Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information
- Zhoutao Chen1,
- Long Pham1,
- Tsai-Chin Wu1,
- Guoya Mo1,
- Yu Xia1,
- Peter L. Chang1,
- Devin Porter1,
- Tan Phan2,
- Huu Che2,
- Hao Tran2,3,
- Vikas Bansal4,
- Justin Shaffer5,
- Pedro Belda-Ferre5,
- Greg Humphrey5,
- Rob Knight5,
- Pavel Pevzner6,
- Son Pham2,
- Yong Wang7 and
- Ming Lei7
- 1Universal Sequencing Technology Corporation, Carlsbad, California 92011, USA;
- 2Bioturing Incorporated, San Diego, California 92121, USA;
- 3Faculty of Information Technology, University of Science, Vietnam National University, Ho Chi Minh City, 700 000 Vietnam;
- 4Department of Pediatrics, University of California San Diego, La Jolla, California 92161, USA;
- 5Center for Microbiome Innovation and Departments of Pediatrics, Bioengineering, and Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA;
- 6Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA;
- 7Universal Sequencing Technology Corporation, Canton, Massachusetts 02021, USA
Abstract
Long-range sequencing information is required for haplotype phasing, de novo assembly, and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirements. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enables a low-cost, high-accuracy, and high-throughput short-read second-generation sequencer to generate over 100 kb of long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcoded linked-reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate megabase-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.260380.119.
- Received December 19, 2019.
- Accepted June 10, 2020.
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