@article{7e9aeea35166440494dd672c337677e7,
title = "Array-based Dynamic Allele Specific Hybridization (Array-DASH): optimization-free microarray processing for multiple simultaneous genomic assays",
abstract = "We report proof-of-principle experiments regarding a dynamic microarray protocol enabling accurate and semi-quantitative DNA analysis for re-sequencing, fingerprinting and genotyping. Single-stranded target molecules hybridise to surface-bound probes during initial gradual cooling with high-fidelity. Real-time tracking of target denaturation (via fluorescence) during a 'dynamic' gradual heating phase permits 'melt-curve' analysis. The probe most closely matching the target sequence is identified based on the highest melting temperature. We demonstrated a >99\% re-sequencing accuracy and a potential detection rate of 1\% for SNPs. Experiments employing Hypericum ribosomal ITS regions and HIV genomes illustrated a reliable detection level of 5\% plus simultaneous re-sequencing and genotyping. Such performance suggests a range of potential real-world applications involving rapid sequence interrogation, for example, in the Covid-19 pandemic. Guidance is offered towards the development of a commercial platform and dedicated software required to bring this technique into mainstream science.",
keywords = "COVID-19/epidemiology, Genome, Plant, Genome, Viral, Genotyping Techniques, HIV-1/genetics, Humans, Hypericum/genetics, Oligonucleotide Array Sequence Analysis, Software",
author = "Gibson, \{Spencer J\} and Nathalie Zahra and Freeman, \{Peter J\} and Caroline Howard and Owen Lancaster and Colin Veal and Fontdevila, \{Maria Casadell{\`a}\} and Roger Paredes and Marc Noguera-Julian and Adrian Slater and Brookes, \{Anthony J\}",
note = "Funding Information: This research received funding from the European Community's Seventh Framework Programme ( FP7 /2007–2013) under grant agreement 201418, entitled READNA; East Midlands Healthcare and Bioscience iNet Higher Education Collaboration Fund, entitled “PlantDASH – a system for the identification of plant material”. Funding Information: By comparison, across the 171 sites not successfully assayed by Array-DASH, 25 (14.6\%) were reported to have a non-reference allele in the NGS data, with 21 (12.3\%) having an abundance greater than 5\%. This higher rate (of non-reference NGS bases) in failed as opposed to successful Array-DASH regions lends further support to the idea that the clustering of Array-DASH failure sites is because of regions containing a higher density of non-reference bases. Additionally, NGS results for such regions might under-represent the true extent of mutations, because of preferential alignment and hence reporting of sequence reads for versions most similar to the reference. In short, being re-sequencing rather than de novo sequencing methods confounds both Array-DASH and NGS (in their own ways).This research received funding from the European Community's Seventh Framework Programme (FP7/2007?2013) under grant agreement 201418, entitled READNA; East Midlands Healthcare and Bioscience iNet Higher Education Collaboration Fund, entitled ?PlantDASH ? a system for the identification of plant material?. Publisher Copyright: {\textcopyright} 2021 Elsevier Inc.",
year = "2021",
month = feb,
day = "16",
doi = "10.1016/j.ab.2021.114124",
language = "English",
volume = "626",
journal = "Analytical Biochemistry",
issn = "0003-2697",
publisher = "Elsevier BV",
}
