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GDBr: genomic signature interpretation tool for DNA double-strand break repair mechanisms.
Nucleic Acids Res
January 2025
Department of Convergent Bioscience and Informatics, College of Bioscience and Biotechnology, Chungnam National University, 99, Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea.
Large genetic variants can be generated via homologous recombination (HR), such as polymerase theta-mediated end joining (TMEJ) or single-strand annealing (SSA). Given that these HR-based mechanisms leave specific genomic signatures, we developed GDBr, a genomic signature interpretation tool for DNA double-strand break repair mechanisms using high-quality genome assemblies. We applied GDBr to a draft human pangenome reference.
View Article and Find Full Text PDFPrognostic Value of Molecular Aberrations in Low- or Intermediate-Risk Neuroblastomas: A Systematic Review.
Cancers (Basel)
December 2024
Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands.
Background: The 5-year prognosis of non-high-risk neuroblastomas is generally good (>90%). However, a proportion of patients show progression and succumb to their disease. We aimed to identify molecular aberrations (not incorporated in the current risk stratification) associated with overall survival (OS) and/or event-free survival (EFS) in patients diagnosed with non-high-risk neuroblastoma.
View Article and Find Full Text PDFClinical, Morphologic, and Genomic Differences in Deep Penetrating Nevi and Deep Penetrating Nevus-like Melanomas.
Mod Pathol
January 2025
Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL. Electronic address:
Deep penetrating nevi (DPNs) are characterized by activating mutations in the MAP kinase and Wnt/beta-catenin pathways that result in large melanocytes with increased nuclear atypia, cytoplasmic pigmentation, and often mitotic activity. Together with a lack of maturation, this constellation of findings creates challenges for pathologists to distinguish deep penetrating nevus (DPN) from DPN-like melanoma. To assess the utility of next generation sequencing (NGS) in resolving this diagnostic dilemma, we performed NGS studies on 35 lesions including 24 DPNs and 11 DPN-like melanomas to characterize the specific genomic differences between the two groups and elucidate the genetic events involved in malignant transformation of DPNs.
View Article and Find Full Text PDFRnd3 Ameliorates Diabetic Cardiac Microvascular Injury via Facilitating Trim40-mediated Rock1 Ubiquitination.
Diabetes
January 2025
Department of Cardiology, Xijing Hospital, Air Force Medical University, Xi'an, Shaanxi, China.
Diabetic microvascular dysfunction is evidenced by disrupted endothelial cell junctions and increased microvascular permeability. However, effective strategies against these injuries remain scarce. In this study, the type 2 diabetes mouse model was established by high-fat diet combined with streptozotocin injection in Rnd3 endothelial- specific transgenic and knockout mice.
View Article and Find Full Text PDFEvolutionarily Developed Alternatively Spliced Exons Containing Translation Initiation Sites.
Cells
December 2024
Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai, Showa-ku, Nagoya 466-8550, Japan.
Alternative splicing is essential for the generation of various protein isoforms that are involved in cell differentiation and tissue development. In addition to internal coding exons, alternative splicing affects the exons with translation initiation codons; however, little is known about these exons. Here, we performed a systematic classification of human alternative exons using coding information.
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