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  1. Article ; Online: Correction to: The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems.

    Daca-Roszak, Patrycja / Fiedorowicz, Joanna / Jankowski, Maciej / Ciesielka, Marzanna / Teresiński, Grzegorz / Lipska-Ziętkiewicz, Beata / Ziętkiewicz, Ewa / Grzybowski, Tomasz / Skonieczna, Katarzyna

    Journal of applied genetics

    2024  

    Language English
    Publishing date 2024-04-13
    Publishing country England
    Document type Published Erratum
    ZDB-ID 1235302-4
    ISSN 2190-3883 ; 1234-1983
    ISSN (online) 2190-3883
    ISSN 1234-1983
    DOI 10.1007/s13353-024-00864-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The effect of library preparation protocol on the efficiency of heteroplasmy detection in mitochondrial DNA using two massively parallel sequencing Illumina systems.

    Daca-Roszak, Patrycja / Fiedorowicz, Joanna / Jankowski, Maciej / Ciesielka, Marzanna / Teresiński, Grzegorz / Lipska-Zietkiewicz, Beata / Zietkiewicz, Ewa / Grzybowski, Tomasz / Skonieczna, Katarzyna

    Journal of applied genetics

    2023  

    Abstract: Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and ... ...

    Abstract Massively parallel sequencing (MPS) technology has become the gold standard in mitochondrial DNA research due to its high sensitivity in detecting mtDNA heteroplasmy, a prognostic marker in various medical applications. Various MPS technologies and platforms used for mtDNA analysis exist. Obtaining reliable and sensitive results requires deep and uniform coverage of the entire mtDNA sequence, which is heavily influenced by the choice of library preparation method and sequencing platform. Here, we present a comparison of the sequencing coverage and the ability to heteroplasmy detection using two library preparation protocols (Nextera XT DNA Library Preparation Kit and Nextera DNA Flex Library Preparation Kit) and two different (MiSeq FGx and ISeq 100) Illumina MPS platforms. Our study indicates that the Nextera DNA Flex Library protocol provides a more balanced coverage along the mitogenome and a reliable heteroplasmy detection with both MiSeq and iSeq Illumina MPS systems.
    Language English
    Publishing date 2023-12-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 1235302-4
    ISSN 2190-3883 ; 1234-1983
    ISSN (online) 2190-3883
    ISSN 1234-1983
    DOI 10.1007/s13353-023-00821-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Genetic diversity in Kashubs: the regional increase in the frequency of several disease-causing variants.

    Jankowski, Maciej / Daca-Roszak, Patrycja / Obracht-Prondzyński, Cezary / Płoski, Rafał / Lipska-Ziętkiewicz, Beata S / Ziętkiewicz, Ewa

    Journal of applied genetics

    2022  Volume 63, Issue 4, Page(s) 691–701

    Abstract: Differential distribution of genetic variants' frequency among human populations is caused by the genetic drift in isolated populations, historical migrations, and demography. Some of these variants are identical by descent and represent founder ... ...

    Abstract Differential distribution of genetic variants' frequency among human populations is caused by the genetic drift in isolated populations, historical migrations, and demography. Some of these variants are identical by descent and represent founder mutations, which - if pathogenic in nature - lead to the increased frequency of otherwise rare diseases. The detection of the increased regional prevalence of pathogenic variants may shed light on the historical processes that affected studied populations and can help to develop effective screening and diagnostic strategies as a part of personalized medicine. Here, we discuss the specific genetic diversity in Kashubs, the minority group living in northern Poland, reflected in the biased distribution of some of the repetitively found disease-causing variants. These include the following: (1) c.662A > G (p.Asp221Gly) in LDLR, causing heterozygous familial hypercholesterolemia; (2) c.3700_3704del in BRCA1, associated with hereditary breast and ovarian cancer syndrome; (3) c.1528G > C (p.Glu510Gln) in HADHA, seen in long-chain 3-hydroxy acyl-CoA dehydrogenase (LCHAD) deficiency, and (4) c.1032delT in NPHS2, associated with steroid-resistant nephrotic syndrome.
    MeSH term(s) Humans ; Genetic Predisposition to Disease ; Mitochondrial Myopathies ; Lipid Metabolism, Inborn Errors ; Genetic Variation ; Mutation
    Language English
    Publishing date 2022-08-15
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1235302-4
    ISSN 2190-3883 ; 1234-1983
    ISSN (online) 2190-3883
    ISSN 1234-1983
    DOI 10.1007/s13353-022-00713-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Discrimination between human populations using a small number of differentially methylated CpG sites: a preliminary study using lymphoblastoid cell lines and peripheral blood samples of European and Chinese origin.

    Daca-Roszak, Patrycja / Jaksik, Roman / Paczkowska, Julia / Witt, Michał / Ziętkiewicz, Ewa

    BMC genomics

    2020  Volume 21, Issue 1, Page(s) 706

    Abstract: Background: Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the ... ...

    Abstract Background: Epigenetics is one of the factors shaping natural variability observed among human populations. A small proportion of heritable inter-population differences are observed in the context of both the genome-wide methylation level and the methylation status of individual CpG sites. It has been demonstrated that a limited number of carefully selected differentially methylated sites may allow discrimination between main human populations. However, most of the few published results have been performed exclusively on B-lymphocyte cell lines.
    Results: The goal of our study was to identify a set of CpG sites sufficient to discriminate between populations of European and Chinese ancestry based on the difference in the DNA methylation profile not only in cell lines but also in primary cell samples. The preliminary selection of CpG sites differentially methylated in these two populations (pop-CpGs) was based on the analysis of two groups of commercially available ethnically-specific B-lymphocyte cell lines, performed using Illumina Infinium Human Methylation 450 BeadChip Array. A subset of 10 pop-CpGs characterized by the best differentiating criteria (|Mdiff| > 1, q < 0.05; lack of the confounding genomic features), and 10 additional CpGs in their immediate vicinity, were further tested using pyrosequencing technology in both B-lymphocyte cell lines and in the primary samples of the peripheral blood representing two analyzed populations. To assess the population-discriminating potential of the selected set of CpGs (further referred to as "composite pop (CEU-CHB)-CpG marker"), three classification methods were applied. The predictive ability of the composite 8-site pop (CEU-CHB)-CpG marker was assessed using 10-fold cross-validation method on two independent sets of samples.
    Conclusions: Our results showed that less than 10 pop-CpG sites may distinguish populations of European and Chinese ancestry; importantly, this small composite pop-CpG marker performs well in both lymphoblastoid cell lines and in non-homogenous blood samples regardless of a gender.
    MeSH term(s) Adult ; Cell Line ; China ; CpG Islands ; DNA Methylation ; Europe ; Female ; Genetics, Population/methods ; Humans ; Leukocytes, Mononuclear ; Male
    Language English
    Publishing date 2020-10-12
    Publishing country England
    Document type Journal Article
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-020-07092-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: In vitro differentiation of ciliated cells in ALI-cultured human airway epithelium - The framework for functional studies on airway differentiation in ciliopathies.

    Bukowy-Bieryłło, Zuzanna / Daca-Roszak, Patrycja / Jurczak, Joanna / Przystałowska-Macioła, Hanna / Jaksik, Roman / Witt, Michał / Ziętkiewicz, Ewa

    European journal of cell biology

    2021  Volume 101, Issue 1, Page(s) 151189

    Abstract: Primary cultures of the human airway epithelium (AE) cells are an indispensable tool in studies of pathophysiology of genetic and environmental pulmonary diseases, including cystic fibrosis (CF), primary ciliary dyskinesia (PCD) and chronic obstructive ... ...

    Abstract Primary cultures of the human airway epithelium (AE) cells are an indispensable tool in studies of pathophysiology of genetic and environmental pulmonary diseases, including cystic fibrosis (CF), primary ciliary dyskinesia (PCD) and chronic obstructive pulmonary disease (COPD). Air-liquid interface (ALI) culture is the best method to follow the differentiation of ciliated cells, whose dysfunction forms the basis of PCD. Here, we used custom-designed Taqman Low Density Array (TLDA), qRT-PCR-based assay, to analyze expression of 14 AE genes in cells from healthy donors, cultured in ALI settings using Pneumacult medium, with the focus on genes involved in cilia differentiation and in PCD pathogenesis. The results of TLDA assay were compared with the bulk RNAseq analysis, and placed in the cellular context using immunofluorescent staining (IF) of ALI cultured cells. Expression analysis revealed culture time-related upregulation of the majority of cilia-related genes, followed by the appearance of respective protein signals visualized by IF. Strong correlation of TLDA with RNAseq results indicated that TLDA assay is a reliable and scalable approach to analyze expression of selected genes specific for different AE cell types. Characterization of temporal and inter-donor changes in the expression of these genes, performed in healthy donors and in well-defined ALI/Pnemacult culture conditions, provides a useful reference relevant for a broad spectrum of functional studies where the in vitro AE differentiation is in focus.
    MeSH term(s) Cell Differentiation ; Cells, Cultured ; Cilia ; Ciliopathies ; Epithelial Cells ; Epithelium ; Humans
    Language English
    Publishing date 2021-12-02
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 391967-5
    ISSN 1618-1298 ; 0070-2463 ; 0171-9335
    ISSN (online) 1618-1298
    ISSN 0070-2463 ; 0171-9335
    DOI 10.1016/j.ejcb.2021.151189
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Identification of Endogenous Control miRNAs for RT-qPCR in T-Cell Acute Lymphoblastic Leukemia.

    Drobna, Monika / Szarzyńska-Zawadzka, Bronisława / Daca-Roszak, Patrycja / Kosmalska, Maria / Jaksik, Roman / Witt, Michał / Dawidowska, Małgorzata

    International journal of molecular sciences

    2018  Volume 19, Issue 10

    Abstract: Optimal endogenous controls enable reliable normalization of microRNA (miRNA) expression in reverse-transcription quantitative PCR (RT-qPCR). This is particularly important when miRNAs are considered as candidate diagnostic or prognostic biomarkers. ... ...

    Abstract Optimal endogenous controls enable reliable normalization of microRNA (miRNA) expression in reverse-transcription quantitative PCR (RT-qPCR). This is particularly important when miRNAs are considered as candidate diagnostic or prognostic biomarkers. Universal endogenous controls are lacking, thus candidate normalizers must be evaluated individually for each experiment. Here we present a strategy that we applied to the identification of optimal control miRNAs for RT-qPCR profiling of miRNA expression in T-cell acute lymphoblastic leukemia (T-ALL) and in normal cells of T-lineage. First, using NormFinder for an iterative analysis of miRNA stability in our miRNA-seq data, we established the number of control miRNAs to be used in RT-qPCR. Then, we identified optimal control miRNAs by a comprehensive analysis of miRNA stability in miRNA-seq data and in RT-qPCR by analysis of RT-qPCR amplification efficiency and expression across a variety of T-lineage samples and T-ALL cell line culture conditions. We then showed the utility of the combination of three miRNAs as endogenous normalizers (hsa-miR-16-5p, hsa-miR-25-3p, and hsa-let-7a-5p). These miRNAs might serve as first-line candidate endogenous controls for RT-qPCR analysis of miRNAs in different types of T-lineage samples: T-ALL patient samples, T-ALL cell lines, normal immature thymocytes, and mature T-lymphocytes. The strategy we present is universal and can be transferred to other RT-qPCR experiments.
    MeSH term(s) Algorithms ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Humans ; Jurkat Cells ; MicroRNAs/metabolism ; Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics ; RNA Stability ; Real-Time Polymerase Chain Reaction
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2018-09-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms19102858
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  7. Article ; Online: CFAP300

    Zietkiewicz, Ewa / Bukowy-Bieryllo, Zuzanna / Rabiasz, Alicja / Daca-Roszak, Patrycja / Wojda, Alina / Voelkel, Katarzyna / Rutkiewicz, Ewa / Pogorzelski, Andrzej / Rasteiro, Margarida / Witt, Michal

    American journal of respiratory cell and molecular biology

    2019  Volume 61, Issue 4, Page(s) 440–449

    Abstract: Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous hereditary disease from a class of ciliopathies. In spite of the recent progress, the genetic basis of PCD in one-third of patients remains unknown. In search for new genes and/or ... ...

    Abstract Primary ciliary dyskinesia (PCD) is a rare, genetically heterogeneous hereditary disease from a class of ciliopathies. In spite of the recent progress, the genetic basis of PCD in one-third of patients remains unknown. In search for new genes and/or mutations, whole-exome sequencing was performed in 120 unrelated Polish patients with PCD, in whom no genetic cause of PCD was earlier identified. Among a number of pathogenic variants in PCD genes, mutations in
    MeSH term(s) Adolescent ; Adult ; Animals ; Axoneme/metabolism ; Axoneme/ultrastructure ; Cell Movement ; Child ; Child, Preschool ; Cilia/physiology ; Cilia/ultrastructure ; Ciliary Motility Disorders/ethnology ; Ciliary Motility Disorders/genetics ; Conserved Sequence ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/physiology ; Dyneins/metabolism ; Ethnic Groups/genetics ; Female ; Helminth Proteins/genetics ; Humans ; INDEL Mutation ; Infant ; Locomotion ; Male ; Poland ; Protein Transport ; RNA Interference ; Whole Exome Sequencing ; Young Adult ; Zebrafish Proteins/genetics
    Chemical Substances CFAP300 protein, human ; Cytoskeletal Proteins ; Helminth Proteins ; Zebrafish Proteins ; Dyneins (EC 3.6.4.2)
    Language English
    Publishing date 2019-03-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1025960-0
    ISSN 1535-4989 ; 1044-1549
    ISSN (online) 1535-4989
    ISSN 1044-1549
    DOI 10.1165/rcmb.2018-0260OC
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies.

    Daca-Roszak, Patrycja / Pfeifer, Aleksandra / Żebracka-Gala, Jadwiga / Rusinek, Dagmara / Szybińska, Aleksandra / Jarząb, Barbara / Witt, Michał / Ziętkiewicz, Ewa

    BMC genomics

    2015  Volume 16, Page(s) 1003

    Abstract: Background: Infinium HumanMethylation 450 BeadChip Arrays by Illumina (Illumina HM450K) are among the most popular CpG microarray platforms widely used in biological and medical research. Several recent studies highlighted the potentially confounding ... ...

    Abstract Background: Infinium HumanMethylation 450 BeadChip Arrays by Illumina (Illumina HM450K) are among the most popular CpG microarray platforms widely used in biological and medical research. Several recent studies highlighted the potentially confounding impact of the genomic variation on the results of methylation studies performed using Illumina's Infinium methylation probes. However, the complexity of SNPs impact on the methylation level measurements (β values) has not been comprehensively described.
    Results: In our comparative study of European and Asian populations performed using Illumina HM450K, we found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. Characteristic tri-modal or bi-modal patterns of β values distribution among individual samples were observed for CpGs with SNPs in the first and second position, respectively. To better understand how SNPs affect methylation readouts, we investigated their impact in the context of SNP position and type, and of the Illumina probe type (Infinium I or II).
    Conclusions: Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes. In addition, it provides important practical clues for discriminating between differences due to the methylation status and to the genomic polymorphisms, based on the inspection of methylation readouts in individual samples. This approach is of special importance when Illumina Infinium assay is used for any comparative population studies, whether related to cancer, disease, ethnicity where SNP frequencies differentiate the studied groups.
    MeSH term(s) Alleles ; CpG Islands ; DNA Methylation ; Epigenesis, Genetic ; Epigenomics/methods ; Gene Frequency ; Genetics, Population ; Genomics/methods ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2015-11-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/s12864-015-2202-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Mild X-linked Alport syndrome due to the COL4A5 G624D variant originating in the Middle Ages is predominant in Central/East Europe and causes kidney failure in midlife.

    Żurowska, Aleksandra M / Bielska, Olga / Daca-Roszak, Patrycja / Jankowski, Maciej / Szczepańska, Maria / Roszkowska-Bjanid, Dagmara / Kuźma-Mroczkowska, Elżbieta / Pańczyk-Tomaszewska, Małgorzata / Moczulska, Anna / Drożdż, Dorota / Hadjipanagi, Despina / Deltas, Constantinos / Ostalska-Nowicka, Danuta / Rabiega, Alina / Taraszkiewicz, Janina / Taranta-Janusz, Katarzyna / Wieczorkiewicz-Plaza, Anna / Jobs, Katarzyna / Mews, Judyta /
    Musiał, Kinga / Jakubowska, Anna / Nosek, Hanna / Jander, Anna E / Koutsofti, Constantina / Stanisławska-Sachadyn, Anna / Kuleszo, Dominka / Ziętkiewicz, Ewa / Lipska-Ziętkiewicz, Beata S

    Kidney international

    2020  Volume 99, Issue 6, Page(s) 1451–1458

    Abstract: A study of 269 children enrolled into a National Registry for children with persistent glomerular hematuria identified 131 individuals with genetically confirmed X-linked Alport Syndrome. A single variant c.1871G>A p.Gly624Asp (G624D) in COL4A5 was ... ...

    Abstract A study of 269 children enrolled into a National Registry for children with persistent glomerular hematuria identified 131 individuals with genetically confirmed X-linked Alport Syndrome. A single variant c.1871G>A p.Gly624Asp (G624D) in COL4A5 was predominant and accounted for 39% of X-linked Alport Syndrome in unrelated Polish families (44 of 113). To evaluate its origins, the genetic variation in a 2.79 Mb segment encompassing the COL4A5 locus on chromosome X was assessed. All G624D alleles were found on the same rare haplotype background, indicating a founder effect dating back to the 12-13th century. The phenotypic data of 131 children with X-linked Alport Syndrome and their 195 affected adult relatives revealed that the G624D variant was associated with a significantly milder clinical course in comparison to other pathogenic COL4A5 variants. Furthermore the clinical course of this genetically uniform cohort was milder than that observed in individuals with other COL4A5 missense mutations. In spite of the benign clinical manifestation throughout childhood and early adulthood, the G624D variant confers significant risk for both kidney failure and deafness in males, albeit 20-30 years later than that observed in individuals with other COL4A5 pathogenic variants (50% cumulative risk of starting dialysis at 54 years (95% confidence interval: 50-62) v. 26 years (95% confidence interval: 22-30)). Thus, males with G624D are candidates for existing and emerging therapies for Alport Syndrome.
    MeSH term(s) Adult ; Child ; Collagen Type IV/genetics ; DNA Mutational Analysis ; Europe ; Founder Effect ; Humans ; Male ; Middle Aged ; Nephritis, Hereditary/genetics ; Renal Insufficiency
    Chemical Substances COL4A5 protein, human ; Collagen Type IV
    Language English
    Publishing date 2020-12-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120573-0
    ISSN 1523-1755 ; 0085-2538
    ISSN (online) 1523-1755
    ISSN 0085-2538
    DOI 10.1016/j.kint.2020.10.040
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