Cytogenetic changes in osteochondroma samples were studied by comparative genomic hybridization and by chromosome banding. No DNA copy number changes (15 patients) or chromosomal aberrations (9 patients) were observed in any of the patients.
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SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.
Brief Bioinform
November 2024
Department of Biology, University of Padova, Via U.Bassi 58/ B, 35131, Italy.
Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner.
View Article and Find Full Text PDFComprehensive evaluation of genomic and functional assays for homologous recombination deficiency with high-grade epithelial ovarian cancer: Platinum sensitivity and prognosis.
Int J Gynecol Cancer
January 2025
Fudan University Shanghai Cancer Center, Department of Gynecologic Oncology, Shanghai, China; Fudan University, Shanghai Medical College, Department of Oncology, Shanghai, China. Electronic address:
Objective: Homologous recombination deficiency assays, guiding treatment of poly (adenosine diphosphate ribose) polymerase inhibitors, are increasingly applied in clinics. This study aimed to evaluate the predictive performance of homologous recombination deficiency status at genomic and functional perspective on the efficacy of platinum-based chemotherapy in ovarian cancer.
Methods: Between 2016 and 2019, 134 patients with high-grade ovarian cancer were retrospectively analyzed.
Fetal hematological phenotypes of various hemoglobinopathies and demonstration of embryonic hemoglobins on capillary electrophoresis: a large cohort data from prenatal screening program.
Diagnosis (Berl)
January 2025
Faculty of Associated Medical Sciences, Centre for Research and Development of Medical Diagnostic Laboratories, Khon Kaen University, Khon Kaen, Thailand.
Objectives: This study reported a large cohort of fetal blood analysis of various hemoglobinopathies.
Methods: A total of 371 fetal blood specimens were recruited. Complete blood count and hemoglobin (Hb) analysis using capillary electrophoresis were performed.
Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes.
Nucleic Acids Res
January 2025
Laboratory of Genome Regeneration, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan.
Article Synopsis
- Sir2 is a histone deacetylase that helps maintain the stability of ribosomal RNA genes in budding yeast by preventing DNA breaks from leading to changes in rDNA copy number.
- It does this by suppressing transcription near issues that arise during DNA replication, which can otherwise provoke double-strand breaks (DSBs) and subsequent DNA repair processes.
- When Sir2 is absent, increased transcription can lead to DSBs, resulting in unstable rDNA copy numbers and the formation of extrachromosomal DNA, highlighting the importance of Sir2 in maintaining rDNA integrity.
Application of copy number variation sequencing combined with whole exome sequencing in prenatal left-right asymmetry disorders.
BMC Genomics
January 2025
Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, Hubei, 430030, China.
Background: Left-right (LR) asymmetry disorders present a complex etiology, with genetic factors emerging as a primary contributor. This study aims to explore the genetic underpinnings of chromosomal variants and individual genes in fetuses afflicted with prenatal LR asymmetry disorder.
Methods: Through a retrospective analysis conducted between 2020 and 2023 at Tongji Hospital, Huazhong University of Science and Technology, genetic outcomes of LR asymmetric disorder were scrutinized utilizing copy number variation sequencing (CNV-seq) and whole exome sequencing (WES) methodologies.
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