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US 8,278,039 B2Granted
Random array DNA analysis by hybridization
AssigneeComplete Genomics, Inc.
InventorRadoje T. Drmanac
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Abstract
The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.
Claims45
A system for determining sequence information for a polynucleotide, comprising:
- (a) an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- (b) a set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula NxByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- (iii) x and z are each at least one;
- and
- (iv) y is 2 to 20;
- (c) a detector configured to detect labeled probes from said set once the probes have hybridized to DNA molecules in the array, and to send data indicating the labeled probes that have been detected to a computer processor;
- and
- (d) a computer processor programmed to receive said data from the detector, and to process the data to obtain said sequence information for the polynucleotide.
7 more elements
A system for determining sequence information for a polynucleotide, comprising:
- (a) an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- (b) a first set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula NxBy or the formula ByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- (iii) x and z are each at least one;
- and
- (iv) y is 2 to 20;
- (c) a detector configured to detect labeled probes from said set once the probes have hybridized to DNA molecules in the array, and to send data indicating the labeled probes that have been detected to a computer processor;
- and
- (d) a computer processor programmed to receive said data from the detector, and to process the data to obtain said sequence information for the polynucleotide.
7 more elements
A product for determining sequence information for a polynucleotide, comprising:
- (a) an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- and
- (b) oligonucleotide probes hybridized to a plurality of the DNA molecules on the array, said probes constituting a first set wherein each probe comprises a label and a nucleotide sequence comprising the formula NxBy or the formula ByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- (iii) x and z are each at least one;
- and
- (iv) y is 2 to 20.
5 more elements
A system for determining sequence information for a polynucleotide, comprising:
- (a) an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- (b) a first set of informative oligonucleotide probes, wherein each probe comprises a label and a nucleotide sequence comprising the formula NxBy or the formula ByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- and
- (iii) x, y, and z are each at least one;
- (c) a second set of oligonucleotide probes, each configured to bind to a site in a DNA molecule of the array adjacent to a probe from the first set;
- (d) a detector configured to detect labeled probes from said set once the probes have hybridized to DNA molecules in the array, and to send data indicating the labeled probes that have been detected to a computer processor;
- and
- (e) a computer processor programmed to receive said data from the detector, and to process the data to obtain said sequence information for the polynucleotide.
7 more elements
A product for determining sequence information for a polynucleotide, comprising:
- (a) an array of DNA molecules, wherein each DNA molecule comprises a fragment of said polynucleotide;
- and
- (b) oligonucleotide probes hybridized to a plurality of the DNA molecules on the array, said probes constituting a first set wherein each probe comprises a label and a nucleotide sequence comprising the formula NxBy or the formula ByNz, wherein:
- (i) each N is independently a degenerate base;
- (ii) each B is independently an informative base;
- (iii) x, y, and z are each at least one;
- and
- (c) a second set of oligonucleotides each hybridized to a plurality of the DNA molecules at a position that is adjacent to an oligonucleotide probe of the first set.
5 more elements
Dependencies are inferred from the claim text.