| CPC C12Q 1/6841 (2013.01) [C12Q 1/6806 (2013.01); C12Q 1/6844 (2013.01); C12Q 2600/16 (2013.01)] | 30 Claims |
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1. A method of determining mislocalization of a nucleic acid within a tissue sample, the method comprising:
(a) obtaining a first image of the tissue sample, wherein the tissue sample is stained with a biomarker that is specific for a second analyte having colocalized expression with the nucleic acid;
(b) hybridizing the nucleic acid to a capture domain of a capture probe on an array, wherein the array comprises a plurality of capture probes, wherein the plurality of capture probes comprise a capture domain;
(c) extending the capture probe using the nucleic acid as a template, thereby generating an extended capture probe on the array;
(d) hybridizing a padlock probe or a snail probe to the extended capture probe on the array;
(e) circularizing the padlock probe or the snail probe on the array;
(f) amplifying the padlock probe or the snail probe on the array, thereby generating an amplified circularized padlock probe or an amplified circularized snail probe on the array;
(g) hybridizing a plurality of detection probes to the amplified circularized padlock probe or the amplified circularized snail probe on the array, wherein a detection probe from the plurality of detection probes comprises:
a nucleic acid sequence that is substantially complementary to a sequence of the padlock probe or the snail probe, and
a detectable label;
(h) obtaining a second image of the tissue sample and detecting a signal intensity from the plurality of detection probes in the second image; and
(i) determining mislocalization of the nucleic acid within the tissue sample by comparing detection of the biomarker in the first image to the signal intensity of the detectable label in the second image.
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