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The Sequencing Bead Array (SBA), a Next-Generation Digital Suspension Array
Stanford Univ, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA..
Stanford Univ, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA..
Stanford Univ, Stanford Genome Technol Ctr, Palo Alto, CA 94304 USA..
Orebro University Hospital.
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2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 10, UNSP e76696Article in journal (Refereed) Published
Abstract [en]

Here we describe the novel Sequencing Bead Array (SBA), a complete assay for molecular diagnostics and typing applications. SBA is a digital suspension array using Next-Generation Sequencing (NGS), to replace conventional optical readout platforms. The technology allows for reducing the number of instruments required in a laboratory setting, where the same NGS instrument could be employed from whole-genome and targeted sequencing to SBA broad-range biomarker detection and genotyping. As proof-of-concept, a model assay was designed that could distinguish ten Human Papillomavirus (HPV) genotypes associated with cervical cancer progression. SBA was used to genotype 20 cervical tumor samples and, when compared with amplicon pyrosequencing, was able to detect two additional co-infections due to increased sensitivity. We also introduce in-house software Sphix, enabling easy accessibility and interpretation of results. The technology offers a multi-parallel, rapid, robust, and scalable system that is readily adaptable for a multitude of microarray diagnostic and typing applications, e. g. genetic signatures, single nucleotide polymorphisms (SNPs), structural variations, and immunoassays. SBA has the potential to dramatically change the way we perform probe-based applications, and allow for a smooth transition towards the technology offered by genomic sequencing.

Place, publisher, year, edition, pages
2013. Vol. 8, no 10, UNSP e76696
National Category
Biomedical Laboratory Science/Technology
Identifiers
URN: urn:nbn:se:oru:diva-56394DOI: 10.1371/journal.pone.0076696ISI: 000325501300080PubMedID: 24116138OAI: oai:DiVA.org:oru-56394DiVA: diva2:1082087
Available from: 2017-03-15 Created: 2017-03-15 Last updated: 2017-03-15Bibliographically approved

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