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Wood HN, Venken T, Willems H, Jacobs A, Reis AJ, Almeida da Silva PE, Homolka S, Niemann S, Rohde KH, Hooyberghs J. Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization. PLoS One 2019; 14:e0212064. [PMID: 30730960 PMCID: PMC6366778 DOI: 10.1371/journal.pone.0212064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/25/2019] [Indexed: 11/19/2022] Open
Abstract
In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (<5%) of drug-resistant Mtb was possible.
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Affiliation(s)
- Hillary N. Wood
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Tom Venken
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Hanny Willems
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - An Jacobs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Ana Júlia Reis
- Laboratory of Tuberculosis, Faculty of Medicine, Universidade Federal do Rio Grande- FURG, Rio Grande so Sul, RS, Brazil
| | - Pedro Eduardo Almeida da Silva
- Laboratory of Tuberculosis, Faculty of Medicine, Universidade Federal do Rio Grande- FURG, Rio Grande so Sul, RS, Brazil
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel, Germany
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
| | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
- Theoretical Physics, Hasselt University, Diepenbeek, Belgium
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Matveeva OV, Ogurtsov AY, Nazipova NN, Shabalina SA. Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes. PLoS One 2018; 13:e0199162. [PMID: 29928000 PMCID: PMC6013149 DOI: 10.1371/journal.pone.0199162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/02/2018] [Indexed: 12/20/2022] Open
Abstract
Off-target oligoprobe's interaction with partially complementary nucleotide sequences represents a problem for many bio-techniques. The goal of the study was to identify oligoprobe sequence characteristics that control the ratio between on-target and off-target hybridization. To understand the complex interplay between specific and genome-wide off-target (cross-hybridization) signals, we analyzed a database derived from genomic comparison hybridization experiments performed with an Affymetrix tiling array. The database included two types of probes with signals derived from (i) a combination of specific signal and cross-hybridization and (ii) genomic cross-hybridization only. All probes from the database were grouped into bins according to their sequence characteristics, where both hybridization signals were averaged separately. For selection of specific probes, we analyzed the following sequence characteristics: vulnerability to self-folding, nucleotide composition bias, numbers of G nucleotides and GGG-blocks, and occurrence of probe's k-mers in the human genome. Increases in bin ranges for these characteristics are simultaneously accompanied by a decrease in hybridization specificity-the ratio between specific and cross-hybridization signals. However, both averaged hybridization signals exhibit growing trends along with an increase of probes' binding energy, where the hybridization specific signal increases significantly faster in comparison to the cross-hybridization. The same trend is evident for the S function, which serves as a combined evaluation of probe binding energy and occurrence of probe's k-mers in the genome. Application of S allows extracting a larger number of specific probes, as compared to using only binding energy. Thus, we showed that high values of specific and cross-hybridization signals are not mutually exclusive for probes with high values of binding energy and S. In this study, the application of a new set of sequence characteristics allows detection of probes that are highly specific to their targets for array design and other bio-techniques that require selection of specific probes.
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Affiliation(s)
- Olga V. Matveeva
- Biopolymer Design LLC, Acton, Massachusetts, United States of America
- * E-mail: (OVM); (SAS)
| | - Aleksey Y. Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nafisa N. Nazipova
- Institute of Mathematical Problems of Biology, RAS – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Svetlana A. Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (OVM); (SAS)
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Willems H, Jacobs A, Hadiwikarta WW, Venken T, Valkenborg D, Van Roy N, Vandesompele J, Hooyberghs J. Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. PLoS One 2017; 12:e0177384. [PMID: 28542229 PMCID: PMC5444680 DOI: 10.1371/journal.pone.0177384] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/26/2017] [Indexed: 01/13/2023] Open
Abstract
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine.
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Affiliation(s)
- Hanny Willems
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - An Jacobs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Wahyu Wijaya Hadiwikarta
- Flemish Institute for Technological Research, VITO, Mol, Belgium.,Institute for Theoretical Physics, KULeuven, Leuven, Belgium
| | - Tom Venken
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research, VITO, Mol, Belgium.,Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Nadine Van Roy
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium.,Theoretical Physics, Hasselt University, Diepenbeek, Belgium
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