Detection of Neighboring Variants

摘要

The present invention relates to methods, kits, probes, and systems for distinguishing between nucleotide variants that are close in proximity on a gene. The methods, kits, probes, and systems can include the use of a small amplicon assay in combination with two unlabeled probes in a high resolution thermal melting analysis of a biological sample containing a locus of interest in order to discern between disease-causing and benign variants that are close in proximity on a gene within the biological sample. The present invention also relates to method of detecting a disease in a patient based on the patient's genotype by determining whether the patient has a disease-causing variant at a locus of interest. The signature melt curves produced by the unlabeled probe tests can be analyzed using HRMA software to distinguish between disease-causing and benign variants that are close in proximity on a gene within the biological sample.

主权项

1. A method of distinguishing between at least two nearby neighbor variants on a nucleic acid having a locus of interest comprising:
(a) providing a first aliquot of said nucleic acid having a locus of interest; (b) incubating said first aliquot of said nucleic acid with a limiting primer, an excess primer, and a first probe that is designed to hybridize to said locus of interest on a target strand of said nucleic acid; (c) performing asymmetric PCR using said first aliquot to produce an excess of amplicons corresponding to the target strand to which the first probe hybridizes, thereby producing a first probe element; (d) providing a second aliquot of said nucleic acid target having a locus of interest; (e) incubating said second aliquot of said nucleic acid target with said limiting primer, said excess primer, and a second probe that is designed to hybridize to said locus of interest on the target strand, wherein said first probe differs in sequence from said second probe; (f) performing asymmetric PCR using said second aliquot to produce an excess of amplicons corresponding to the target strand to which the second probe hybridizes, thereby producing a second probe element; (g) generating a first melting curve for the first probe element in a first mixture with a saturating binding dye by measuring fluorescence from said dye as the first mixture is heated; (h) generating a second melting curve for the second probe element in a second mixture with said saturating binding dye by measuring fluorescence from said dye as the second mixture is heated; and (i) analyzing said first melting curve and said second melting curve to distinguish between said at least two nearby neighbor variants, wherein a melting signature curve of each of said at least two nearby neighbor variants is different in said first and second melting curves.