Tagging nucleic acids for sequence assembly
First Claim
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1. A method of nucleic acid analysis comprising:
- a) providing a crosslinked DNA sample comprising a first DNA molecule, wherein said first DNA molecule comprises a first sequence segment and a second sequence segment held together independent of a common phosphodiester bond of the first DNA molecule;
b) cleaving said first DNA molecule using an endonuclease such that said first segment and said second segment no longer share a common phosphodiester backbone;
c) isolating said first sequence segment and said second sequence segment in a first reaction volume;
d) attaching a label to said first sequence segment and to said second sequence segment in said first reaction volume;
e) obtaining sequence information of said label and said first sequence segment and said second sequence segment; and
f) assigning sequence of the first sequence segment and the second sequence segment to a first data contig indicated by the label.
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Abstract
Various approaches for generating long-distance contiguity information to facilitate contig assembly and phase determination are disclosed. Nucleic acids are assembled into complexes using binding moieties such that, when the nucleic acid backbones are cleaved, the ensuing fragments remain bound. Exposed ends are tagged and ligated either to one another or to tagging moieties such as oligo labels. Ligated junctions are sequenced, and the sequence information is used to assemble contigs into common scaffolds or to assign phase information. Various approaches to tagging the exposed ends are presented.
117 Citations
24 Claims
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1. A method of nucleic acid analysis comprising:
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a) providing a crosslinked DNA sample comprising a first DNA molecule, wherein said first DNA molecule comprises a first sequence segment and a second sequence segment held together independent of a common phosphodiester bond of the first DNA molecule; b) cleaving said first DNA molecule using an endonuclease such that said first segment and said second segment no longer share a common phosphodiester backbone; c) isolating said first sequence segment and said second sequence segment in a first reaction volume; d) attaching a label to said first sequence segment and to said second sequence segment in said first reaction volume; e) obtaining sequence information of said label and said first sequence segment and said second sequence segment; and f) assigning sequence of the first sequence segment and the second sequence segment to a first data contig indicated by the label. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24)
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Specification