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  1. Artikel ; Online: A Small De Novo CNV Deletion of the Paternal Copy of

    Szafranski, Przemyslaw / Stankiewicz, Paweł

    Non-coding RNA

    2023  Band 9, Heft 5

    Abstract: Pathogenic single-nucleotide variants (SNVs) and copy-number variant (CNV) deletions involving ... ...

    Abstract Pathogenic single-nucleotide variants (SNVs) and copy-number variant (CNV) deletions involving the
    Sprache Englisch
    Erscheinungsdatum 2023-10-09
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article
    ZDB-ID 2813993-8
    ISSN 2311-553X ; 2311-553X
    ISSN (online) 2311-553X
    ISSN 2311-553X
    DOI 10.3390/ncrna9050061
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Buch ; Online: Genomic Disorders

    Lupski, James R. / Stankiewicz, Pawel

    The Genomic Basis of Disease

    2006  

    Verfasserangabe edited by James R. Lupski, Pawel Stankiewicz
    Schlagwörter Pathology
    Sprache Englisch
    Verlag Humana Press Inc
    Erscheinungsort Totowa, NJ
    Dokumenttyp Buch ; Online
    HBZ-ID TT050387104
    ISBN 978-1-588-29559-0 ; 978-1-597-45039-3 ; 1-588-29559-1 ; 1-597-45039-1
    DOI 10.1007/978-1-59745-039-3
    Datenquelle ZB MED Katalog Medizin, Gesundheit, Ernährung, Umwelt, Agrar

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  3. Artikel ; Online: Cloud-native distributed genomic pileup operations.

    Wiewiórka, Marek / Szmurło, Agnieszka / Stankiewicz, Paweł / Gambin, Tomasz

    Bioinformatics (Oxford, England)

    2023  Band 39, Heft 1

    Abstract: Motivation: Pileup analysis is a building block of many bioinformatics pipelines, including variant calling and genotyping. This step tends to become a bottleneck of the entire assay since the straightforward pileup implementations involve processing of ...

    Abstract Motivation: Pileup analysis is a building block of many bioinformatics pipelines, including variant calling and genotyping. This step tends to become a bottleneck of the entire assay since the straightforward pileup implementations involve processing of all base calls from all alignments sequentially. On the other hand, a distributed version of the algorithm faces the intrinsic challenge of splitting reads-oriented file formats into self-contained partitions to avoid costly data exchange between computational nodes.
    Results: Here, we present a scalable, distributed and efficient implementation of a pileup algorithm that is suitable for deploying in cloud computing environments. In particular, we implemented: (i) our custom data-partitioning algorithm optimized to work with the alignment reads, (ii) a novel and unique approach to process alignment events from sequencing reads using the MD tags, (iii) the source code micro-optimizations for recurrent operations, and (iv) a modular structure of the algorithm. We have proven that our novel approach consistently and significantly outperforms other state-of-the-art distributed tools in terms of execution time (up to 6.5× faster) and memory usage (up to 2× less), resulting in a substantial cloud cost reduction. SeQuiLa is a cloud-native solution that can be easily deployed using any managed Kubernetes and Hadoop services available in public clouds, like Microsoft Azure Cloud, Google Cloud Platform, or Amazon Web Services. Together with the already implemented distributed range join and coverage calculations, our package provides end-users with a unified SQL interface for convenient analyses of population-scale genomic data in an interactive way.
    Availability and implementation: https://biodatageeks.github.io/sequila/.
    Mesh-Begriff(e) Software ; Genomics/methods ; Algorithms ; Genome ; Computational Biology/methods
    Sprache Englisch
    Erscheinungsdatum 2023-01-03
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac804
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Long Non-Coding RNA

    Szafranski, Przemyslaw / Stankiewicz, Paweł

    Genes

    2021  Band 12, Heft 2

    Abstract: ... ...

    Abstract The
    Mesh-Begriff(e) Disease Susceptibility ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation ; Genetic Loci ; Genetic Structures ; Humans ; Promoter Regions, Genetic ; RNA Interference ; RNA, Long Noncoding/genetics ; Regulatory Sequences, Nucleic Acid ; Transcription, Genetic
    Chemische Substanzen Forkhead Transcription Factors ; RNA, Long Noncoding
    Sprache Englisch
    Erscheinungsdatum 2021-01-27
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12020177
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel: One pedigree we all may have come from - did Adam and Eve have the chromosome 2 fusion?

    Stankiewicz, Paweł

    Molecular cytogenetics

    2016  Band 9, Seite(n) 72

    Abstract: Background: In contrast to Great Apes, who have 48 chromosomes, modern humans and likely Neandertals and Denisovans have and had, respectively, 46 chromosomes. The reduction in chromosome number was caused by the head-to-head fusion of two ancestral ... ...

    Abstract Background: In contrast to Great Apes, who have 48 chromosomes, modern humans and likely Neandertals and Denisovans have and had, respectively, 46 chromosomes. The reduction in chromosome number was caused by the head-to-head fusion of two ancestral chromosomes to form human chromosome 2 (HSA2) and may have contributed to the reproductive barrier with Great Apes.
    Results: Next generation sequencing and molecular clock analyses estimated that this fusion arose prior to our last common ancestor with Neandertal and Denisovan hominins ~ 0.74 - 4.5 million years ago.
    Hypotheses: I propose that, unlike recurrent Robertsonian translocations in humans, the HSA2 fusion was a single nonrecurrent event that spread through a small polygamous clan population bottleneck. Its heterozygous to homozygous conversion, fixation, and accumulation in the succeeding populations was likely facilitated by an evolutionary advantage through the genomic loss rather than deregulation of expression of the gene(s) flanking the HSA2 fusion site at 2q13.
    Conclusions: The origin of HSA2 might have been a critical evolutionary event influencing higher cognitive functions in various early subspecies of hominins. Next generation sequencing of
    Sprache Englisch
    Erscheinungsdatum 2016-09-26
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2420849-8
    ISSN 1755-8166
    ISSN 1755-8166
    DOI 10.1186/s13039-016-0283-3
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel: Long Non-Coding RNA FENDRR: Gene Structure, Expression, and Biological Relevance

    Szafranski, Przemyslaw / Stankiewicz, Paweł

    Genes. 2021 Jan. 27, v. 12, no. 2

    2021  

    Abstract: The FOXF1 Adjacent Noncoding Developmental Regulatory RNA (Fendrr) plays an important role in the control of gene expression in mammals. It is transcribed in the opposite direction to the neighboring Foxf1 gene with which it shares a region containing ... ...

    Abstract The FOXF1 Adjacent Noncoding Developmental Regulatory RNA (Fendrr) plays an important role in the control of gene expression in mammals. It is transcribed in the opposite direction to the neighboring Foxf1 gene with which it shares a region containing promoters. In humans, FENDRR is located on chromosome 16q24.1, and is positively regulated both by the FOXF1 distant lung-specific cis-acting enhancer and by trans-acting FOXF1. Fendrr has been shown to function as a competing endogenous RNA, sponging microRNAs and protein factors that control stability of mRNAs, and as an epigenetic modifier of chromatin structure around gene promoters and other regulatory sites, targeting them with histone methyltrasferase complexes. In mice, Fendrr is essential for development of the heart, lungs, and gastrointestinal system; its homozygous loss causes embryonic or perinatal lethality. Importantly, deregulation of FENDRR expression has been causatively linked also to tumorigenesis, resistance to chemotherapy, fibrosis, and inflammatory diseases. Here, we review the current knowledge on the FENDRR structure, expression, and involvement in development and tissue maintenance.
    Schlagwörter carcinogenesis ; chromatin ; death ; drug therapy ; epigenetics ; fibrosis ; gastrointestinal system ; gene expression ; genes ; heart ; histones ; homozygosity ; microRNA ; non-coding RNA
    Sprache Englisch
    Erscheinungsverlauf 2021-0127
    Erscheinungsort Multidisciplinary Digital Publishing Institute
    Dokumenttyp Artikel
    Anmerkung NAL-AP-2-clean
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes12020177
    Datenquelle NAL Katalog (AGRICOLA)

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  7. Artikel ; Online: Revised time estimation of the ancestral human chromosome 2 fusion.

    Poszewiecka, Barbara / Gogolewski, Krzysztof / Stankiewicz, Paweł / Gambin, Anna

    BMC genomics

    2022  Band 23, Heft Suppl 6, Seite(n) 616

    Abstract: Background: The reduction of the chromosome number from 48 in the Great Apes to 46 in modern humans is thought to result from the end-to-end fusion of two ancestral non-human primate chromosomes forming the human chromosome 2 (HSA2). Genomic signatures ... ...

    Abstract Background: The reduction of the chromosome number from 48 in the Great Apes to 46 in modern humans is thought to result from the end-to-end fusion of two ancestral non-human primate chromosomes forming the human chromosome 2 (HSA2). Genomic signatures of this event are the presence of inverted telomeric repeats at the HSA2 fusion site and a block of degenerate satellite sequences that mark the remnants of the ancestral centromere. It has been estimated that this fusion arose up to 4.5 million years ago (Mya).
    Results: We have developed an enhanced algorithm for the detection and efficient counting of the locally over-represented weak-to-strong (AT to GC) substitutions. By analyzing the enrichment of these substitutions around the fusion site of HSA2 we estimated its formation time at 0.9 Mya with a 95% confidence interval of 0.4-1.5 Mya. Additionally, based on the statistics derived from our algorithm, we have reconstructed the evolutionary distances among the Great Apes (Hominoidea).
    Conclusions: Our results shed light on the HSA2 fusion formation and provide a novel computational alternative for the estimation of the speciation chronology.
    Mesh-Begriff(e) Animals ; Centromere/genetics ; Chromosomes, Human ; Evolution, Molecular ; Genome ; Hominidae/genetics ; Humans
    Sprache Englisch
    Erscheinungsdatum 2022-08-25
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-022-08828-7
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Parental mosaicism for apparent de novo genetic variants: Scope, detection, and counseling challenges.

    Zemet, Roni / Van den Veyver, Ignatia B / Stankiewicz, Paweł

    Prenatal diagnosis

    2022  Band 42, Heft 7, Seite(n) 811–821

    Abstract: The disease burden of de novo mutations (DNMs) has been evidenced only recently when the common application of next-generation sequencing technologies enabled their reliable and affordable detection through family-based clinical exome or genome ... ...

    Abstract The disease burden of de novo mutations (DNMs) has been evidenced only recently when the common application of next-generation sequencing technologies enabled their reliable and affordable detection through family-based clinical exome or genome sequencing. Implementation of exome sequencing into prenatal diagnostics revealed that up to 63% of pathogenic or likely pathogenic variants associated with fetal structural anomalies are apparently de novo, primarily for autosomal dominant disorders. Apparent DNMs have been considered to primarily occur as germline or zygotic events, with consequently negligible recurrence risks. However, there is now evidence that a considerable proportion of them are in fact inherited from a parent mosaic for the variant. Here, we review the burden of DNMs in prenatal diagnostics and the influence of parental mosaicism on the interpretation of apparent DNMs and discuss the challenges with detecting and quantifying parental mosaicism and its effect on recurrence risk. We also describe new bioinformatic and technological tools developed to assess mosaicism and discuss how they improve the accuracy of reproductive risk counseling when parental mosaicism is detected.
    Mesh-Begriff(e) Counseling ; Female ; Humans ; Mosaicism ; Mutation ; Parents ; Pregnancy ; Pregnancy Trimester, First ; Ultrasonography, Prenatal
    Sprache Englisch
    Erscheinungsdatum 2022-04-14
    Erscheinungsland England
    Dokumenttyp Journal Article ; Review
    ZDB-ID 82031-3
    ISSN 1097-0223 ; 0197-3851
    ISSN (online) 1097-0223
    ISSN 0197-3851
    DOI 10.1002/pd.6144
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: PhaseDancer: a novel targeted assembler of segmental duplications unravels the complexity of the human chromosome 2 fusion going from 48 to 46 chromosomes in hominin evolution.

    Poszewiecka, Barbara / Gogolewski, Krzysztof / Karolak, Justyna A / Stankiewicz, Paweł / Gambin, Anna

    Genome biology

    2023  Band 24, Heft 1, Seite(n) 205

    Abstract: Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler PhaseDancer that extends SD-rich regions of ... ...

    Abstract Resolving complex genomic regions rich in segmental duplications (SDs) is challenging due to the high error rate of long-read sequencing. Here, we describe a targeted approach with a novel genome assembler PhaseDancer that extends SD-rich regions of interest iteratively. We validate its robustness and efficiency using a golden-standard set of human BAC clones and in silico-generated SDs with predefined evolutionary scenarios. PhaseDancer enables extension of the incomplete complex SD-rich subtelomeric regions of Great Ape chromosomes orthologous to the human chromosome 2 (HSA2) fusion site, informing a model of HSA2 formation and unravelling the evolution of human and Great Ape genomes.
    Mesh-Begriff(e) Humans ; Animals ; Hominidae/genetics ; Segmental Duplications, Genomic ; Telomere ; Genomics ; Chromosomes, Human
    Sprache Englisch
    Erscheinungsdatum 2023-09-11
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-023-03022-8
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel: SNV/indel hypermutator phenotype in biallelic RAD51C variant - Fanconi anemia.

    Zemet, Roni / Du, Haowei / Gambin, Tomasz / Lupski, James R / Liu, Pengfei / Stankiewicz, Paweł

    Research square

    2023  

    Abstract: We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants ... ...

    Abstract We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving
    Sprache Englisch
    Erscheinungsdatum 2023-03-02
    Erscheinungsland United States
    Dokumenttyp Preprint
    DOI 10.21203/rs.3.rs-2628288/v1
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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