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

被引:7
|
作者
Schwartz, Jerrod J. [1 ]
Lee, Choli [1 ]
Hiatt, Joseph B. [1 ]
Adey, Andrew [1 ]
Shendure, Jay [1 ]
机构
[1] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA
基金
美国国家科学基金会;
关键词
molecular biophysics; transposase; jumping reads;
D O I
10.1073/pnas.1202680109
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页码:18749 / 18754
页数:6
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