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Ambient storage of genomic time capsules.
Trends Genet
December 2024
Department of Medicine (Cardiovascular Medicine), Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address:
While the cost of genome sequencing has decreased, -80°C DNA preservation and raw sequence data archiving remain expensive. Transitioning to room-temperature DNA preservation could reduce costs, lessen researchers' reliance on the electrical grid, and encourage a future proofing strategy of periodical updating with higher quality sequencing instead of long-term storage of raw signal data. A new technology recently described by Prince et al.
View Article and Find Full Text PDFProof of Concept Study: Comparison of Semi-Automated RNA Isolation Methods from Archived Formalin-Fixed, Paraffin-Embedded Tissues with Clinical Routine RNA Isolation Methods.
Methods Protoc
December 2024
Department of Pathology, Herlev University Hospital, 2730 Herlev, Denmark.
High-quality RNA is crucial in clinical diagnostics and precision medicine. Formalin-fixed and paraffin-embedded (FFPE) tissues pose a challenge due to nucleic acid fragmentation and crosslinking. In this pilot study, various commercially available techniques for extracting RNA from small FFPE samples were compared.
View Article and Find Full Text PDFOptimizing RNA extraction methods for high-throughput transcriptome sequencing of formalin-fixed paraffin-embedded cardiac tissue specimens.
PLoS One
December 2024
Program for Hypoplastic Left Heart Syndrome, Mayo Clinic Rochester, Rochester, Minnesota, United States of America.
Archived FFPE cardiac tissue specimens are valuable for molecular studies aimed at identifying biomarkers linked to mortality in cardiovascular disease. Establishing a reliable and reproducible RNA extraction method is critical for generating high-quality transcriptome sequences for molecular assays. Here, the efficiency of four RNA extraction methods: Qiagen AllPrep DNA/RNA method (Method QP); Qiagen AllPrep DNA/RNA method with protocol modification on the ethanol wash step after deparaffinization (Method QE); CELLDATA RNA extraction (Method BP) and CELLDATA RNA extraction with protocol modifications on the lysis step (Method BL) was compared on 23 matching FFPE cardiac tissue specimens (n = 92).
View Article and Find Full Text PDFAssessment of MGMT promoter methylation status in glioblastoma using deep learning features from multi-sequence MRI of intratumoral and peritumoral regions.
Cancer Imaging
December 2024
Department of Radiology, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, 7 Weiwu Road, Zhengzhou, 450000, PR China.
Objective: This study aims to evaluate the effectiveness of deep learning features derived from multi-sequence magnetic resonance imaging (MRI) in determining the O-methylguanine-DNA methyltransferase (MGMT) promoter methylation status among glioblastoma patients.
Methods: Clinical, pathological, and MRI data of 356 glioblastoma patients (251 methylated, 105 unmethylated) were retrospectively examined from the public dataset The Cancer Imaging Archive. Each patient underwent preoperative multi-sequence brain MRI scans, which included T1-weighted imaging (T1WI) and contrast-enhanced T1-weighted imaging (CE-T1WI).
Molecular characterization of archival adrenal tumor tissue from patients with ACTH-independent Cushing syndrome.
J Steroid Biochem Mol Biol
December 2024
Department of Pathology, University of Michigan, Ann Arbor, MI, United States; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, United States.
Cushing syndrome represents a multitude of signs and symptoms associated with long-term and excessive exposure to glucocorticoids. Solitary cortisol-producing adenomas (CPAs) account for most cases of ACTH-independent Cushing syndrome (CS). Technological advances in next-generation sequencing have significantly increased our understanding about the genetic landscape of CPAs.
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