DNA Diagnostics by Surface-Bound Melt-Curve Reactions

Meuzelaar, Linda Strömqvist; Hopkins, Katie L.; Liébana, Ernesto; Brookes, Anthony J.

doi:10.2353/jmoldx.2007.060057

Cited by 12 publications

(6 citation statements)

References 33 publications

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“… DASH, dynamic allele-specific hybridization [ 80 ]; PRT, paralogue ratio test [ 81 ]; MAQ, multiple amplicon quantification [ 82 ]; qPCR, quantitative PCR. …”

Section: Combination Of Snp and Cnv Genotyping In Common Disordersmentioning

confidence: 99%

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies

Estivill¹,

Armengol²

2007

PLoS Genet

193

135

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Genome-wide association scans (GWASs) using single nucleotide polymorphisms (SNPs) have been completed successfully for several common disorders and have detected over 30 new associations. Considering the large sample sizes and genome-wide SNP coverage of the scans, one might have expected many of the common variants underpinning the genetic component of various disorders to have been identified by now. However, these studies have not evaluated the contribution of other forms of genetic variation, such as structural variation, mainly in the form of copy number variants (CNVs). Known CNVs account for over 15% of the assembled human genome sequence. Since CNVs are not easily tagged by SNPs, might have a wide range of copy number variability, and often fall in genomic regions not well covered by whole-genome arrays or not genotyped by the HapMap project, current GWASs have largely missed the contribution of CNVs to complex disorders. In fact, some CNVs have already been reported to show association with several complex disorders using candidate gene/region approaches, underpinning the importance of regions not investigated in current GWASs. This reveals the need for new generation arrays (some already in the market) and the use of tailored approaches to explore the full dimension of genome variability beyond the single nucleotide scale.

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“… DASH, dynamic allele-specific hybridization [ 80 ]; PRT, paralogue ratio test [ 81 ]; MAQ, multiple amplicon quantification [ 82 ]; qPCR, quantitative PCR. …”

Section: Combination Of Snp and Cnv Genotyping In Common Disordersmentioning

confidence: 99%

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies

Estivill¹,

Armengol²

2007

PLoS Genet

193

135

View full text Add to dashboard Cite

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“…Other systems for array based denaturation studies have been developed for the purpose such as multithermal microarray washers [22], surface plasmon resonance (SPR) based detection [24] and membrane-based dynamic allele-specific hybridization (DASH) systems [25,26]. The system presented in this work has the potential advantage of employing magnetic particles as labels.…”

Section: Melting Curvementioning

confidence: 97%

On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

Rizzi¹,

Østerberg²,

Henriksen³

et al. 2015

Journal of Magnetism and Magnetic Materials

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“…It is possible to determine the temperature and salt concentration condition that causes DNA hybrids to denature by continuously increasing temperature or decreasing ionic concentration ( Figure 1b). In the literature, measurements of the melting of DNA hybrids have been performed as function of increasing temperature using readouts based on fluorescence [5][6][7] , electrochemistry [8][9][10] , surface plasmon resonance (SPR) 11,12 , surface enhanced Raman spectroscopy (SERS) 13 , and magnetoresistive sensors 14 . Several of these readouts have significant cross-sensitivities to temperature and salt concentration and thus require extra care.…”

Section: Introductionmentioning

confidence: 99%

Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

2017

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We present a microfluidic system and its use to measure DNA denaturation curves by varying the temperature or salt (Na) concentration. The readout is based on real-time measurements of DNA hybridization using magnetoresistive sensors and magnetic nanoparticles (MNPs) as labels. We report the first melting curves of DNA hybrids measured as a function of continuously decreasing salt concentration at fixed temperature and compare them to the corresponding curves obtained vs. temperature at fixed salt concentration. The magnetoresistive sensor platform provided reliable results under varying temperature as well as salt concentration. The salt concentration melting curves were found to be more reliable than temperature melting curves. We performed a two-dimensional mapping of the melting profiles of a target to probes targeting its wild type (WT) and mutant type (MT) variants in the temperature-salt concentration plane. This map clearly showed a region of optimum ability to differentiate between the two variants. We finally demonstrated single nucleotide polymorphysm (SNP) genotyping using both denaturation methods on both separate sensors but also using a differential measurement on a single sensor. The results demonstrate that concentration melting provides an attractive alternative to temperature melting in on-chip DNA denaturation experiments and further show that the magnetoresistive platform is attractive due to its low cross-sensitivity to temperature and liquid composition.

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DNA Diagnostics by Surface-Bound Melt-Curve Reactions

Cited by 12 publications

References 33 publications

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies

On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

Two-dimensional salt and temperature DNA denaturation analysis using a magnetoresistive sensor

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