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

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 46, 2012, Pages 18749-18754

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

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Jumping reads; Molecular biophysics; Transposase

Indexed keywords

ARTICLE; DNA LIBRARY; DNA SEQUENCE; ESCHERICHIA COLI; FLOW CYTOMETRY; ILLUMINATION; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

DNA, BACTERIAL; ESCHERICHIA COLI; GENOME, BACTERIAL; GENOMIC LIBRARY; SEQUENCE ANALYSIS, DNA;

ESCHERICHIA COLI;

EID: 84869234142     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1202680109     Document Type: Article

References (21)

1. Lander ES, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860-921, and errata (2001) 411(6838):720 and (2001)412(6846):565.
2. Waterston RH, et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420(6915):520-562.
3. Alkan C, Sajjadian S, Eichler EE (2011) Limitations of next-generation genome sequence assembly. Nat Methods 8(1):61-65.
4. Li R, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463(7279):311-317.
5. Li R, et al. (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20(2):265-272.
6. Korbel JO, et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science 318(5849):420-426.
7. Hillmer AM, et al. (2011) Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res 21(5):665-675.
8. Williams LJ, et al. (2012) Paired-end sequencing of Fosmid libraries by Illumina. Genome Res, 10.1101/gr.138925.112.
9. Roach JC, Boysen C, Wang K, Hood L (1995) Pairwise end sequencing: A unified approach to genomic mapping and sequencing. Genomics 26(2):345-353.
10. Kitzman JO, et al. (2011) Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nat Biotechnol 29(1):59-63.
11. Fan HC, Wang J, Potanina A, Quake SR (2011) Whole-genome molecular haplotyping of single cells. Nat Biotechnol 29(1):51-57.
12. Peters BA, et al. (2012) Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 487(7406):190-195.
13. Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J (2010) Parallel, tag-directed assembly of locally derived short sequence reads. Nat Methods 7(2):119-122.
14. Schwartz DC, et al. (1993) Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262(5130):110-114.
15. Zhou S, et al. (2007) Validation of rice genome sequence by optical mapping. BMC Genomics 8(1):278.
16. Zhou S, et al. (2009) A single molecule scaffold for the maize genome. PLoS Genet 5(11):e1000711.
17. Riehn R, et al. (2005) Restriction mapping in nanofluidic devices. Proc Natl Acad Sci USA 102(29):10012-10016.
18. Ramanathan A, et al. (2004) An integrative approach for the optical sequencing of single DNA molecules. Anal Biochem 330(2):227-241.
19. Eid J, et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323(5910):133-138.
20. Branton D, et al. (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26(10):1146-1153.
21. Geiss GK, et al. (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26(3):317-325.