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Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling.
Genome Res
January 2025
University Medical Center Utrecht, Utrecht University, Oncode Institute, Cyclomics
Shallow genome-wide cell-free DNA (cfDNA) sequencing holds great promise for non-invasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single nucleotide variations (SNVs) are, however, much harder to identify with low sequencing depth due to sequencing errors. Here we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA and consensus calling based on genome-wide long-read nanopore sequencing to enable simultaneous multimodal tumor fraction estimation through SNVs, CNAs, and fragmentomics.
View Article and Find Full Text PDFAccurate Molecular Sensing based on a Modular and Customizable CRISPR/Cas-Assisted Nanopore Operational Nexus (CANON).
Angew Chem Int Ed Engl
January 2025
Changchun Institute of Applied Chemistry Chinese Academy of Sciences: Chang Chun Institute of Applied Chemistry Chinese Academy of Sciences, State Key Lab of Electroanalytical Chemistry, 5625 Renmin Street, 130022, Changchun, CHINA.
Solid-state nanopore is a promising single molecular detection technique, but is largely limited by relatively low resolution to small-size targets and laborious design of signaling probes. Here we establish a universal, CRISPR/Cas-Assisted Nanopore Operational Nexus (CANON), which can accurately transduce different targeting sources/species into different DNA structural probes via a "Signal-ON" mode. Target recognition activates the cleavage activity of a Cas12a/crRNA system and then completely digest the blocker of an initiator.
View Article and Find Full Text PDFNanopore adaptive sampling accurately detects nucleotide variants and improves the characterization of large-scale rearrangement for the diagnosis of cancer predisposition.
Clin Transl Med
January 2025
Unit of Molecular Biology, Georges-François Leclerc Cancer center, UNICANCER, Dijon, France.
Background: Molecular diagnosis has become highly significant for patient management in oncology.
Methods: Here, 30 well-characterized clinical germline samples were studied with adaptive sampling to enrich the full sequence of 152 cancer predisposition genes. Sequencing was performed on Oxford Nanopore (ONT) R10.
A Y-Shaped Peptide-Based Antifouling Electrochemical Aptasensor for Sensitive Aflatoxin B1 Detection in Food.
J Agric Food Chem
January 2025
Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China.
Conquering surface fouling of sensors caused by nonspecific adsorption and accumulation of foulants in a food matrix is of significance in accurate food safety analysis. Herein, an antifouling electrochemical aptasensor based on a Y-shaped peptide and nanoporous gold (NPG) for aflatoxin B1 detection in milk, tofu, and rice flour was proposed. The self-designed Y-shaped peptide involves an anchoring segment (-C), a support structure (-PPPP-), and an antifouling domain with two branches (-EK(KSRE)DER-) inspired by two bioactive peptides.
View Article and Find Full Text PDFA novel and sensitive trefoil-structured biosensor based on nanoporous gold for simultaneous determination of microRNA-21 and microRNA-16.
Biosens Bioelectron
December 2024
State Key Laboratory of Quality Research in Chinese Medicines & School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau 999078, China. Electronic address:
Although electrochemical biosensors have been developed to detect multiple microRNAs (miRNAs) simultaneously through loading different capture probes, high surface-induced perturbation and competition among probes have reduced the detection sensitivity. To address these challenges, a trefoil DNA capture probe (TDCP) was designed for microRNA-21 (miR-21) and microRNA-16 (miR-16) detection simultaneously. The TDCP exhibits a stable structure, low spatial resistance, and integral rigidity, which decreases high surface-induced perturbations and competition to improve the accessibility of the target miRNA.
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