title: Capturing native long-range contiguity by in situ library construction and optical sequencing.
abstract: The relatively short read lengths associated with the most cost-effective DNA sequencing technologies have limited their use in de novo genome assembly, structural variation detection, and haplotype-resolved genome sequencing. Consequently, there is a strong need for methods that capture various scales of contiguity information at a throughput commensurate with the current scale of massively parallel sequencing. We propose in situ library construction and optical sequencing on the flow cells of currently available massively parallel sequencing platforms as an efficient means of capturing both contiguity information and primary sequence with a single technology. In this proof-of-concept study, we demonstrate basic feasibility by generating >30,000 Escherichia coli paired-end reads separated by 1, 2, or 3 kb using in situ library construction on standard Illumina flow cells. We also show that it is possible to stretch single molecules ranging from 3 to 8 kb on the surface of a flow cell before in situ library construction, thereby enabling the production of clusters whose physical relationship to one another on the flow cell is related to genomic distance.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Jerrod J
authors.initials: JJ
authors.lastname: Schwartz
authors.forename: Choli
authors.initials: C
authors.lastname: Lee
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Hiatt
authors.forename: Andrew
authors.initials: A
authors.lastname: Adey
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D015698:Genomic Library; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004269:DNA, Bacterial