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AssigneesThe Broad Institute, Inc., Baylor College of Medicine
InventorsErez LIEBERMAN-AIDEN, Suhas RAO, Elena STAMENOVA, Olga DUDCHENKO, Eric LANDER
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Disclosed is an in situ method for detecting spatial proximity relationships between nucleic acid sequences, such as DNA, in a cell. The method includes: providing a sample of one or more cells comprising nucleic acids; fragmenting the nucleic acids present in the cells that leaves 5′ overhanging ends; filling in the overhanging ends with at least one labeled nucleotide; joining the filled in end of the fragmented nucleic acids that are in close physical proximity to create one or more end joined nucleic acid fragments having a junction; isolating the one or more end joined nucleic acid fragments using the labeled nucleotide; and determining the sequence at the junction of the one or more end joined nucleic acid fragments.
An in situ method for detecting spatial proximity relationships between nucleic acid sequences in a cell, comprising:
The method of any one of claims, 1-36, further comprising treating the sample with one or more agents prior to performing a PCR amplification step.
The method of claim 55, wherein the cells in the sample are synchronized in metaphase.
A method for diagnosing a disease or condition, the method comprising:
An isolated nucleic acid probe that specifically binds to a junction in a end joined nucleic acid fragment, wherein the probe specifically hybridizes to the end joined nucleic acid fragment both 5′ and 3′ of the site of the junction and spans the site of the junction.
An isolated nucleic acid probe that specifically binds a specific nucleic acid sequence in a junction in a end joined nucleic acid fragment.
A system for visualizing the information from one or more ligation junctions.
The system according to any one of claims 111-117, wherein multiple interaction matrices can be simultaneously viewer and compared.
Dependencies are inferred from the claim text.