Analysis of polynucleotides
AssigneeBionano Genomics, Inc.
InventorsHan Cao, Alex R. Hastie, Ernest Tsz-Tsun Lam, Željko Džakula
Life of this patent
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Abstract
According to some embodiments herein, methods and kits for labeling and analyzing nucleic acids are provided. In some embodiments, sequence-specific labeling is performed on polynucleotide sequences associated with a host genome, and the presence or absence of patterns characteristic of extragenomic sequences are determined.
Claims16
1-89. (canceled)
A method of characterizing de novo a first polynucleotide integrated into a second polynucleotide, which together comprise a combined polynucleotide that is integrated into a host organism's genome, the method comprising:
- labeling the first polynucleotide in a sequence-specific manner to provide a pattern of sequence-specific first labels on the first polynucleotide and labeling the second polynucleotide in a sequence-specific manner to provide a sequence-specific pattern of second labels on the second polynucleotide, wherein the first polynucleotide comprises a nucleic acid sequence that did not originate from the host organism's genome, and wherein the origin of the nucleic acid sequence in the labeled first polynucleotide is unknown;
- linearizing the combined polynucleotide following the labeling;
- detecting patterns of sequence-specific labels on the first and second polynucleotides;
- identifying a first region of the combined polynucleotide as comprising the first polynucleotide that did not originate from the host genome by comparing a labeling pattern characteristic of the first polynucleotide to a reference pattern of the host genome;
- and
- characterizing a labeling pattern of the second polynucleotide adjacent to the first polynucleotide to determine the location and/or orientation of integration of said first polynucleotide into the host genome.
A method of characterizing de novo a first polynucleotide associated covalently or non-covalently with a host genome, the method comprising:
- labeling the first polynucleotide and sequences flanking the first polynucleotide in a sequence-specific manner to provide a pattern of sequence-specific first labels on the first polynucleotide and flanking sequences, wherein the first polynucleotide comprises a nucleic acid sequence that did not originate from the host organism's genome, and wherein the origin is unknown for the first polynucleotide comprising the pattern of sequence-specific first labels;
- linearizing the first polynucleotide following labeling;
- detecting patterns of sequence-specific first labels on the first polynucleotide;
- and
- determining a presence or absence of the first polynucleotide in the host genome based on a presence or absence of a pattern characteristic of the host genome on the sequences flanking the first polynucleotide.
Dependencies are inferred from the claim text.