Capturing native long-range contiguity by in situ library construction and optical sequencing

Jerrod J. Schwartz, Choli Lee, Joseph B. Hiatt, Andrew Adey, Jay Shendure

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)18749-18754
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number46
StatePublished - Nov 13 2012
Externally publishedYes


  • Jumping reads
  • Molecular biophysics
  • Transposase

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Capturing native long-range contiguity by in situ library construction and optical sequencing'. Together they form a unique fingerprint.

Cite this