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Chase M, Neumann A, Erickson B, Komonski D. Concentrating Forensic DNA Sample Extracts on the Microlab® STARlet using the Microlab® Monitored Multi-Flow, Positive Pressure, Evaporative Extraction Module Unit. Forensic Sci Int 2022; 335:111287. [DOI: 10.1016/j.forsciint.2022.111287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/27/2022] [Indexed: 11/29/2022]
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Cain-Hom C, Pabalate R, Pham A, Patel HN, Wiler R, Cox JC. Mammalian Genotyping Using Acoustic Droplet Ejection for Enhanced Data Reproducibility, Superior Throughput, and Minimized Cross-Contamination. ACTA ACUST UNITED AC 2015; 21:37-48. [PMID: 26311060 DOI: 10.1177/2211068215601637] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 12/20/2022]
Abstract
Genetically engineered animal models are major tools of a drug discovery pipeline because they facilitate understanding of the molecular and biochemical basis of disease. These highly complex models of human disease often require increasingly convoluted genetic analysis. With growing needs for throughput and consistency, we find that traditional aspiration-and-dispense liquid-handling robots no longer have the required speed, quality, or reproducibility.We present an adaptation and installation of an acoustic droplet ejection (ADE) liquid-handling system for ultra-high-throughput screening of genetically engineered models. An ADE system is fully integrated with existing laboratory processes and platforms to facilitate execution of PCR and quantitative PCR (qPCR) reactions. Such a configuration permits interrogation of highly complex genetic models in a variety of backgrounds. Our findings demonstrate that a single ADE system replaces 8-10 traditional liquid-handling robots while increasing quality and reproducibility.We demonstrate significant improvements achieved by transitioning to an ADE device: extremely low detectable cross-contamination in PCR and qPCR despite extensive use, greatly increased data reproducibility (large increases in data quality and Cq consistency), lowered reaction volumes for large cost savings, and nearly a magnitude increase in speed per instrument. We show several comparisons between traditional- and ADE-based pipetting for a qPCR-based workflow.
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Affiliation(s)
- Carol Cain-Hom
- Department of Transgenic Technology, Genentech Inc., San Francisco, CA, USA
| | - Ryan Pabalate
- Department of Transgenic Technology, Genentech Inc., San Francisco, CA, USA
| | - Anna Pham
- Department of Transgenic Technology, Genentech Inc., San Francisco, CA, USA
| | - Hetal N Patel
- Department of Transgenic Technology, Genentech Inc., San Francisco, CA, USA
| | - Rhonda Wiler
- Department of Transgenic Technology, Genentech Inc., San Francisco, CA, USA
| | - J Colin Cox
- Department of Transgenic Technology, Genentech Inc., San Francisco, CA, USA
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Stangegaard M, Frøslev TG, Frank-Hansen R, Hansen AJ, Morling N. Automated Extraction of DNA from Blood and PCR Setup using a Tecan Freedom EVO Liquid Handler for Forensic Genetic STR Typing of Reference Samples. ACTA ACUST UNITED AC 2011; 16:134-40. [DOI: 10.1016/j.jala.2010.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Indexed: 10/18/2022]
Abstract
We have implemented and validated automated protocols for DNA extraction and PCR setup using a Tecan Freedom EVO liquid handler mounted with the Te-MagS magnetic separation device (Tecan, Mannedorf, Switzerland). The protocols were validated for accredited forensic genetic work according to ISO 17025 using the Qiagen MagAttract DNA Mini M48 kit (Qiagen GmbH, Hilden, Germany) from fresh whole blood and blood from deceased individuals. The workflow was simplified by returning the DNA extracts to the original tubes minimizing the risk of misplacing samples. The tubes that originally contained the samples were washed with MilliQ water before the return of the DNA extracts. The PCR was setup in 96-well microtiter plates. The methods were validated for the kits: AmpFSTR Identifier, SGM Plus and Yfiler (Applied Biosystems, Foster City, CA), GenePrint FFFL and PowerPlex Y (Promega, Madison, Wl). The automated protocols allowed for extraction and addition of PCR master mix of 96 samples within 3.5 h. In conclusion, we demonstrated that (1) DNA extraction with magnetic beads and (2) PCR setup for accredited, forensic genetic short tandem repeat typing can be implemented on a simple automated liquid handler leading to the reduction of manual work, and increased quality and throughput.
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Affiliation(s)
- Michael Stangegaard
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tobias G. Frøslev
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Frank-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders J. Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Weibel R, Iten M, König I, Beckbissinger R, Benthien T, Hälg W, Ingenhoven N, Lehnert A, Oeltjen L, Zaborosch C. Development of Standard Test Procedures for Quantifying Carry over from Fixed Pipetting Tips in Liquid-Handling Systems. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.jala.2009.08.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Robotic liquid-handling systems using fixed reusable pipetting tips are used not only in fully integrated in vitro clinical diagnostic analyzers, but also in open platform robotic liquid-handling systems. These are not confined to particular diagnostic assays, as customers adapt a large variety of assays on these platforms. One major problem with the use of fixed, reusable tips is the carry over (CO) of analyte from sample to sample. Despite widespread use of fixed tips in open platform systems, systematic studies on procedures to quantify CO for analytes other than nucleic acids are missing. In a consortium with three liquid-handling system suppliers and one coating specialist, we developed test procedures for the quantification of CO. The procedures were standardized and tested with the analytes fluorescein, immunoglobulin G, and hepatitis B surface antigen as model substances for small organic molecules, antibodies, and complex biomolecules. The test procedures allow the reproducible quantification of the CO with intra- and interassay precisions of less than 6% coefficient of variation. They were used to investigate the effect of different tip coatings on the CO of the three analytes. Fluoropolymers, inorganic-organic nanocomposites, sodium-silicate glass, titanium dioxide, and silicone resins, which are used in special applications, showed only small differences in CO. The CO test procedures can be easily transferred to different liquid-handling systems and used with different analytes.
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Affiliation(s)
- Roland Weibel
- Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Wädenswil, Switzerland
| | - Miriam Iten
- Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Wädenswil, Switzerland
| | - Iwo König
- Zurich University of Applied Sciences, Institute of Chemistry and Biological Chemistry, Wädenswil, Switzerland
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Reduction of Carry over in Liquid-Handling Systems with a Decontamination Step Integrated in the Washing Procedure. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.jala.2010.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Robotic liquid-handling systems can be equipped with disposable pipetting tips or fixed reusable pipetting tips. The use of disposable tips is perceived as the best option to avoid carry over (CO) of analyte from sample to sample. We recently developed standardized CO test procedures that allow precise and reproducible quantification of CO for fixed reusable tips. We used these test procedures to reduce CO of the analytes fluorescein, IgG, and hepatitis B surface antigen (HBsAg) to minimal levels. Variations of washing intensity, using water as a washing solution, did not lower CO below acceptable target levels. These target levels would preclude a false-positive detection of IgG and HBsAg in human serum when a negative sample is measured subsequent to a sample with a high analyte concentration. We therefore integrated a decontamination step into the washing procedure. Screening of 12 decontamination solutions showed that sodium hypochlorite solution was very efficient in reducing CO. Optimization led to a final washing routine in which tips are exposed for 0.2 s to 0.17 M NaOCI and subsequently rinsed with 2 mL of water to remove any remaining decontaminant solution. The washing procedure only takes 15 s and is thus suitable for high-throughput applications. The procedure was able to lower CO of IgG and HBsAg in human sera below relevant levels. The decontamination step with hypochlorite can easily be integrated into different liquid-handling systems and is likely to be effective against CO of most proteins and peptides.
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Park ES, Brown AC, DiFeo MA, Barker TH, Lu H. Continuously perfused, non-cross-contaminating microfluidic chamber array for studying cellular responses to orthogonal combinations of matrix and soluble signals. LAB ON A CHIP 2010; 10:571-580. [PMID: 20162232 DOI: 10.1039/b919294h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We present a microfluidic cell culture array with unique versatility and parallelization for experimental trials requiring perfusion cultures. Specifically, we realize a rectangular chamber array in a PDMS device with three attributes: (i) continuous perfusion; (ii) flow paths that forbid cross-chamber contamination; and (iii) chamber shielding from direct perfusion to minimize shear-induced cell behaviour. These attributes are made possible by a bridge-and-underpass architecture, where flow streams travel vertically to pass over (or under) channels and on-chip valves. The array is also designed for considerable versatility, providing subarray, row, column, or single chamber addressing. It allows for incubation with adsorbed molecules, perfusion of differing media, seeding or extraction of cells, and assay staining. We use the device to characterize different phenotypes of alveolar epithelial type II (ATII) cells, particularly the extent of epithelial-to-mesenchymal transition (EMT), a highly suspected pathway in tissue regeneration and fibrosis. Cells are cultured on combinations of matrix proteins (fibronectin or laminin by row) and soluble signals (with or without transforming growth factor-beta1 by column) with two repeats per chip. Fluorescent assays are performed in the array to assess viability, cytoskeletal organization, and cell-cell junction formation. Assay and morphological data are used to tease-out effects of cues driving each phenotype, confirming this as an effective and versatile combinatorial screening platform.
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Affiliation(s)
- Edward S Park
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
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Optimized manual and automated recovery of amplifiable DNA from tissues preserved in buffered formalin and alcohol-based fixative. Forensic Sci Int Genet 2010; 4:80-8. [DOI: 10.1016/j.fsigen.2009.06.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 05/12/2009] [Accepted: 06/06/2009] [Indexed: 11/23/2022]
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Poon H, Elliott J, Modler J, Frégeau C. The Use of Hemastix®and the Subsequent Lack of DNA Recovery Using the Promega DNA IQTMSystem. J Forensic Sci 2009; 54:1278-86. [DOI: 10.1111/j.1556-4029.2009.01173.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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