title: Phasing of single DNA molecules by massively parallel barcoding.
abstract: High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-171 65 Solna, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Borgström
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-171 65 Solna, Sweden.
authors.forename: David
authors.initials: D
authors.lastname: Redin
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-171 65 Solna, Sweden.
authors.forename: Sverker
authors.initials: S
authors.lastname: Lundin
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-171 65 Solna, Sweden.
authors.forename: Emelie
authors.initials: E
authors.lastname: Berglund
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-171 65 Solna, Sweden.
authors.forename: Anders F
authors.initials: AF
authors.lastname: Andersson
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, Royal Institute of Technology (KTH), SE-171 65 Solna, Sweden.
authors.forename: Afshin
authors.initials: A
authors.lastname: Ahmadian
mesh_terms: D004247:DNA / Q000737:chemistry*; D058893:DNA Barcoding, Taxonomic
chemical_list: D004247:DNA