Methods of diagnosing and treating medullary cystic kidney disease
AssigneesThe Broad Institute, Inc., The General Hospital Corporation, Instituto Carlos Slim De La Salud, A.C.
InventorsAndrew Kirby, Andreas Gnirke, Brendan Blumenstiel, Matthew Defelice, Mark Daly
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Abstract
The present invention features a highly sensitive assay for detecting frameshift mutations for high throughput use. Also provided herein are methods for diagnosing or determining a predisposition for developing medullary cystic kidney disease type 1 (MCKD1) in a subject by detecting a frameshift mutation in the GC-rich variable number of tandem repeats (VNTR) sequence of the mucin 1 gene (MUC-1).
Claims18
A method of treating a medullary cystic kidney disease type 1 (MCKD1) comprising detecting a point mutation resulting in insertion of a cytosine in the GC-rich variable number of tandem repeats (VNTR) sequence of the coding region of the mucin 1 gene (MUC-1) in a nucleic acid sample, wherein the presence of said point mutation indicates that the subject has or is predisposed to developing MCKD1;
- said method comprising:
- a. performing an endonuclease digestion on a nucleic acid sample;
- wherein said endonuclease selectively cleaves a wild-type MUC-1 nucleic acid sequence and not a mutant MUC-1 sequence having a cytosine insertion in the GC-rich variable number of tandem repeats (VNTR) region to produce a first plurality of nucleic acid fragments;
- b. performing a PCR reaction on said first plurality of nucleic acid fragments to produce a plurality of amplified nucleic acid products;
- c. performing a second endonuclease digestion on the plurality of amplified nucleic acid products, wherein said endonuclease selectively cleaves a wild-type MUC-1 nucleic acid sequence and not a mutant MUC-1 sequence having a cytosine insertion in the GC-rich variable number of tandem repeats (VNTR) region to produce a second plurality of nucleic acid fragments;
- d. performing a probe extension reaction on said second plurality of nucleic acid fragments using a probe that specifically binds upstream of the cytosine insertion to produce a plurality of reaction products;
- and
- e. measuring the mass or size of the reaction product and calculating the difference in mass or size from the wild type sequence, thereby determining a cytosine insertion in the GC-rich variable number of tandem repeats (VNTR) sequence of the coding region of the mucin 1 gene (MUC-1), and,
- f. administering to a subject in need thereof a MUC-1 inhibitor, wherein the MUC-1 inhibitor is a MUC-1 nucleic acid, a MUC-1 specific short-interfering RNA, a MUC-1 specific ribozyme, a MUC-1 specific peptide inhibitor or a MUC-1 specific small molecule, wherein the MUC-1 inhibitor reduces MUC-1 production in a target cell.
A method of treating a medullary cystic kidney disease type 1 (MCKD 1) comprising
- detecting a point mutation resulting in insertion of a cytosine in the GC-rich variable number of tandem repeats (VNTR) sequence of the coding region of the mucin 1 gene (MUC-1) in a nucleic acid sample, wherein the presence of said point mutation indicates that the subject has or is predisposed to developing MCKD1 and
- administering to a subject in need thereof a MUC-1 inhibitor, wherein the MUC-1 inhibitor is a MUC-1 nucleic acid, a MUC-1 specific short-interfering RNA, a MUC-1 specific ribozyme, a MUC-1 specific peptide inhibitor or a MUC-1 specific small molecule,
- wherein the MUC-1 inhibitor reduces MUC-1 production in a target cell.
Dependencies are inferred from the claim text.