1
|
Kucharski M, Tripathi J, Nayak S, Zhu L, Wirjanata G, van der Pluijm RW, Dhorda M, Dondorp A, Bozdech Z. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 2020; 19:363. [PMID: 33036628 PMCID: PMC7547485 DOI: 10.1186/s12936-020-03436-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Sequencing technology advancements opened new opportunities to use transcriptomics for studying malaria pathology and epidemiology. Even though in recent years the study of whole parasite transcriptome proved to be essential in understanding parasite biology there is no compiled up-to-date reference protocol for the efficient generation of transcriptome data from growing number of samples. Here, a comprehensive methodology on how to preserve, extract, amplify, and sequence full-length mRNA transcripts from Plasmodium-infected blood samples is presented that can be fully streamlined for high-throughput studies. Results The utility of various commercially available RNA-preserving reagents in a range of storage conditions was evaluated. Similarly, several RNA extraction protocols were compared and the one most suitable method for the extraction of high-quality total RNA from low-parasitaemia and low-volume blood samples was established. Furthermore, the criteria needed to evaluate the quality and integrity of Plasmodium RNA in the presence of human RNA was updated. Optimization of SMART-seq2 amplification method to better suit AT-rich Plasmodium falciparum RNA samples allowed us to generate high-quality transcriptomes from as little as 10 ng of total RNA and a lower parasitaemia limit of 0.05%. Finally, a modified method for depletion of unwanted human haemoglobin transcripts using in vitro CRISPR-Cas9 treatment was designed, thus improving parasite transcriptome coverage in low parasitaemia samples. To prove the functionality of the pipeline for both laboratory and field strains, the highest 2-hour resolution RNA-seq transcriptome for P. falciparum 3D7 intraerythrocytic life cycle available to date was generated, and the entire protocol was applied to create the largest transcriptome data from Southeast Asian field isolates. Conclusions Overall, the presented methodology is an inclusive pipeline for generation of good quality transcriptomic data from a diverse range of Plasmodium-infected blood samples with varying parasitaemia and RNA inputs. The flexibility of this pipeline to be adapted to robotic handling will facilitate both small and large-scale future transcriptomic studies in the field of malaria.
Collapse
Affiliation(s)
- Michal Kucharski
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| | - Jaishree Tripathi
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| | - Sourav Nayak
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Grennady Wirjanata
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Rob W van der Pluijm
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mehul Dhorda
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,WorldWide Antimalarial Resistance Network-Asia Regional Centre, Bangkok, Thailand
| | - Arjen Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
| |
Collapse
|
2
|
Klein S, Müller TG, Khalid D, Sonntag-Buck V, Heuser AM, Glass B, Meurer M, Morales I, Schillak A, Freistaedter A, Ambiel I, Winter SL, Zimmermann L, Naumoska T, Bubeck F, Kirrmaier D, Ullrich S, Barreto Miranda I, Anders S, Grimm D, Schnitzler P, Knop M, Kräusslich HG, Dao Thi VL, Börner K, Chlanda P. SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP. Viruses 2020; 12:E863. [PMID: 32784757 PMCID: PMC7472728 DOI: 10.3390/v12080863] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 01/01/2023] Open
Abstract
Rapid large-scale testing is essential for controlling the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The standard diagnostic pipeline for testing SARS-CoV-2 presence in patients with an ongoing infection is predominantly based on pharyngeal swabs, from which the viral RNA is extracted using commercial kits, followed by reverse transcription and quantitative PCR detection. As a result of the large demand for testing, commercial RNA extraction kits may be limited and, alternatively, non-commercial protocols are needed. Here, we provide a magnetic bead RNA extraction protocol that is predominantly based on in-house made reagents and is performed in 96-well plates supporting large-scale testing. Magnetic bead RNA extraction was benchmarked against the commercial QIAcube extraction platform. Comparable viral RNA detection sensitivity and specificity were obtained by fluorescent and colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) using a primer set targeting the N gene, as well as RT-qPCR using a primer set targeting the E gene, showing that the RNA extraction protocol presented here can be combined with a variety of detection methods at high throughput. Importantly, the presented diagnostic workflow can be quickly set up in a laboratory without access to an automated pipetting robot.
Collapse
Affiliation(s)
- Steffen Klein
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
- Schaller Research Groups, Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Thorsten G. Müller
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Dina Khalid
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Vera Sonntag-Buck
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Anke-Mareil Heuser
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Bärbel Glass
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Matthias Meurer
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; (M.M.); (D.K.); (S.A.); (M.K.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ivonne Morales
- Center of Infectious Diseases, Clinical Tropical Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany;
| | - Angelika Schillak
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Andrew Freistaedter
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Ina Ambiel
- Center of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany;
| | - Sophie L. Winter
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
- Schaller Research Groups, Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Liv Zimmermann
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Tamara Naumoska
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Felix Bubeck
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Daniel Kirrmaier
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; (M.M.); (D.K.); (S.A.); (M.K.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stephanie Ullrich
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Isabel Barreto Miranda
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; (M.M.); (D.K.); (S.A.); (M.K.)
| | - Dirk Grimm
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
- German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Paul Schnitzler
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
| | - Michael Knop
- Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; (M.M.); (D.K.); (S.A.); (M.K.)
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
- German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Viet Loan Dao Thi
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
- Schaller Research Groups, Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Kathleen Börner
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
- German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Petr Chlanda
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; (S.K.); (T.G.M.); (D.K.); (V.S.-B.); (A.-M.H.); (B.G.); (A.S.); (A.F.); (S.L.W.); (L.Z.); (T.N.); (F.B.); (S.U.); (I.B.M.); (D.G.); (P.S.); (H.-G.K.); (V.L.D.T.)
- Schaller Research Groups, Center of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| |
Collapse
|
3
|
Thakore N, Norville R, Franke M, Calderon R, Lecca L, Villanueva M, Murray MB, Cooney CG, Chandler DP, Holmberg RC. Automated TruTip nucleic acid extraction and purification from raw sputum. PLoS One 2018; 13:e0199869. [PMID: 29975759 PMCID: PMC6033430 DOI: 10.1371/journal.pone.0199869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022] Open
Abstract
Automated nucleic acid extraction from primary (raw) sputum continues to be a significant technical challenge for molecular diagnostics. In this work, we developed a prototype open-architecture, automated nucleic acid workstation that includes a mechanical homogenization and lysis function integrated with heating and TruTip purification; optimized an extraction protocol for raw sputum; and evaluated system performance on primary clinical specimens. Eight samples could be processed within 70 min. The system efficiently homogenized primary sputa and doubled nucleic acid recovery relative to an automated protocol that did not incorporate sample homogenization. Nucleic acid recovery was at least five times higher from raw sputum as compared to that of matched sediments regardless of smear or culture grade, and the automated workstation reproducibly recovered PCR-detectable DNA to at least 80 CFU mL-1 raw sputum. M. tuberculosis DNA was recovered and detected from 122/123 (99.2%) and 124/124 (100%) primary sputum and sediment extracts, respectively. There was no detectable cross-contamination across 53 automated system runs and amplification or fluorescent inhibitors (if present) were not detectable. The open fluidic architecture of the prototype automated workstation yields purified sputum DNA that can be used for any molecular diagnostic test. The ability to transfer TruTip protocols between personalized, on-demand pipetting tools and the fully automated workstation also affords public health agencies an opportunity to standardize sputum nucleic acid sample preparation procedures, reagents, and quality control across multiple levels of the health care system.
Collapse
Affiliation(s)
- Nitu Thakore
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Ryan Norville
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Molly Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Perú, Carabayllo, Lima, Peru
| | | | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | | |
Collapse
|
4
|
A bench-top automated workstation for nucleic acid isolation from clinical sample types. J Microbiol Methods 2018; 148:174-180. [PMID: 29678500 DOI: 10.1016/j.mimet.2018.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 11/23/2022]
Abstract
Systems that automate extraction of nucleic acid from cells or viruses in complex clinical matrices have tremendous value even in the absence of an integrated downstream detector. We describe our bench-top automated workstation that integrates our previously-reported extraction method - TruTip - with our newly-developed mechanical lysis method. This is the first report of this method for homogenizing viscous and heterogeneous samples and lysing difficult-to-disrupt cells using "MagVor": a rotating magnet that rotates a miniature stir disk amidst glass beads confined inside of a disposable tube. Using this system, we demonstrate automated nucleic acid extraction from methicillin-resistant Staphylococcus aureus (MRSA) in nasopharyngeal aspirate (NPA), influenza A in nasopharyngeal swabs (NPS), human genomic DNA from whole blood, and Mycobacterium tuberculosis in NPA. The automated workstation yields nucleic acid with comparable extraction efficiency to manual protocols, which include commercially-available Qiagen spin column kits, across each of these sample types. This work expands the scope of applications beyond previous reports of TruTip to include difficult-to-disrupt cell types and automates the process, including a method for removal of organics, inside a compact bench-top workstation.
Collapse
|
5
|
Centrifugation-free extraction of circulating nucleic acids using immiscible liquid under vacuum pressure. Sci Rep 2018; 8:5467. [PMID: 29615736 PMCID: PMC5883035 DOI: 10.1038/s41598-018-23766-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/20/2018] [Indexed: 12/11/2022] Open
Abstract
Extraction of cell-free DNA (cfDNA), which exists at an extremely low concentration in plasma, is a critical process for either targeted-sensing or massive sequencing of DNAs. However, such small amount of DNA cannot be fully obtained without high-speed centrifugation (<20,000 g). Here, we developed a centrifugation-free cfDNA extraction method and system that utilizes an immiscible solvent under single low vacuum pressure throughout the entire process. It has been named Pressure and Immiscibility-Based EXtraction (PIBEX). The amounts of extracted cfDNA by PIBEX were compared with those extracted by the conventional gold standards such as QIAGEN using quantitative PCR (qPCR). The PIBEX system showed equal performance regarding extraction amount and efficiency compared to the existing method. Because the PIBEX eliminates the troublous and repetitive centrifugation processes in DNA extraction, it can be further utilized in microfluidic-sample preparation systems for circulating nucleic acids, which would lead to an integrated sample-to-answer system in liquid biopsies.
Collapse
|
6
|
Bonacci S, Buccato S, Maione D, Petracca R. Successful completion of a semi-automated enzyme-free cloning method. ACTA ACUST UNITED AC 2016; 17:57-66. [PMID: 27507291 DOI: 10.1007/s10969-016-9207-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 08/02/2016] [Indexed: 12/13/2022]
Abstract
Nowadays, in scientific fields such as Structural Biology or Vaccinology, there is an increasing need of fast, effective and reproducible gene cloning and expression processes. Consequently, the implementation of robotic platforms enabling the automation of protocols is becoming a pressing demand. The main goal of our study was to set up a robotic platform devoted to the high-throughput automation of the polymerase incomplete primer extension cloning method, and to evaluate its efficiency compared to that achieved manually, by selecting a set of bacterial genes that were processed either in the automated platform (330) or manually (94). Here we show that we successfully set up a platform able to complete, with high efficiency, a wide range of molecular biology and biochemical steps. 329 gene targets (99 %) were effectively amplified using the automated procedure and 286 (87 %) of these PCR products were successfully cloned in expression vectors, with cloning success rates being higher for the automated protocols respect to the manual procedure (93.6 and 74.5 %, respectively).
Collapse
|
7
|
Holmberg RC, Gindlesperger A, Stokes T, Lopez D, Hyman L, Freed M, Belgrader P, Harvey J, Li Z. Akonni TruTip(®) and Qiagen(®) methods for extraction of fetal circulating DNA--evaluation by real-time and digital PCR. PLoS One 2013; 8:e73068. [PMID: 23936545 PMCID: PMC3735556 DOI: 10.1371/journal.pone.0073068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/30/2013] [Indexed: 12/18/2022] Open
Abstract
Due to the low percentage of fetal DNA present in maternal plasma (< 10%) during early gestation, efficient extraction processes are required for successful downstream detection applications in non-invasive prenatal diagnostic testing. In this study, two extraction methods using similar chemistries but different workflows were compared for isolation efficiency and percent fetal DNA recovery. The Akonni Biosystems TruTip technology uses a binding matrix embedded in a pipette tip; the Circulating Nucleic Acids Kit from Qiagen employs a spin column approach. The TruTip method adds an extra step to decrease the recovery of DNA fragments larger than 600 bp from the sample to yield an overall higher percentage of smaller molecular weight DNA, effectively enriching for fetal DNA. In this evaluation, three separate extraction comparison studies were performed - a dilution series of fragmented DNA in plasma, a set of clinical maternal samples, and a blood collection tube time point study of maternal samples. Both extraction methods were found to efficiently extract small fragment DNA from large volumes of plasma. In the amended samples, the TruTip extraction method was ~15% less efficient with overall DNA recovery, but yielded an 87% increase in % fetal DNA relative to the Qiagen method. The average percent increase of fetal DNA of TruTip extracted samples compared to the Qiagen method was 55% for all sets of blinded clinical samples. A study comparing extraction efficiencies from whole blood samples incubated up to 48 hours prior to processing into plasma resulted in more consistent % fetal DNA recoveries using TruTip. The extracted products were tested on two detection platforms, quantitative real-time PCR and droplet digital PCR, and yielded similar results for both extraction methods.
Collapse
|
8
|
Griesemer SB, Holmberg R, Cooney CG, Thakore N, Gindlesperger A, Knickerbocker C, Chandler DP, St George K. Automated, simple, and efficient influenza RNA extraction from clinical respiratory swabs using TruTip and epMotion. J Clin Virol 2013; 58:138-43. [PMID: 23880159 DOI: 10.1016/j.jcv.2013.06.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND Rapid, simple and efficient influenza RNA purification from clinical samples is essential for sensitive molecular detection of influenza infection. Automation of the TruTip extraction method can increase sample throughput while maintaining performance. OBJECTIVES To automate TruTip influenza RNA extraction using an Eppendorf epMotion robotic liquid handler, and to compare its performance to the bioMerieux easyMAG and Qiagen QIAcube instruments. STUDY DESIGN Extraction efficacy and reproducibility of the automated TruTip/epMotion protocol was assessed from influenza-negative respiratory samples spiked with influenza A and B viruses. Clinical extraction performance from 170 influenza A and B-positive respiratory swabs was also evaluated and compared using influenza A and B real-time RT-PCR assays. RESULTS TruTip/epMotion extraction efficacy was 100% in influenza virus-spiked samples with at least 745 influenza A and 370 influenza B input gene copies per extraction, and exhibited high reproducibility over four log10 concentrations of virus (<1% CV). RNA yields between the three automated methods differed by less than 0.5 log10 gene copies. 99% of clinical specimens that were PCR-positive after easyMAG or QIAcube extraction were also positive following TruTip extraction. Overall Ct value differences obtained between TruTip/epMotion and easyMAG/QIAcube clinical extracts ranged from 1.24 to 1.91. Pairwise comparisons of Ct values showed a high correlation of the TruTip/epMotion protocol to the other methods (R2>0.90). CONCLUSION The automated TruTip/epMotion protocol is a simple and rapid extraction method that reproducibly purifies influenza RNA from respiratory swabs, with comparable efficacy and efficiency to both the easyMAG and QIAcube instruments.
Collapse
Affiliation(s)
- Sara B Griesemer
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, United States.
| | | | | | | | | | | | | | | |
Collapse
|