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US 2010/0062947 A1Published application
Circular chromosome conformation capture (4c)
AssigneeErasmus University Medical Center
InventorsWouter De Laat, Frank Grosveld
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AssigneeErasmus University Medical Center
InventorsWouter De Laat, Frank Grosveld
Estimating the term…
The present invention relates in one aspect to 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: (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) optionally digesting the nucleotide sequences with a secondary restriction enzyme; (f) optionally 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 sequences 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 two or more target nucleotide sequences with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of:
(canceled)
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:
The method according to 27, wherein an inversed pattern of DNA-DNA interaction frequencies for the subject sample as compared to the control is indicative of a balanced and/or unbalanced inversion.
A method for analysing the frequency of interaction of one or more target nucleotide sequences with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of:
A method for determining the presence of a genomic rearrangement in a sample comprising the steps of:
A database of nucleic acid sequences of about 6-50 basepairs that directly flank, and optionally include, the primary restriction enzyme recognition site or the secondary restriction enzyme recognition site of each target sequence.
A database of nucleic acid sequences of about 12-50 basepairs that directly flank all relevant primary and secondary restriction enzyme recognition sites in the genome.
A method or an agent or a database or a use substantially as described herein and with reference to any of the Examples or Figures.
Dependencies are inferred from the claim text.