The accurate identification of somatic mutations has become a pivotal component of tumor profiling and precision medicine. In molecular diagnostics laboratories, somatic mutation analyses on the Ion Torrent sequencing platform are typically performed on the Ion Reporter platform, which requires extensive manual review of the results and lacks optimized analysis workflows for custom targeted sequencing panels. Alternative solutions that involve custom bioinformatics pipelines involve the sequential execution of software tools with numerous parameters, leading to poor reproducibility and portability. We describe PipeIT, a stand-alone Singularity container of a somatic mutation calling and filtering pipeline for matched tumor-normal Ion Torrent sequencing data. PipeIT is able to identify pathogenic variants in BRAF, KRAS, PIK3CA, CTNNB1, TP53, and other cancer genes that the clinical-grade Oncomine workflow identified. In addition, PipeIT analysis of tumor-normal paired data generated on a custom targeted sequencing panel achieved 100% positive predictive value and 99% sensitivity compared with the 68% to 80% positive predictive value and 92% to 96% sensitivity using the default tumor-normal paired Ion Reporter workflow, substantially reducing the need for manual curation of the results. PipeIT can be rapidly deployed to and ensures reproducible results in any laboratory and can be executed with a single command with minimal input files from the users.
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http://dx.doi.org/10.1016/j.jmoldx.2019.05.001 | DOI Listing |
BMC Cancer
December 2024
Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.
Background: Colorectal cancer (CRC) is the second leading cause of cancer death worldwide. Early detection of precursor lesions or early-stage cancer could hamper cancer development or improve survival rates. Liquid biopsy, which detects tumor biomarkers, such as mutations, in blood, is a promising avenue for cancer screening.
View Article and Find Full Text PDFActa Microbiol Immunol Hung
December 2024
4Department of Biomedical Sciences, School of Health Sciences, International Hellenic University, 5400, Thessaloniki, Greece.
Klebsiella pneumoniae is a major pathogen associated with hospital-acquired infections, particularly those involving multidrug-resistant strains. Carbapenem resistance, often driven by carbapenemases such as KPC, VIM, OXA-48, and NDM, poses a significant challenge in clinical settings. This study reports on K.
View Article and Find Full Text PDFNat Commun
December 2024
Department of Physics, University of Texas at Arlington, Arlington, TX, USA.
The imaging of individual Ba ions in high pressure xenon gas is one possible way to attain background-free sensitivity to neutrinoless double beta decay and hence establish the Majorana nature of the neutrino. In this paper we demonstrate selective single Ba ion imaging inside a high-pressure xenon gas environment. Ba ions chelated with molecular chemosensors are resolved at the gas-solid interface using a diffraction-limited imaging system with scan area of 1 × 1 cm located inside 10 bar of xenon gas.
View Article and Find Full Text PDFEndocr Relat Cancer
November 2024
M Gild, Department of Endocrinology, Royal North Shore Hospital, St Leonards, Australia.
Liquid biopsies are a minimally invasive approach to obtain biomarkers including cell free DNA (cfDNA) from peripheral blood. Our study evaluated the utility of cfDNA in advanced thyroid cancers. Patients aged >18 years with metastatic medullary thyroid cancer (MTC), poorly differentiated thyroid cancer (PDTC), or anaplastic thyroid cancer (ATC) were enrolled in this prospective study between 2020 and 2024.
View Article and Find Full Text PDFActa Microbiol Immunol Hung
December 2024
3Hippokration General Hospital, Konstantinoupoleos 49, 54642, Thessaloniki, Greece.
This study investigated a strain of Klebsiella pneumoniae, identified as GRTHES, which exhibited extensive antibiotic resistance. The strain was resistant to all beta-lactams, including combinations with newer agents such as meropenem/vaborbactam and imipenem/relebactam, as well as to aminoglycosides, fluoroquinolones, fosfomycin, trimethoprim-sulfamethoxazole and colistin. It remained susceptible to tigecycline.
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