1
|
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.
Collapse
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
| |
Collapse
|
2
|
Hadiwikarta WW, Van Dorst B, Hollanders K, Stuyver L, Carlon E, Hooyberghs J. Targeted resequencing of HIV variants by microarray thermodynamics. Nucleic Acids Res 2013; 41:e173. [PMID: 23935070 PMCID: PMC3794611 DOI: 10.1093/nar/gkt682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Within a single infected individual, a virus population can have a high genomic variability. In the case of HIV, several mutations can be present even in a small genomic window of 20–30 nucleotides. For diagnostics purposes, it is often needed to resequence genomic subsets where crucial mutations are known to occur. In this article, we address this issue using DNA microarrays and inputs from hybridization thermodynamics. Hybridization signals from multiple probes are analysed, including strong signals from perfectly matching (PM) probes and a large amount of weaker cross-hybridization signals from mismatching (MM) probes. The latter are crucial in the data analysis. Seven coded clinical samples (HIV-1) are analyzed, and the microarray results are in full concordance with Sanger sequencing data. Moreover, the thermodynamic analysis of microarray signals resolves inherent ambiguities in Sanger data of mixed samples and provides additional clinically relevant information. These results show the reliability and added value of DNA microarrays for point-of-care diagnostic purposes.
Collapse
Affiliation(s)
- Wahyu W Hadiwikarta
- Flemish Institute for Technological Research, VITO, Boeretang 200, B-2400 Mol, Belgium, Institute for Theoretical Physics, KULeuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium, Janssen Diagnostics bvba, Turnhoutseweg 30, B-2340 Beerse, Belgium and Theoretical Physics, Hasselt University, Campus Diepenbeek, Agoralaan - Building D, B-3590, Diepenbeek, Belgium
| | | | | | | | | | | |
Collapse
|
3
|
Microarray-based DNA resequencing using 3' blocked primers. Anal Biochem 2007; 374:41-7. [PMID: 18023400 DOI: 10.1016/j.ab.2007.10.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 10/22/2007] [Accepted: 10/23/2007] [Indexed: 11/22/2022]
Abstract
To exceed the throughput and accuracy of conventional sequencing technologies, we tested a method (pyrophosphorolysis-activated polymerization [PAP]) of nucleic acid amplification that uses 3' blocked primers (P*s). As proof-of-principle, we resequenced a 20-bp region of the factor IX gene with a microarray of P*s. P*s discriminate 3' end mismatches with ultra-high specificity as well as mismatches along their lengths with high specificity. We correctly identified two wild-type samples as well as all mismatches, including three single-base substitutions, one microdeletion, one microinsertion, and one heterozygous mutation. Despite limitations in the primer purity, the signal/noise ratio between the matched and mismatched P*s sometimes exceeded 1000. Thus, PAP resequencing shows great potential for accurate and high-throughput microarray-based resequencing.
Collapse
|
4
|
Liu Q, Sommer SS. PAP: detection of ultra rare mutations depends on P* oligonucleotides: "sleeping beauties" awakened by the kiss of pyrophosphorolysis. Hum Mutat 2004; 23:426-36. [PMID: 15108273 DOI: 10.1002/humu.20036] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Pyrophosphorolysis-activated polymerization (PAP) was initially developed to enhance the specificity of allele-specific PCR for detection of known mutations in the presence of a great excess of wild-type allele. The high specificity of PAP derives from the serial coupling of activation of a 3' blocked pyrophosphorolysis-activable oligonucleotide (P(*)) with extension of the unblocked, activated P(*). In theory, PAP can detect a copy of a single base mutation present in 3x10(11) copies of the wild-type allele. In practice, the selectivity of detection is limited by polymerase extension errors, a bypass reaction, from the unblocked oligonucleotide annealed to the opposing strand. Bi-directional PAP allele-specific amplification (Bi-PAP-A) is a derivative of PAP that uses two opposing pyrophosphorolysis activable oligonucleotides (P(*)) with one nucleotide overlap at their 3' termini. This eliminates the problematic bypass reaction. The selectivity of Bi-PAP-A was examined using lambda phage DNA as a model system. Bi-PAP-A selectively detected two copies of a rare mutated allele in the presence of at least 2x10(9) copies of the wild-type lambda phage DNA. We then applied Bi-PAP-A to direct detection of spontaneous somatic mutations in the lacI transgene in BigBlue transgenic mice at a frequency as low as 3x10(-9). A 370-fold variation in the frequency of a specific somatic mutation among different mouse samples was found, implying hyper-Poisson variance and clonal expansion of mutation occurring during early development. Bi-PAP-A is a simple, rapid, and general method capable of automation and particularly suited to detection of ultra rare mutations. We also show that P(*) oligonucleotides have the novel and unexpected property of high specificity to mismatches with the template throughout lengths of the P(*). Thus, PAP also can form the basis of microarray-based scanning or resequencing methods to detect virtually all mutations.
Collapse
Affiliation(s)
- Qiang Liu
- Department of Molecular Genetics, City of Hope National Medical Center, Duarte, California 91010-3000, USA
| | | |
Collapse
|
5
|
Liu Q, Sommer SS. Pyrophosphorolysis-activatable oligonucleotides may facilitate detection of rare alleles, mutation scanning and analysis of chromatin structures. Nucleic Acids Res 2002; 30:598-604. [PMID: 11788724 PMCID: PMC99816 DOI: 10.1093/nar/30.2.598] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pyrophosphorolysis-activated polymerization (PAP) was initially developed to enhance the specificity of allele-specific PCR for detection of known mutations in the presence of a great excess of wild-type allele. The high specificity of PAP derives from the serial coupling of pyrophosphorolysis-mediated activation of a pyrophosphorolysis-activatable oligonucleotide (P*) followed by extension of the activated oligonucleotide. Herein, we demonstrate that genetically engineered DNA polymerases greatly improve the efficiency of PAP, making it a practical technique for detection of rare mutations. We also show that P* oligonucleotides have the novel and unexpected property of high sensitivity to mismatches throughout at least the 16 3'-terminal nucleotides. Thus, PAP constitutes a technology platform of potential utility whenever high specificity is required along the length of an oligonucleotide.
Collapse
Affiliation(s)
- Qiang Liu
- Departments of Molecular Genetics, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | | |
Collapse
|
6
|
Trévisiol E, Defrancq E, Lhomme J, Laayoun A, Cros P. Synthesis of Methylketone Containing Nucleoside Triphosphates for RNA Labelling. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00577-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
7
|
Skobeltsyna LM, Pyshnyi DV, Shishkina IG, Tabatadze DR, Dymshits GM, Zarytova VF, Ivanova EM. Development of a colorimetric test system for detection of point mutations via ligation of a tandem of short oligonucleotides on methacrylate beads. Mol Biol 2000. [DOI: 10.1007/bf02759660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
8
|
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) gene studies are now one of the most frequent activities in clinical molecular genetics laboratories. The number of requests is growing, owing to the increasingly wide range of recognized CFTR gene diseases (cystic fibrosis, congenital bilateral absence of the vas deferens, disseminated bronchiectasis, allergic bronchopulmonary aspergillosis and chronic pancreatitis), and the availability of efficient molecular tools for detecting mutations. A growing number of tests capable of simultaneously detecting several frequent CF mutations are being developed, and commercial kits are now available. The most recent kits detect nearly 90% of defective alleles in Caucasians, a rate high enough for carrier screening and for the majority of diagnostic requests. However, because of the wide variety of molecular defects documented in the CFTR gene, only a limited number of laboratories have mastered the entire panoply of necessary techniques, while other laboratories have to refer certain cases to specialized centers with complementary and/or scanning tools at their disposal. A good knowledge of CFTR diseases and their molecular mechanisms, together with expertise in the various techniques, is crucial for interpreting the results. Diagnostic strategies must take into account the indication, the patient's ethnic origin, and the time available in the framework of genetic counseling. This review presents the methods most frequently used for detecting CFTR gene mutations, and discusses the strategies most suited to the different clinical settings.
Collapse
Affiliation(s)
- E Girodon-Boulandet
- Service de Biochimie et de Génétique, INSERM U468, Hôpital Henri-Mondor, Créteil, France
| | | | | |
Collapse
|
9
|
Yuan B, Thomas JP, von Kodolitsch Y, Pyeritz RE. Comparison of heteroduplex analysis, direct sequencing, and enzyme mismatch cleavage for detecting mutations in a large gene, FBN1. Hum Mutat 1999; 14:440-6. [PMID: 10533071 DOI: 10.1002/(sici)1098-1004(199911)14:5<440::aid-humu11>3.0.co;2-p] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Analysis of large genes for mutations of clinical relevance is complicated by intragenic heterogeneity, sensitivity, and cost of the methods available, and in the case of many conditions, specificity of the genetic alterations detected. We examined the FBN1 gene for mutations in people who had Marfan syndrome using three methods: single-chain polymorphism analysis (SSCP) with heteroduplex (HA) analysis, enzyme-mediated cleavage (EMC) of heteroduplexes, and direct sequencing. We also used these methods to search for mutations in the P53 gene in patients with hepatocellular carcinoma. The results showed that EMC was most efficient for detecting mutations. However, the cost favored SSCP with heteroduplex analysis, provided conditions did not need to be optimized to detect a mutation. Until more cost-effective and sensitive methods are developed to detect unknown mutations in large genes, diagnosis of many genetic disorders will depend on the willingness of an investigator who is studying a particular disorder to perform clinical molecular testing and have the laboratory accredited.
Collapse
Affiliation(s)
- B Yuan
- Department of Human Genetics, MCP Hahnemann School of Medicine, Pittsburgh, PA, USA
| | | | | | | |
Collapse
|
10
|
Dubiley S, Kirillov E, Mirzabekov A. Polymorphism analysis and gene detection by minisequencing on an array of gel-immobilized primers. Nucleic Acids Res 1999. [DOI: 10.1093/nar/27.18.e19-i] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
11
|
Abstract
Automated mutation analysis brings with it a vastly increased capacity in the number of test samples that can be processed at a time, as well as much improved test reproducibility. Until now, the introduction of automation into this field had been restricted to the use of semiautomated sequencing systems to make the most of the sequence information extractable from a single lane in an electrophoretic gel or in a polymer-filled glass capillary. Much effort is now being directed into harnessing the potential of DNA microarrays (DNA chips) and there is increasing interest in the potential of matrix-assisted mass spectrometry for determining the detail of large nucleic acid molecules. Meanwhile, there are other important recent developments already available, including robotic workstations, the further development of the allele-specific oligonucleotide assay into microtitre formats, and its use with fluorescence for real-time quantitative PCR analysis. Implementation of these developments in appropriate settings can further streamline the routine of molecular diagnostic laboratories, allowing them to take greater advantage of the recent surge of gene discoveries and their associated disease-causing mutations.
Collapse
Affiliation(s)
- D Ravine
- Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, UK
| |
Collapse
|
12
|
Neel JV. A unified approach to the study of mutation, from bacteria to humans: some potentialities of the new DNA technologies. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 1999; 33:266-272. [PMID: 10398373 DOI: 10.1002/(sici)1098-2280(1999)33:4<266::aid-em2>3.0.co;2-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- J V Neel
- Department of Human Genetics, The University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
13
|
Affiliation(s)
- A Blanchard
- Rosetta Inpharmatics, Kirland, WA 98034, USA
| |
Collapse
|
14
|
Abstract
The technology and applications of microarrays of immobilized DNA or oligonucleotides are reviewed. DNA arrays are fabricated by high-speed robotics on glass or nylon substrates, for which labeled probes are used to determine complementary binding allowing massively parallel gene expression and gene discovery studies. Oligonucleotide microarrays are fabricated either by in situ light-directed combinational synthesis or by conventional synthesis followed by immobilization on glass substrates. Sample DNA is amplified by the polymerase chain reaction (PCR), and a fluorescent label is inserted and hybridized to the microarray. This technology has been successfully applied to the simultaneous expression of many thousands of genes and to large-scale gene discovery, as well as polymorphism screening and mapping of genomic DNA clones.
Collapse
Affiliation(s)
- G Ramsay
- Wolpert Polymers, Inc., Richmond, VA 23225-4636, USA.
| |
Collapse
|