Ruler arrays
OwnerDavid K. Gifford, P. Alexander Rolfeinventors
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Abstract
The invention in some aspects relates to methods for measuring distances between locations in a nucleic acid. The invention relates to methods of genetic analysis useful for detecting genomic alterations. In some aspects, the invention relates to methods for detecting genomic insertions, deletions, and inversions.
Claims47
A method for measuring the distance between locations in a nucleic acid, wherein the locations are a predefined location and a test location, comprising:
- (a) preparing nucleic acid fragments from the nucleic acid, wherein each fragment comprises (i) only one predefined region, wherein the predefined region is complementary to a predefined location of the nucleic acid and (ii) at least one test region, wherein a test region is complementary to a test location of the nucleic acid, and
- (b) measuring the frequency of occurrence of each test region in the nucleic acid fragments, wherein the frequency of occurrence of a particular test region is inversely related to the distance between the test location in the nucleic acid that is complementary to the particular test region and the predefined location in the nucleic acid.
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A method for detecting a difference between a test nucleic acid and a reference nucleic acid comprising:
- (a) contacting (i) a collection of labeled test nucleic acid fragments with (ii) a set of query probes, wherein test nucleic acid fragments are labeled at one or more defined site to produce the labeled test nucleic acid fragments and wherein a query probe is a polynucleotide and the set of query probes comprises at least three different polynucleotides, each of whose sequence identifies a known region in the reference nucleic acid, under conditions appropriate for hybridization of labeled test nucleic acid fragments with query probes;
- (b) determining the extent of hybridization between each query probe and labeled test nucleic acid fragments;
- (c) associating the extent of hybridization for each query probe, characteristic(s) of the known region identified by the query probe, and characteristic(s) of the defined sites, thereby producing a test hybridization pattern;
- (d) determining distance in the test hybridization pattern by evaluating the extent of hybridization for a query probe within the resolution limit of a defined site within the test hybridization pattern with (i) the extent of hybridization of the query probe in a reference hybridization pattern and (ii) distance from the query probe to the defined site in the reference hybridization pattern, wherein distance is the number of bases between a defined site and a region identified by a query probe;
- and
- (e) identifying a difference in distance between the reference hybridization pattern and the test hybridization pattern, thereby detecting a difference between a test nucleic acid and a reference nucleic acid.
A method for detecting a difference between a test nucleic acid and a reference nucleic acid comprising:
- (a) contacting (i) a collection of labeled test nucleic acid fragments with (ii) a set of query probes, wherein test nucleic acid fragments are labeled at one or more defined sites to produce the labeled test nucleic acid fragments and wherein a query probe is a polynucleotide and the set of query probes comprises at least three different polynucleotides, each of whose sequence identifies a known region in the reference nucleic acid, under conditions appropriate for hybridization of labeled test nucleic acid fragments with query probes;
- (b) determining the extent of hybridization between each query probe and labeled test nucleic acid fragments;
- (c) associating the extent of hybridization for each query probe, characteristic(s) of the known region identified by the query probe, and characteristic(s) of the defined sites, thereby producing a test hybridization pattern;
- (d) comparing the test hybridization pattern with a reference hybridization pattern to produce a ratio hybridization pattern;
- and
- (e) identifying a significant local maximum or a significant local minimum in the ratio hybridization pattern,
- thereby detecting a difference between a test nucleic acid and a reference nucleic acid.
The method of 31, further comprising contacting labeled nucleic acid fragments with the one or more restriction enzymes under conditions suitable for digestion of the nucleic acid fragments by the one or more restriction enzymes at defined sites, thereby producing digested labeled nucleic acid fragments.
A method for labeling DNA, comprising:
- (a) combining:
- (i) linear DNA that comprises DNA to be labeled and adapter 10 DNA that tags each end of the DNA to be labeled, wherein the adapter DNA flanks the DNA to be labeled.
- (ii) primer capable of hybridizing to the adapter DNA;
- and
- (iii) labeled nucleotides or combining:
- (i) linear DNA to be labeled
- (ii) a primer capable of hybridizing to a specific sequence in the linear DNA;
- and
- (iii) labeled nucleotides, thereby producing a combination;
- and
- (b) maintaining the combination under conditions appropriate for amplification of the linear DNA to occur, thereby producing amplified DNA comprising at least one labeled nucleotide, thereby producing labeled DNA.
A method of producing a pool of labeled DNA fragments, wherein the pool comprises a random distribution of labeled DNA fragments of from about 3 kilobases to about 5 kilobases, comprising:
- (a) combining:
- (i) linear DNA that comprises DNA to be labeled and adapter DNA that tags each end of the DNA to be labeled, wherein the adapter DNA flanks the DNA to be labeled.
- (ii) primer capable of hybridizing to the adapter DNA;
- and
- (iii) labeled nucleotides
- or combining:
- (i) linear DNA to be labeled
- (ii) a primer capable of hybridizing to a specific sequence in the linear DNA;
- and
- (iii) labeled nucleotides, thereby producing a combination;
- and
- (b) maintaining the combination under conditions appropriate for amplification of the linear DNA to occur, thereby producing amplified DNA comprising at least one labeled nucleotide, thereby producing a pool of labeled DNA fragments.
Dependencies are inferred from the claim text.