Methods and related devices for single molecule whole genome analysis
AssigneeBionano Genomics, Inc.
InventorsMing Xiao, Someskumar Das
Life of this patent
Estimating the term…
Abstract
Provided are methods of labeling and analyzing features along at least one macro molecule such as a linear biopolymer, including methods of mapping the distribution and frequency of specific sequence motifs or the chemical or proteomic modification state of such sequence motifs along individual unfolded nucleic acid molecules. The present invention also provides methods of identifying signature patterns of sequence or epigenetic variations along such labeled macro molecules for direct massive parallel single molecule level analysis. The present invention also provides systems suitable for high throughput analysis of such labeled macro mo lecules.
Claims39
A method of analyzing a double-stranded DNA sample, comprising:
- processing a double-stranded DNA sample so as to give rise to a flap of the first strand of the double-stranded DNA sample being displaced from the double-stranded DNA sample,
- the flap having a length in the range of from about 1 to about 1000 bases, and
- the flap giving rise to a gap in the first strand of the double-stranded DNA sample corresponding to the flap;
- incorporating one or more bases into the double-stranded DNA so as to eliminate at least a portion of the gap;
- labeling at least a portion of the processed double-stranded DNA with one or more tags;
- and
- correlating the location of one or more labels to a structural characteristic of the DNA sample.
(canceled)
(canceled)
(canceled)
(canceled)
(canceled)
(canceled)
(canceled)
(canceled)
(canceled)
(canceled)
(canceled)
A method of obtaining structural information from DNA, comprising:
- labeling, on a first double-stranded DNA sample, one or more sequence-specific locations on the first sample;
- labeling, on a second double-stranded DNA sample, the corresponding one or more sequence-specific locations on the second double-stranded DNA sample;
- elongating at least a portion of the first double-stranded DNA sample;
- elongating at least a portion of the second double-stranded DNA sample;
- and
- comparing the intensity, location, or both of a signal of the at least one label of the first, elongated double-stranded DNA sample to the intensity, location, or both of the signal of the at least one label of the second, elongated double-stranded DNA sample.
(canceled)
(canceled)
A method of obtaining structural information from DNA, comprising:
- labeling, with two or more probes, two or more regions on a flap of a single-stranded DNA member of a double-stranded DNA sample and correlating the locations of the probes to the spatial relationship between the two or more regions to the structure, sequence, or both, of one or more of the regions.
A method of identifying pathogenic genetic material, comprising:
- binding one or more labeled probes to one or more regions of a DNA sample;
- determining the position of one or more probes based on a signal unique to the region upon which the one or more probes reside;
- and
- comparing the position, color, or both of one or more probes bound to the DNA sample to a corresponding signal from a DNA region known to correspond to one or more pathogenic states.
An analysis system, comprising:
- one or more regions for nicking and labeling single- or double-stranded nucleic acid biopolymers;
- one or more regions adapted for elongating nucleic acid biopolymers;
- and
- an imaging device adapted to gather visual information from a labeled nucleic acid biopolymer.
(canceled)
Dependencies are inferred from the claim text.