorczyk, Filip Wolbach, Daria Kołodziejska, Katarzyna Ferdyn, Alicja Woźna, Marcin Żytkiewicz, Anna Bodora-Troińska, Waldemar Elikowski, Zbigniew Król, Artur Zaczyński, Agnieszka Pawlak, Robert Gil, Waldemar Wierzba, Paula Dobosz, Katarzyna Zawadzka, Paweł Zawadzki, Paweł Sztromwasser
bioRxiv 2021.07.07.451425; doi: https://doi.org/10.1101/2021.07.07.451425
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‘The Thousand Polish Genomes Project’ - a national database of Polish variant allele frequencies
Elżbieta Kaja, Adrian Lejman, Dawid Sielski, Mateusz Sypniewski, Tomasz Gambin, Tomasz Suchocki, Mateusz Dawidziuk, Paweł Golik, Marzena Wojtaszewska, Maria Stępień, Joanna Szyda, Karolina Lisiak-Teodorczyk, Filip Wolbach, Daria Kołodziejska, Katarzyna Ferdyn, Alicja Woźna, Marcin Żytkiewicz, Anna Bodora-Troińska, Waldemar Elikowski, Zbigniew Król, Artur Zaczyński, Agnieszka Pawlak, Robert Gil, Waldemar Wierzba, Paula Dobosz, Katarzyna Zawadzka, Paweł Zawadzki, Paweł Sztromwasser
bioRxiv 2021.07.07.451425; doi: https://doi.org/10.1101/2021.07.07.451425

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