scholarly journals High-Sensitivity High-Throughput Detection of Nucleic Acid Targets on Metasurface Fluorescence Biosensors

Biosensors ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 33
Author(s):  
Masanobu Iwanaga
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
High Performance ◽  
Direct Detection ◽  
Fluorescence Emission ◽  
High Sensitivity ◽  
Nanorod Array ◽  
Silicon On Insulator ◽  
Detection Methods ◽  
High Throughput Detection

Worldwide infection disease due to SARS-CoV-2 is tremendously affecting our daily lives. High-throughput detection methods for nucleic acids are emergently desired. Here, we show high-sensitivity and high-throughput metasurface fluorescence biosensors that are applicable for nucleic acid targets. The all-dielectric metasurface biosensors comprise silicon-on-insulator nanorod array and have prominent electromagnetic resonances enhancing fluorescence emission. For proof-of-concept experiment on the metasurface biosensors, we have conducted fluorescence detection of single-strand oligoDNAs, which model the partial sequences of SARS-CoV-2 RNA indicated by national infection institutes, and succeeded in the high-throughput detection at low concentrations on the order of 100 amol/mL without any amplification technique. As a direct detection method, the metasurface fluorescence biosensors exhibit high performance.

scholarly journals Development of a Highly Sensitive Device for Counting the Number of Disease-Specific Exosomes in Human Sera

2018 ◽  
Vol 64 (10) ◽  
pp. 1463-1473 ◽  
Author(s):  
Yasuaki Kabe ◽  
Makoto Suematsu ◽  
Satoshi Sakamoto ◽  
Miwa Hirai ◽  
Ikko Koike ◽  
...  
Keyword(s):  
High Performance ◽  
Direct Detection ◽  
Cancer Cell Line ◽  
Detection Sensitivity ◽  
Detection Methods ◽  
Optical Disc ◽  
Liquid Biopsies ◽  
Her2 Positive ◽  
Cross Sectional ◽  
Human Sera

Abstract BACKGROUND Although circulating exosomes in blood play crucial roles in cancer development and progression, difficulties in quantifying exosomes hamper their application for reliable clinical testing. By combining the properties of nanobeads with optical disc technology, we have developed a novel device named the ExoCounter to determine the exact number of exosomes in the sera of patients with various types of cancer. METHOD In this system, individual exosomes were captured in the groove of an optical disc coated with antibodies against exosome surface antigens. The captured exosomes were labeled with antibody-conjugated magnetic nanobeads, and the number of the labeled exosomes was counted with an optical disc drive. RESULTS We showed that the ExoCounter could detect specific exosomes derived from cells or human serum without any enrichment procedures. The detection sensitivity and linearity with this system were higher than those with conventional detection methods such as ELISA or flow cytometry. In addition to the ubiquitous exosome markers CD9 and CD63, the cancer-related antigens CD147, carcinoembryonic antigen, and human epidermal growth factor receptor 2 (HER2) were also used to quantify cancer cell line-derived exosomes. Furthermore, analyses of a cross-sectional cohort of sera samples revealed that HER2-positive exosomes were significantly increased in patients with breast cancer or ovarian cancer compared with healthy individuals and those with noncancer diseases. CONCLUSIONS The ExoCounter system exhibits high performance in the direct detection of exosomes in cell culture and human sera. This method may enable reliable analysis of liquid biopsies.

scholarly journals Alignment-free filtering for cfNA fusion fragments

2019 ◽  
Vol 35 (14) ◽  
pp. i225-i232 ◽  
Author(s):  
Xiao Yang ◽  
Yasushi Saito ◽  
Arjun Rao ◽  
Hyunsung John Kim ◽  
Pranav Singh ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Cell Line ◽  
De Novo ◽  
High Sensitivity ◽  
Detection Methods ◽  
Rna Seq ◽  
Sequencing Data ◽  
Alignment Free ◽  
Fusion Detection ◽  
High Depth

Abstract Motivation Cell-free nucleic acid (cfNA) sequencing data require improvements to existing fusion detection methods along multiple axes: high depth of sequencing, low allele fractions, short fragment lengths and specialized barcodes, such as unique molecular identifiers. Results AF4 was developed to address these challenges. It uses a novel alignment-free kmer-based method to detect candidate fusion fragments with high sensitivity and orders of magnitude faster than existing tools. Candidate fragments are then filtered using a max-cover criterion that significantly reduces spurious matches while retaining authentic fusion fragments. This efficient first stage reduces the data sufficiently that commonly used criteria can process the remaining information, or sophisticated filtering policies that may not scale to the raw reads can be used. AF4 provides both targeted and de novo fusion detection modes. We demonstrate both modes in benchmark simulated and real RNA-seq data as well as clinical and cell-line cfNA data. Availability and implementation AF4 is open sourced, licensed under Apache License 2.0, and is available at: https://github.com/grailbio/bio/tree/master/fusion.

scholarly journals High-throughput sequencing for noninvasive disease detection in hematologic malignancies

Blood ◽  
2017 ◽  
Vol 130 (4) ◽  
pp. 440-452 ◽  
Author(s):  
Florian Scherer ◽  
David M. Kurtz ◽  
Maximilian Diehn ◽  
Ash A. Alizadeh
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Residual Disease ◽  
High Sensitivity ◽  
Hematologic Malignancies ◽  
Circulating Tumor Dna ◽  
Detection Methods ◽  
Disease Detection ◽  
Molecular Testing ◽  
Molecular Features

Abstract Noninvasive monitoring of minimal residual disease (MRD) has led to significant advances in personalized management of patients with hematologic malignancies. Improved therapeutic options and prolonged survival have further increased the need for sensitive tumor assessment that can inform treatment decisions and patient outcomes. At diagnosis or relapse of most hematologic neoplasms, malignant cells are often easily accessible in the blood as circulating tumor cells (CTCs), making them ideal targets to noninvasively profile the molecular features of each patient. In other cancer types, CTCs are generally rare and noninvasive molecular detection relies on circulating tumor DNA (ctDNA) shed from tumor deposits into circulation. The ability to precisely detect and quantify CTCs and ctDNA could minimize invasive procedures and improve prediction of clinical outcomes. Technical advances in MRD detection methods in recent years have led to reduced costs and increased sensitivity, specificity, and applicability. Among currently available tests, high-throughput sequencing (HTS)–based approaches are increasingly attractive for noninvasive molecular testing. HTS-based methods can simultaneously identify multiple genetic markers with high sensitivity and specificity without individual optimization. In this review, we present an overview of techniques used for noninvasive molecular disease detection in selected myeloid and lymphoid neoplasms, with a focus on the current and future role of HTS-based assays.

Performance of a silicon-on-insulator direct electron detector in a low-voltage transmission electron microscope

Microscopy ◽  
2020 ◽  
Author(s):  
Takafumi Ishida ◽  
Akira Shinozaki ◽  
Makoto Kuwahara ◽  
Toshinobu Miyoshi ◽  
Koh Saitoh ◽  
...  
Keyword(s):  
Electron Microscope ◽  
Transmission Electron Microscope ◽  
High Efficiency ◽  
Low Voltage ◽  
Direct Detection ◽  
High Sensitivity ◽  
Silicon On Insulator ◽  
Modulation Transfer ◽  
Electron Detector ◽  
Transmission Electron

Abstract The performance of a direct electron detector using silicon-on-insulator (SOI) technology in a low-voltage transmission electron microscope (LVTEM) is evaluated. The modulation transfer function and detective quantum efficiency of the detector are measured under backside illumination. The SOI-type detector is demonstrated to have high sensitivity and high efficiency for the direct detection of low-energy electrons. The detector is thus considered suitable for low-dose imaging in an LVTEM.

scholarly journals CRISPR-Based COVID-19 Testing: Toward Next-Generation Point-of-Care Diagnostics

2021 ◽  
Vol 11 ◽  
Author(s):  
Uyanga Ganbaatar ◽  
Changchun Liu
Keyword(s):  
Nucleic Acid ◽  
Point Of Care ◽  
High Sensitivity ◽  
Detection Methods ◽  
Molecular Testing ◽  
Practical Applications ◽  
Food Industries ◽  
Resource Limited ◽  
Point Of Care Diagnostics ◽  
Agriculture And Food

As the COVID-19 pandemic continues, people are becoming infected at an alarming rate, individuals are unknowingly spreading disease, and more lives are lost every day. There is an immediate need for a simple, rapid, early and sensitive point-of-care testing for COVID-19 disease. However, current testing approaches do not meet such need. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based detection methods have received substantial attention for nucleic acid-based molecular testing due to their simplicity, high sensitivity and specificity. This review explores the various CRISPR-based COVID-19 detection methods and related diagnostic devices. As with any emerging technology, CRISPR/Cas-based nucleic acid testing methods have several challenges that must be overcome for practical applications in clinics and hospitals. More importantly, these detection methods are not limited to COVID-19 but can be applied to detect any type of pathogen, virus, and fungi that may threaten humans, agriculture, and food industries in resource-limited settings. CRISPR/Cas-based detection methods have the potential to become simpler, more reliable, more affordable, and faster in the near future, which is highly important for achieving point-of-care diagnostics.

scholarly journals A simple, safe and sensitive method for SARS-CoV-2 inactivation and RNA extraction for RT-qPCR

2020 ◽  
Author(s):  
Lelde Kalnina ◽  
Àngels Mateu-Regué ◽  
Stephanie Oerum ◽  
Annemette Hald ◽  
Jan Gerstoft ◽  
...  
Keyword(s):  
High Throughput ◽  
Diagnostic Tests ◽  
Rna Extraction ◽  
High Sensitivity ◽  
Viral Rna ◽  
Extraction Protocol ◽  
Rna Purification ◽  
High Throughput Detection ◽  
Very High ◽  
Sensitive Method

ABSTRACTThe SARS-CoV-2 pandemic has created an urgent need for large amounts of diagnostic tests to detect viral RNA, which commercial suppliers are increasingly unable to deliver. In addition to the lack of availability, the current methods do not always fully inactivate the virus. Together, this calls for the development of safer methods for extraction and detection of viral RNA from patient samples that utilise readily available reagents and equipment present in most standard laboratories. We present a rapid and straightforward RNA extraction protocol for inactivating the SARS-CoV-2 virus that uses standard lab reagents. This protocol expands analysis capacity as the inactivated samples can be used in RT-qPCR detection tests at laboratories not otherwise classified for viral work. The method circumvents the need for commercial RNA purification kits, takes about 30 minutes from swab to PCR-ready viral RNA, and enables downstream detection of SARS-CoV-2 by RT-qPCR with very high sensitivity (~4 viral RNA copies per RT-qPCR). In summary, we present a rapid, safe and sensitive method for high-throughput detection of SARS-CoV-2, that can be conducted in any laboratory equipped with a qPCR machine.

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