Array-based Dynamic Allele Specific Hybridization (Array-DASH): optimization-free microarray processing for multiple simultaneous genomic assays

Spencer J Gibson, Nathalie Zahra, Peter J Freeman, Caroline Howard, Owen Lancaster, Colin Veal, Maria Casadellà Fontdevila, Roger Paredes, Marc Noguera-Julian, Adrian Slater, Anthony J Brookes

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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.

Original languageEnglish
Article number114124
JournalAnalytical Biochemistry
Volume626
DOIs
Publication statusPublished - 16 Feb 2021

Keywords

  • COVID-19/epidemiology
  • Genome, Plant
  • Genome, Viral
  • Genotyping Techniques
  • HIV-1/genetics
  • Humans
  • Hypericum/genetics
  • Oligonucleotide Array Sequence Analysis
  • Software

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