Rapid and automated sample preparation for nucleic acid extraction on a microfluidic CD (compact disk)

2006 ◽  
Author(s):  
Jitae Kim ◽  
Horacio Kido ◽  
Jim V. Zoval ◽  
Dominic Gagné ◽  
Régis Peytavi ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Acid Extraction ◽  
Compact Disk ◽  
Nucleic Acid Extraction ◽  
Automated Sample Preparation

scholarly journals Towards a “Sample-In, Answer-Out” Point-of-Care Platform for Nucleic Acid Extraction and Amplification: Using an HPV E6/E7 mRNA Model System

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Anja Gulliksen ◽  
Helen Keegan ◽  
Cara Martin ◽  
John O'Leary ◽  
Lars A. Solli ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Clinical Sample ◽  
Point Of Care ◽  
Fluorescent Detection ◽  
Clinical Samples ◽  
Microfluidic Channels ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Hpv E6

The paper presents the development of a “proof-of-principle” hands-free and self-contained diagnostic platform for detection of human papillomavirus (HPV) E6/E7 mRNA in clinical specimens. The automated platform performs chip-based sample preconcentration, nucleic acid extraction, amplification, and real-time fluorescent detection with minimal user interfacing. It consists of two modular prototypes, one for sample preparation and one for amplification and detection; however, a common interface is available to facilitate later integration into one single module. Nucleic acid extracts (n=28) from cervical cytology specimens extracted on the sample preparation chip were tested using the PreTect HPV-Proofer and achieved an overall detection rate for HPV across all dilutions of 50%–85.7%. A subset of 6 clinical samples extracted on the sample preparation chip module was chosen for complete validation on the NASBA chip module. For 4 of the samples, a 100% amplification for HPV 16 or 33 was obtained at the 1 : 10 dilution for microfluidic channels that filled correctly. The modules of a “sample-in, answer-out” diagnostic platform have been demonstrated from clinical sample input through sample preparation, amplification and final detection.

Nucleic acid extraction: Fundamentals of sample preparation methodologies, current advancements, and future endeavors

2020 ◽  
Vol 130 ◽  
pp. 115985
Author(s):  
Miranda N. Emaus ◽  
Marcelino Varona ◽  
Derek R. Eitzmann ◽  
Shu-An Hsieh ◽  
Victoria R. Zeger ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Acid Extraction ◽  
Nucleic Acid Extraction

scholarly journals An inexpensive semi-automated sample processing pipeline for cell-free RNA

2020 ◽  
Author(s):  
Mira N. Moufarrej ◽  
Stephen R. Quake
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Low Cost ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Sample Processing ◽  
Processing Pipeline ◽  
Liquid Handling ◽  
Sample Throughput ◽  
Automated Pipeline

AbstractDespite advances in automated liquid handling and microfluidics, preparing samples for RNA sequencing at scale generally requires expensive equipment, which is beyond the reach of many academic labs. Manual sample preparation remains a slow, expensive, and error-prone process. Here, we describe a low-cost, semi-automated pipeline to extract cell-free RNA (cfRNA) that increases sample throughput by 12-fold while reducing time spent and cost by nearly 11-fold and 3-fold respectively. This pipeline is generalizable for many nucleic acid extraction applications, thereby increasing the scale of studies, which can be performed in small research labs.

scholarly journals An Automated and Miniaturized Rotating-Disk Device for Rapid Nucleic Acid Extraction

Micromachines ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 204 ◽  
Author(s):  
Rui Tong ◽  
Lijuan Zhang ◽  
Chuandeng Hu ◽  
Xuee Chen ◽  
Qi Song ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Magnetic Beads ◽  
Rotating Disk ◽  
Molecular Diagnostic ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Time Saving ◽  
Central Controller ◽  
Acid Sample

The result of molecular diagnostic and detection greatly dependent on the quality and integrity of the isolated nucleic acid. In this work, we developed an automated miniaturized nucleic acid extraction device based on magnetic beads method, consisting of four components including a sample processing disc and its associated rotary power output mechanism, a pipetting module, a magnet module and an external central controller to enable a customizable and automated robust nucleic acid sample preparation. The extracted nucleic acid using 293T cells were verified using real-time polymerase chain reaction (PCR) and the data implies a comparable efficiency to a manual process, with the advantages of performing a flexible, time-saving (~10 min), and simple nucleic acid sample preparation.

Design and Application of a High-Throughput Sample Processing Module Based on Magnetic Beads

2018 ◽  
Vol 10 (3) ◽  
pp. 320-328 ◽  
Author(s):  
Yile Fang ◽  
Yanqi Wu ◽  
Pei Liao ◽  
Zhu Chen ◽  
Hui Chen ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Sample Preparation ◽  
Magnetic Separation ◽  
High Throughput ◽  
Magnetic Beads ◽  
Performance Evaluations ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Dc Power ◽  
Processing Module

One of key challenges in diagnosis of infectious diseases is collecting a large quantity of purified nucleic acids from pathogens immediately. To address this challenge, a high-throughput magnetic separation module and a heating and vibrating module were developed to optimize the operation of biological sample preparation (like nucleic acid extraction) on our home-built liquid handing system. Both of the two modules have 4 working locations for Biomolecular Screening (BS) standard labware, and three functions (magnetic separation, heating and vibrating) were elaborately integrated into the two modules. Each module has its own core control circuit and a unique interface port containing a 24 V DC power supply connector and a CAN bus communication connector. When equipping with the two modules, the home-built liquid handing system transformed into an integrated automatic sample preparation workstation. Performance evaluations were carried out on the two modules and finally a nucleic acid extraction of human's whole blood was carried out on the workstation. Results showed that the two modules could cooperate well with the liquid handing system, and the workstation exhibited its ability for high-throughput sample preparation.

scholarly journals Differing Effects of Standard and Harsh Nucleic Acid Extraction Procedures on Diagnostic Helminth Real-Time PCRs Applied to Human Stool Samples

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 188
Author(s):  
Tanja Hoffmann ◽  
Andreas Hahn ◽  
Jaco J. Verweij ◽  
Gérard Leboulle ◽  
Olfert Landt ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Real Time Pcr ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Pcr Assay ◽  
Bead Beating ◽  
Stool Samples ◽  
Pcr Assays ◽  
Human Stool

This study aimed to assess standard and harsher nucleic acid extraction schemes for diagnostic helminth real-time PCR approaches from stool samples. A standard procedure for nucleic acid extraction from stool and a procedure including bead-beating as well as proteinase K digestion were compared with group-, genus-, and species-specific real-time PCR assays targeting helminths and nonhelminth pathogens in human stool samples. From 25 different in-house and commercial helminth real-time PCR assays applied to 77 stool samples comprising 67 historic samples and 10 external quality assessment scheme samples positively tested for helminths, higher numbers of positive test results were observed after bead-beating-based nucleic acid extraction for 5/25 (20%) real-time PCR assays irrespective of specificity issues. Lower cycle threshold values were observed for one real-time PCR assay after the standard extraction scheme, and for four assays after the bead-beating-based scheme. Agreement between real-time PCR results after both nucleic acid extraction strategies according to Cohen’s kappa ranged from poor to almost perfect for the different assays. Varying agreement was observed in eight nonhelminth real-time PCR assays applied to 67 historic stool samples. The study indicates highly variable effects of harsh nucleic acid extraction approaches depending on the real-time PCR assay used.

scholarly journals Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 615
Author(s):  
Allen Wing-Ho Chu ◽  
Cyril Chik-Yan Yip ◽  
Wan-Mui Chan ◽  
Anthony Chin-Ki Ng ◽  
Dream Lok-Sze Chan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Rna Extraction ◽  
Nasopharyngeal Swab ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Nucleic Acid Extraction ◽  
Suitable Alternative ◽  
Pcr Inhibitors ◽  
Pcr Targeting

SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFYTM) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors.

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