Evaluation of Cobas Ampliprep Automated Nucleic Acid Extraction for Genotyping Human Papillomavirus (HPV) by the Roche linear array HPV Test

2008 ◽  
Vol 26 (3) ◽  
pp. 180-181 ◽  
Author(s):  
Ana Fernández-Olmos ◽  
Jesús Chacón ◽  
María Luisa Mateos ◽  
Fernando Baquero
Keyword(s):  
Human Papillomavirus ◽  
Nucleic Acid ◽  
Linear Array ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Hpv Test ◽  
Roche Linear Array

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.

Synergistic use of electroosmotic flow and magnetic forces for nucleic acid extraction

The Analyst ◽  
2020 ◽  
Vol 145 (6) ◽  
pp. 2412-2419 ◽  
Author(s):  
Rachel N. Deraney ◽  
Lindsay Schneider ◽  
Anubhav Tripathi
Keyword(s):  
Nucleic Acid ◽  
Electric Field ◽  
Microfluidic Chip ◽  
Applied Electric Field ◽  
Electroosmotic Flow ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Magnetic Forces ◽  
Extraction And Purification

NA extraction and purification utilitzing a microfluidic chip with applied electric field to induce electroosmotic flow opposite the magnetic NA-bound bead mix.

scholarly journals Evaluation of simple nucleic acid extraction methods for the detection of SARS-CoV-2 in nasopharyngeal and saliva specimens during global shortage of extraction kits

2020 ◽  
Vol 129 ◽  
pp. 104519 ◽  
Author(s):  
Allen Wing-Ho Chu ◽  
Wan-Mui Chan ◽  
Jonathan Daniel Ip ◽  
Cyril Chik-Yan Yip ◽  
Jasper Fuk-Woo Chan ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Extraction Methods ◽  
Acid Extraction ◽  
Nucleic Acid Extraction

Comparison of 2 highly automated nucleic acid extraction systems for quantitation of human cytomegalovirus in whole blood

2011 ◽  
Vol 69 (2) ◽  
pp. 161-166 ◽  
Author(s):  
Catherine Mengelle ◽  
Jean-Michel Mansuy ◽  
Isabelle Da Silva ◽  
Chistian Davrinche ◽  
Jacques Izopet
Keyword(s):  
Nucleic Acid ◽  
Human Cytomegalovirus ◽  
Whole Blood ◽  
Acid Extraction ◽  
Nucleic Acid Extraction

scholarly journals NEATTILL: A simplified procedure for nucleic acid extraction from arrayed tissue for TILLING and other high-throughput reverse genetic applications

Plant Methods ◽  
2010 ◽  
Vol 6 (1) ◽  
pp. 3 ◽  
Author(s):  
Yellamaraju Sreelakshmi ◽  
Soni Gupta ◽  
Reddaiah Bodanapu ◽  
Vineeta Chauhan ◽  
Mickey Hanjabam ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
High Throughput ◽  
Acid Extraction ◽  
Reverse Genetic ◽  
Nucleic Acid Extraction ◽  
Simplified Procedure

scholarly journals Limited-Resource Preparable Chitosan Magnetic Particles for Extracting Amplification-Ready Zeptomole-Range Nucleic Acid from Complex Biofluid

2021 ◽  
Author(s):  
Sayantan Tripathy ◽  
Arunansu Talukdar ◽  
Goutam Pramanik ◽  
P. V. Rajesh ◽  
Souradyuti Ghosh
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Real Time Pcr ◽  
Magnetic Particles ◽  
Limited Resource ◽  
Nucleic Acid Amplification ◽  
Acid Extraction ◽  
Analytical Sensitivity ◽  
Nucleic Acid Extraction ◽  
Spin Column

<b>Layman Summary: </b>Nucleic acid extraction is a key prerequisite for any nucleic acid amplification test (NAAT) or isothermal NAAT (iNAAT) based molecular diagnosis assays.<b> </b>Existing methods utilizes spin column system for nucleic acid extraction which are unsuitable for limited resource settings. Our work explores two methods for chitosan coated magnetic particle preparation that can be executed within 6 h from commonly available chemicals with nothing but a magnetic stirrer and water bath and doable by a minimally trained person. We will also investigated the compatibility of the extracted nucleic acid with downstream NAATs such as real time LAMP, colorimetric LAMP, and real time PCR. In the process, we established the analytical sensitivity of the overall method.<div><br><div><b>Characterization methods</b>: SEM, XRD, EDX, FT-IR</div><div><br></div><div><b>Bioanalytical methods:</b> Real time LAMP, Colorimetric LAMP, Real time PCR</div></div>

Functional Magnetite Nanoparticle: A Review on the Particles Lysis and Nucleic Acid Separation

2021 ◽  
Vol 33 ◽  
pp. 13-27
Author(s):  
Puspita Nurlilasari ◽  
Camellia Panatarani ◽  
Mia Miranti ◽  
Savira Ekawardhani ◽  
Ferry Faizal ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Magnetite Nanoparticles ◽  
Magnetic Beads ◽  
Functional Materials ◽  
Cell Lysis ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Coating Materials ◽  
Magnetite Nanoparticle ◽  
Separation Cell

The functional magnetite nanoparticles are one of the most important functional materials for nucleic acid separation. Cell lysis and magnetic separation are two essential steps involve in optimizing nucleic acid extraction using the magnetic beads method. Many coating materials, coupling agents, chemical cell lysis, and several methods have been proposed to produce the specific desired properties for nucleic acid extraction. The important properties, such as biocompatibility, stability, linking ability, hydrophobicity, and biodegradable, were considered. The appropriate coating material of magnetite core and coupling agent are necessary to give biomolecules a possibility to link with each other through chemical conjugation. In this review, progress in functional magnetite nanoparticles to optimize the high binding performance in nucleic acid extraction is discussed.

Use of a Linear Array for the Detection of Human Papillomavirus Genotypes in Head and Neck Cancer

2010 ◽  
Vol 134 (12) ◽  
pp. 1813-1817
Author(s):  
Candice C. Black ◽  
Heather A. Bentley ◽  
Thomas H. Davis ◽  
Gregory J. Tsongalis
Keyword(s):  
Human Papillomavirus ◽  
Head And Neck ◽  
Linear Array ◽  
Hpv Genotyping ◽  
Formalin Fixed Paraffin ◽  
Hpv Status ◽  
Test Kit ◽  
Formalin Fixed Paraffin Embedded ◽  
Roche Linear Array ◽  
Formalin Fixed

Abstract Context—Tumors of the head and neck commonly arise from the squamous and respiratory mucosa that lines the nasal and oral cavity, sinuses, pharynx, and larynx. The rate of oropharyngeal cancers diagnosed among Americans younger than 50 years is increasing. Infection of the oropharynx and tonsils by the human papillomavirus (HPV) has been linked to preneoplasia and cancer. Objectives—To evaluate the Roche Linear Array HPV Genotyping test kit to identify, and then specifically genotype, HPV in formalin-fixed, paraffin-embedded tissues. Design—We evaluated the performance of this assay for accuracy, for intra-assay and interassay precision, and for its limit of detection, using materials with known HPV status. Sixteen tumor tissues with the following origins were evaluated: 1 ocular, 1 hypopharynx, 8 tonsil, 1 retromolar trigone, 3 tongue, 1 anal, and 1 lymph node. DNA from formalin-fixed, paraffin-embedded tumor sections was isolated and amplified in duplicate, with positive and negative controls, using primers specific to the polymorphic L1 region of the HPV genome. Thirty-seven genotypes were tested using the linear array. The amplified product (450 base pairs) was visualized by gel electrophoresis and, if positive, reflexed to HPV genotyping. Results—Nine of the 16 tumors analyzed were HPV positive. The detected genotypes included HPV 6, 16, and 69. Conclusions—The Roche Linear Array HPV Genotyping test is an easy-to-use method for determining HPV genotype in the routine analysis of formalin-fixed, paraffin-embedded tumors. This assay is robust and can be performed routinely in a clinical laboratory setting.

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