MASSIVELY PARALLEL CONTIGUITY MAPPING
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Abstract
Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.
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Citations
48 Claims
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1-23. -23. (canceled)
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24. A method for capturing contiguity information comprising:
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treating a target DNA sequence with a transposase resulting in one or more fragmentation or insertion events; adding or inserting one or more recognition sequences to the target DNA sequence; sequencing the treated DNA; and capturing contiguity information by identifying target DNA sequences or recognition sequences having a shared property. - View Dependent Claims (25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42)
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43. A method of bisulfite sequencing comprising:
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a) performing in vitro transposition into target DNA molecules with transposase complexes, each transposase complex comprising a double stranded DNA transposase recognition sequence and a single stranded DNA adaptor overhang having methylated cytosine (C) residues b) subjecting transposed target DNA molecules to bisulfite treatment; c) performing nucleic acid amplification d) sequencing the resulting nucleic acid library - View Dependent Claims (44, 45)
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46. A method for inferring chromosome conformation comprising:
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a) cross-linking DNA within cells; b) isolating cross-linked DNA from cells; c) fragmenting the cross-linked DNA; d) end-modifying fragmented, cross-linked DNA molecules with an adaptor that is complementary to or that corresponds to a first surface-bound primer; e) hybridizing ends of the fragmented, end-modified target DNA molecules to the first surface-bound primer; f) performing transposition with non-surface-bound transposase complexes, each non-surface-bound transposase complex comprising a DNA transposase and one or more sequences corresponding to a second surface-bound primer; g) performing cluster amplification to produce clusters of clonally derived nucleic acids; h) sequencing clusters of clonally derived nucleic acids; and i) determining physical interactions between chromosomal positions by paring neighboring clusters together. - View Dependent Claims (47, 48)
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Specification