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2. Comprehensive analysis of runs of homozygosity and heterozygosity in Holstein cattle on the basis of medium and high density SNP panels and large population sample.

Author

Szmatoła, Tomasz, Gurgul, Artur, Jasielczuk, Igor, and Ropka-Molik, Katarzyna

Subjects
HOLSTEIN-Friesian cattle, INBREEDING, HOMOZYGOSITY, SINGLE nucleotide polymorphisms, HETEROZYGOSITY, CATTLE genetics, CATTLE breeding, DENSITY
Abstract

This study reports runs of homozygosity (ROH) and heterozygosity (ROHet) distributed in a large population of Holstein cattle on the basis of two microarrays of medium (50k; 2163 animals; 54 609 SNPs) and high single nucleotide polymorphism (SNP) density (HD; 600 animals; 777 692 SNPs). To assess the inbreeding values of Holstein cattle, the ROH-based genomic inbreeding coefficient (FROH) was calculated. The comparison of SNP panels suggested that FROH values above 4 Mb should be considered for panels of medium densities as a relatively reliable measure of inbreeding. Moreover, ROH hotspots and coldspots were identified and compared between the HD and 50k SNP panels and were carefully examined for association with production and functional traits. The obtained results pinpointed genomic regions presumably under selection pressure in Holstein cattle. The regions overlapped with a large number of genes, including GHR, GBF1, SUMF1, CCL28, NIM1K, U6, BTRC and FABP1, many of which are involved in important Holstein cattle characteristics. We also found that some ROH hotspots and coldspots identified with the HD panel were not detected with the 50k panel, mainly because of insufficient SNP density in certain genomic regions. This suggests that using medium-density panels might not be the best choice when precise identification of ROH patterns is the main goal. In summary, in this work, we confirmed that a high-density SNP panel compared to a medium-density SNP panel allows for more precise identification of ROH patterns, especially in the case of short ROH that could be associated with ancestral inbreeding. [ABSTRACT FROM AUTHOR]

Published
2024
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6. The distinguishable DNA whole genome methylation profile of 2 cases of pediatric precursor B acute lymphoblastic leukaemia (BCP ALL) with prodromal, preleukemic phase: A case report

Author

Chaber, Radosław, Gurgul, Artur, Wróbel, Grażyna, Tomoń, Anna, Paszek, Sylwia, Potocka, Natalia, Haus, Olga, Lejman, Monika, Łach, Kornelia, Szmatoła, Tomasz, Jasielczuk, Igor, Rybka, Blanka, Ryczan-Krawczyk, Renata, Stąpor, Sylwia, Ciebiera, Krzysztof, Arthur, Christopher J., and Zawlik, Izabela

Published
2018
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8. MicroRNA gene methylation landscape in pediatric B-cell precursor acute lymphoblastic leukemia

Author

Chaber, Radosław, primary, Gurgul, Artur, additional, Tabarkiewicz, Jacek, additional, Wróbel, Grażyna, additional, Szmatoła, Tomasz, additional, Jasielczuk, Igor, additional, Haus, Olga, additional, Lejman, Monika, additional, Rybka, Blanka, additional, Ryczan-Krawczyk, Renata, additional, Jaśkowiec, Anna, additional, Paszek, Sylwia, additional, Potocka, Natalia, additional, Arthur, Christopher J., additional, Bal, Wioletta, additional, Łach, Kornelia, additional, Kowal, Aneta, additional, Zawlik, Izabela, additional, and Latos-Grażyńska, Elżbieta, additional

Published
2022
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10. Maternal atopy and offspring epigenome-wide methylation signature

Author

Danielewicz, Hanna, primary, Gurgul, Artur, additional, Dębińska, Anna, additional, Myszczyszyn, Grzegorz, additional, Szmatoła, Tomasz, additional, Myszkal, Anna, additional, Jasielczuk, Igor, additional, Drabik-Chamerska, Anna, additional, Hirnle, Lidia, additional, and Boznański, Andrzej, additional

Published
2020
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13. Additional file 7: of A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

Author

Gurgul, Artur, Jasielczuk, Igor, Ropka-Molik, Katarzyna, Semik-Gurgul, Ewelina, Pawlina-Tyszko, Klaudia, Szmatoła, Tomasz, Szyndler-Nędza, Magdalena, Bugno-Poniewierska, Monika, Blicharski, Tadeusz, Szulc, Karolina, Skrzypczak, Ewa, and Jędrzej Krupiński

Abstract

Comparison of selected phenotypic traits for the studied pig breeds. (DOCX 19 kb)

Published
2018
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17. Maternal atopy and offspring epigenome-wide methylation signature.

Author

Danielewicz, Hanna, Gurgul, Artur, Dębińska, Anna, Myszczyszyn, Grzegorz, Szmatoła, Tomasz, Myszkal, Anna, Jasielczuk, Igor, Drabik-Chamerska, Anna, Hirnle, Lidia, and Boznański, Andrzej

Subjects
DNA methylation, EPIGENETICS, ALLERGIES, ATOPY, MATERNAL health
Abstract

The increase in the prevalence of allergic diseases is believed to partially depend on environmental changes. DNA methylation is a major epigenetic mechanism, which is known to respond to environmental factors. A number of studies have revealed that patterns of DNA methylation may potentially predict allergic diseases. Here, we examined how maternal atopy is associated with methylation patterns in the cord blood of neonates. We conducted an epigenome-wide association study in a cohort of 96 mother-child pairs. Pregnant women aged not more than 35 years old, not currently smoking or exposed to environmental tobacco smoke, who did not report obesity before conception were considered eligible. They were further tested for atopy. Converted DNA from cord blood was analysed using Infinium MethylationEPIC; for statistical analysis, RnBeads software was applied. Gestational age and sex were included as covariates in the final analysis. 83 DM sites were associated with maternal atopy. Within the top DM sites, there were CpG sites which mapped to genes SCD, ITM2C, NT5C3A and NPEPL1. Regional analysis revealed 25 tiling regions, 4 genes, 3 CpG islands and 5 gene promoters, (including PIGCP1, ADAM3A, ZSCAN12P1) associated with maternal atopy. Gene content analysis revealed pointwise enrichments in pathways related to purine-containing compound metabolism, the G1/S transition of the mitotic cell cycle, stem cell division and cellular glucose homoeostasis. These findings suggest that maternal atopy provides a unique intrauterine environment that may constitute the first environment in which exposure is associated with methylation patterns in newborn. [ABSTRACT FROM AUTHOR]

Published
2021
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20. Whole-genome DNA methylation characteristics in pediatric precursor B cell acute lymphoblastic leukemia (BCP ALL)

Author

Chaber, Radosław, primary, Gurgul, Artur, additional, Wróbel, Grażyna, additional, Haus, Olga, additional, Tomoń, Anna, additional, Kowalczyk, Jerzy, additional, Szmatoła, Tomasz, additional, Jasielczuk, Igor, additional, Rybka, Blanka, additional, Ryczan-Krawczyk, Renata, additional, Duszeńko, Ewa, additional, Stąpor, Sylwia, additional, Ciebiera, Krzysztof, additional, Paszek, Sylwia, additional, Potocka, Natalia, additional, Arthur, Christopher J., additional, and Zawlik, Izabela, additional

Published
2017
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21. Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis

Author

Deregowska, Anna, primary, Adamczyk, Jagoda, additional, Kwiatkowska, Aleksandra, additional, Gurgul, Artur, additional, Skoneczny, Marek, additional, Skoneczna, Adrianna, additional, Szmatola, Tomasz, additional, Jasielczuk, Igor, additional, Magda, Michal, additional, Rawska, Ewa, additional, Pabian, Sylwia, additional, Panek, Anita, additional, Kaplan, Jakub, additional, Lewinska, Anna, additional, and Wnuk, Maciej, additional

Published
2015
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