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Article

The Thousand Polish Genomes—A Database of Polish Variant Allele Frequencies

by
Elżbieta Kaja
1,2,3,†,
Adrian Lejman
1,2,†,
Dawid Sielski
1,2,
Mateusz Sypniewski
1,4,
Tomasz Gambin
5,
Mateusz Dawidziuk
6,
Tomasz Suchocki
7,8,
Paweł Golik
9,
Marzena Wojtaszewska
1,10,
Magdalena Mroczek
11,
Maria Stępień
1,12,13,
Joanna Szyda
7,8,
Karolina Lisiak-Teodorczyk
1,
Filip Wolbach
1,
Daria Kołodziejska
1,
Katarzyna Ferdyn
1,14,
Maciej Dąbrowski
1,15,
Alicja Woźna
1,16,
Marcin Żytkiewicz
17,
Anna Bodora-Troińska
17,
Waldemar Elikowski
17,
Zbigniew J. Król
2,
Artur Zaczyński
2,
Agnieszka Pawlak
2,18,
Robert Gil
2,18,
Waldemar Wierzba
2,
Paula Dobosz
1,2,19,
Katarzyna Zawadzka
1,
Paweł Zawadzki
1,16 and
Paweł Sztromwasser
1,*add Show full author list remove Hide full author list
1
MNM Bioscience Inc., Cambridge, MA 02142, USA
2
Central Clinical Hospital of Ministry of the Interior and Administration in Warsaw, 02-507 Warsaw, Poland
3
Department of Medical Chemistry and Laboratory Medicine, Poznan University of Medical Sciences, 60-101 Poznan, Poland
4
Department of Genetics and Animal Breeding, Poznań University of Life Sciences, 60-637 Poznan, Poland
5
Institute of Computer Science, Warsaw University of Technology, 00-665 Warsaw, Poland
6
Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
7
Biostatistics Group, Wrocław University of Environmental and Life Sciences, 51-631 Wrocław, Poland
8
National Research Institute of Animal Production, 32-083 Balice, Poland
9
Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
10
Department of Hematology, Frederic Chopin Provincial Specialist Hospital, 35-055 Rzeszów, Poland
11
Department of Neurology and Neurophysiology, Balgrist University Hospital, University of Zurich, 8008 Zurich, Switzerland
12
Department of Infectious Diseases, Medical University of Lublin, 20-059 Lublin, Poland
13
Department of Sports Medicine, Medical University of Lublin, 20-059 Lublin, Poland
14
Medical and Science Sp. z o.o., 08-455 Podebłocie, Poland
15
Institute of Human Genetics Polish Academy of Sciences, 60-479 Poznan, Poland
16
Faculty of Physics, Adam Mickiewicz University, 61-614 Poznan, Poland
17
Department of Internal Medicine, Józef Struś Multidisciplinary Municipal Hospital, 61-285 Poznan, Poland
18
Mossakowski Medical Research Centre, Polish Academy of Science, 02-106 Warsaw, Poland
19
Department of Hematology, Transplantation and Internal Medicine, University Clinical Center of the Medical University of Warsaw, 02-091 Warsaw, Poland
 
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*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Academic Editor: Alessandra Rampazzo
Int. J. Mol. Sci. 2022, 23(9), 4532; https://doi.org/10.3390/ijms23094532
Received: 21 March 2022 / Revised: 13 April 2022 / Accepted: 14 April 2022 / Published: 20 April 2022
(This article belongs to the Collection State-of-the-Art Molecular Genetics and Genomics in Poland)
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Abstract

Although Slavic populations account for over 4.5% of world inhabitants, no centralised, open-source reference database of genetic variation of any Slavic population exists to date. Such data are crucial for clinical genetics, biomedical research, as well as archeological and historical studies. The Polish population, which is homogenous and sedentary in its nature but influenced by many migrations of the past, is unique and could serve as a genetic reference for the Slavic nations. In this study, we analysed whole genomes of 1222 Poles to identify and genotype a wide spectrum of genomic variation, such as small and structural variants, runs of homozygosity, mitochondrial haplogroups, and de novo variants. Common variant analyses showed that the Polish cohort is highly homogenous and shares ancestry with other European populations. In rare variant analyses, we identified 32 autosomal-recessive genes with significantly different frequencies of pathogenic alleles in the Polish population as compared to the non-Finish Europeans, including C2, TGM5, NUP93, C19orf12, and PROP1. The allele frequencies for small and structural variants, calculated for 1076 unrelated individuals, are released publicly as The Thousand Polish Genomes database, and will contribute to the worldwide genomic resources available to researchers and clinicians. View Full-Text
Keywords: variant; allele frequency; genome; whole-genome sequencing; population genomics; allelic distribution; Polish genomes variant; allele frequency; genome; whole-genome sequencing; population genomics; allelic distribution; Polish genomes
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MDPI and ACS Style

Kaja, E.; Lejman, A.; Sielski, D.; Sypniewski, M.; Gambin, T.; Dawidziuk, M.; Suchocki, T.; Golik, P.; Wojtaszewska, M.; Mroczek, M.; Stępień, M.; Szyda, J.; Lisiak-Teodorczyk, K.; Wolbach, F.; Kołodziejska, D.; Ferdyn, K.; Dąbrowski, M.; Woźna, A.; Żytkiewicz, M.; Bodora-Troińska, A.; Elikowski, W.; Król, Z.J.; Zaczyński, A.; Pawlak, A.; Gil, R.; Wierzba, W.; Dobosz, P.; Zawadzka, K.; Zawadzki, P.; Sztromwasser, P. The Thousand Polish Genomes—A Database of Polish Variant Allele Frequencies. Int. J. Mol. Sci. 2022, 23, 4532. https://doi.org/10.3390/ijms23094532

AMA Style

Kaja E, Lejman A, Sielski D, Sypniewski M, Gambin T, Dawidziuk M, Suchocki T, Golik P, Wojtaszewska M, Mroczek M, Stępień M, Szyda J, Lisiak-Teodorczyk K, Wolbach F, Kołodziejska D, Ferdyn K, Dąbrowski M, Woźna A, Żytkiewicz M, Bodora-Troińska A, Elikowski W, Król ZJ, Zaczyński A, Pawlak A, Gil R, Wierzba W, Dobosz P, Zawadzka K, Zawadzki P, Sztromwasser P. The Thousand Polish Genomes—A Database of Polish Variant Allele Frequencies. International Journal of Molecular Sciences. 2022; 23(9):4532. https://doi.org/10.3390/ijms23094532

Chicago/Turabian Style

Kaja, Elżbieta, Adrian Lejman, Dawid Sielski, Mateusz Sypniewski, Tomasz Gambin, Mateusz Dawidziuk, Tomasz Suchocki, Paweł Golik, Marzena Wojtaszewska, Magdalena Mroczek, Maria Stępień, Joanna Szyda, Karolina Lisiak-Teodorczyk, Filip Wolbach, Daria Kołodziejska, Katarzyna Ferdyn, Maciej Dąbrowski, Alicja Woźna, Marcin Żytkiewicz, Anna Bodora-Troińska, Waldemar Elikowski, Zbigniew J. Król, Artur Zaczyński, Agnieszka Pawlak, Robert Gil, Waldemar Wierzba, Paula Dobosz, Katarzyna Zawadzka, Paweł Zawadzki, and Paweł Sztromwasser. 2022. "The Thousand Polish Genomes—A Database of Polish Variant Allele Frequencies" International Journal of Molecular Sciences 23, no. 9: 4532. https://doi.org/10.3390/ijms23094532

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