METHODS AND DEVICES FOR SINGLE-MOLECULE WHOLE GENOME ANALYSIS
Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g. determining structural variations and copy number variations between individuals.
1 - 58 . (canceled)
59 . A method of characterizing a DNA, comprising:
labeling a plurality of sequence-specific locations on a first DNA comprising from 50 kb to about 100 mb;
linearizing at least a portion of the labeled first DNA;
detecting a recognizable pattern of labels on the linearized first DNA, wherein the labels are indicative of a sequence characteristic of the first DNA; and
comparing the recognizable pattern of labels on the linearized first DNA to a pattern of labels indicative of a known sequence characteristic of a reference DNA to ascertain a similarity or difference in a sequence characteristic of the first DNA and the reference DNA.
60 . The method of claim 59 , wherein the labeling does not comprise hybridization of a sequence-specific nucleic acid probe.
61 . The method of claim 59 , wherein the linearizing comprises transporting the DNA into a nanochannel.
62 . The method of claim 59 , further comprising correlating a recognizable pattern of labels to one or more selected from the group consisting of a structure, a sequence assembly, a genetic map, a cytogenetic map, a methylation pattern, a physiological characteristic, a location of a CpG island, an epigenomic pattern, and a combination thereof.
63 . The method of claim 59 , wherein the first DNA is double stranded.
64 . The method of claim 59 , wherein the labeling is effected with one or more selected from the group consisting of a methyltransferase, a zinc finger protein, an antibody, a transcription factor, a DNA binding protein, a hairpin polyamide, a triplex-forming oligodeoxynucleotide, a peptide nucleic acid, and any combination thereof.
65 . The method of claim 59 , wherein the labeling is effected with a methyltransferase.
66 . The method of claim 59 , wherein the label further comprises a fluorophore or quantum dot.
67 . The method of claim 59 , further comprising labeling at least one additional sequence-specific location on the first DNA with a label that differs from the label of claim 59 .
68 . The method of claim 67 , wherein one label identifies genomic information, and wherein the other label identifies epigenomic information.
69 . The method of claim 59 , wherein the sequence characteristic of the reference DNA is obtained from a reference database genome assembly sequencing or an in silico barcode computationally generated based on same sequence-specific motifs.
70 . A method of generating a non-virtual genome assembly, wherein the non-virtual genome assembly comprises an observed scaffold comprising the recognizable pattern of labels on the linearized first DNA of claim 59 .
71 . The method of claim 70 , wherein the recognizable pattern of labels comprises raw images of observed barcode of the plurality of fragments of a first batch of a chromosome or genome sample.
72 . The method of claim 71 , further comprising extracting the observed barcode of the plurality of fragments.
73 . The method of claim 72 , further comprising assembling the observed barcode of the plurality of fragments into an observed scaffold.
74 . The method of claim 71 , further comprising fragmenting a second batch of the chromosome or genome sample
75 . The method of claim 74 , further comprising generating random short reads of 35 to 850 bps.
76 . The method of claim 75 , further comprising computationally assembling the random short reads into contigs of 10 to 100 kb.
77 . The method of claim 76 , further comprising computationally generating in Silico barcode on the contigs.
78 . The method of claim 77 , further comprising mapping an in Silico barcode onto an observed scaffold.