Compositions and methods for intramolecular nucleic acid rearrangement
First Claim
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1. A method of analyzing genomic DNA, comprising:
- a) generating a first plurality of different segments of a first nucleic acid molecule of a contiguous region in the genomic DNA, wherein said contiguous region in the genomic DNA is represented by a plurality of nucleic acid molecules, and wherein each of said first plurality of different segments is appended to a first multiplex identifier (MID) sequence;
b) generating a second plurality of different segments of a second nucleic acid molecule of said contiguous region, wherein each of said second plurality of different segments is appended to a second MID sequence and said first MID sequence and said second MID sequence are different; and
c) sequencing the first and second plurality of different segments and the appended first and second MID sequences, respectively, to analyze the genomic DNA.
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Abstract
Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or multiplex identifier). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.
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13 Claims
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1. A method of analyzing genomic DNA, comprising:
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a) generating a first plurality of different segments of a first nucleic acid molecule of a contiguous region in the genomic DNA, wherein said contiguous region in the genomic DNA is represented by a plurality of nucleic acid molecules, and wherein each of said first plurality of different segments is appended to a first multiplex identifier (MID) sequence; b) generating a second plurality of different segments of a second nucleic acid molecule of said contiguous region, wherein each of said second plurality of different segments is appended to a second MID sequence and said first MID sequence and said second MID sequence are different; and c) sequencing the first and second plurality of different segments and the appended first and second MID sequences, respectively, to analyze the genomic DNA. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method of analyzing nucleic acids, comprising:
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a) generating a first plurality of different segments of a first nucleic acid molecule from a contiguous region of genomic DNA, and wherein each of said first plurality of different segments is appended to a first multiplex identifier (MID) sequence; b) generating a second plurality of different segments of a second nucleic acid molecule from said contiguous region, wherein each of said second plurality of different segments is appended to a second MID sequence and said first MID sequence and said second MID sequence are different, c) sequencing the first plurality of different segments and appended first MID sequences, and the second plurality of different segments and appended second MID sequences; and d) identifying the first plurality of different segments as segments of the first nucleic acid molecule from the first MID sequence, and identifying the second plurality of different segments as segments of the second nucleic acid molecule from the second MID sequence.
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13. A method of analyzing a plurality of contiguous genomic sequences, comprising:
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a) providing a sample comprising the plurality of contiguous genomic sequences; b) tagging a plurality of fragments of the contiguous genomic sequences with a multiplex identifier (MID) sequence such that fragments of a first contiguous nucleic acid sequence share a common MID sequence that is different from an MID sequence of fragments of a second contiguous nucleic acid sequence; and c) sequencing the plurality of fragments and MID sequences to identify fragments of the contiguous sequence.
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Specification