1. Array-based Dynamic Allele Specific Hybridization (Array-DASH): optimization-free microarray processing for multiple simultaneous genomic assays
- Author
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Nathalie Zahra, Colin Veal, Caroline Howard, Maria Casadellà Fontdevila, Roger Paredes, Anthony J. Brookes, Spencer J. Gibson, Peter Freeman, Owen Lancaster, Marc Noguera-Julian, and Adrian Slater
- Subjects
Genotyping ,HIV-1/genetics ,Microarray ,Coronavirus disease 2019 (COVID-19) ,Genotyping Techniques ,Computer science ,Biophysics ,Human immunodeficiency virus (HIV) ,Hybridization Array ,Computational biology ,Genome, Viral ,medicine.disease_cause ,01 natural sciences ,Biochemistry ,Genome ,Semi-quantitative ,03 medical and health sciences ,Hypericum/genetics ,medicine ,Humans ,Molecular Biology ,Allele specific ,030304 developmental biology ,COVID-19/epidemiology ,Oligonucleotide Array Sequence Analysis ,0303 health sciences ,010401 analytical chemistry ,COVID-19 ,HIV ,Cell Biology ,0104 chemical sciences ,HIV-1 ,Re-sequencing ,Hypericum ,Genome, Plant ,Software - 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.
- Published
- 2021