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AssigneeErasmus University Medical Center Faculty of Medicine Department of Cell Biology and Genetics
InventorsWouter De Laat, Frank Grosveld
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The present invention relates in one aspect to a method for analyzing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest (e.g., one or more genomic loci) comprising the steps of: (a) providing a sample of cross-linked DNA; (b) digesting the cross-linked DNA with a primary restriction enzyme; (c) ligating the cross-linked nucleotide sequences; (d) reversing the cross linking; (e) digesting the nucleotide sequences with a secondary restriction enzyme; (f) ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest; (g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridises to the DNA sequences that flank the nucleotide sequence of interest; (h) hybridising the amplified sequence(s) to an array; and (i) determining the frequency of interaction between the DNA sequences.
A method for analysing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of:
The method according to any of the preceding claims, wherein the target nucleotide sequence is a nucleotide sequence that is associated with or causes a disease, or is located up to or greater than 15 Mb on a linear DNA template from a locus that is associated with or causes a disease.
A method for analysing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences (eg. one or more genomic loci) comprising the steps of:
A circularised nucleotide sequence comprising a first and a second nucleotide sequence, wherein each end of the first and a second nucleotide sequences are separated by different restriction enzyme recognition sites, and wherein said first nucleotide sequence is a target nucleotide sequence and said second nucleotide sequence is obtainable by cross-linking genomic DNA.
A method for preparing a circularised nucleotide sequence comprising the steps of:
A set of probes complementary in sequence to the nucleic acid sequence adjacent to each one of the primary restriction enzyme recognition sites of a primary restriction enzyme in genomic DNA.
A process for preparing a set of probes comprising the steps of:
The method according to 41, wherein an inversed pattern of DNA-DNA interaction frequencies for the subject sample as compared to the control is indicative of an balanced and/or unbalanced inversion.
A method, an array of probes, a set of probes, a process, an array, an assay method, an agent, or a use substantially as described herein and with reference to any of the Examples or Figures.
Dependencies are inferred from the claim text.