A method of in situ detection of a nucleotide variation of a target nucleic acid in a sample of fixed and permeabilized cells, comprising: contacting the sample with a nucleotide variation probe and a neighbor probe, wherein the SP comprises a target anchor segment (SPAT) that can specifically hybridize to a region of the target nucleic acid comprising the nucleotide variation and a pre-amplifier anchor segment (SPAP), and wherein the NP comprises a target anchor segment (NPAT) that can hybridize to a region of the target nucleic acid adjacent to the binding site of the SP and a pre-amplifier anchor segment (NPAP); contacting the sample with an SP pre-amplifier and an NP pre-amplifier, wherein the SPM comprises a segment that can bind to the SP and comprises two or more SP collaboration anchors (SPCAs), and wherein the NPM comprises a segment that can bind to the NP and comprises two or more NP collaboration anchors (NPCAs); contacting the sample with a collaboration amplifier, wherein the COM comprises a first segment complementary to the SPCA, a second segment complementary to the NPCA, and a third segment comprising a plurality of label amplifier anchor segments; contacting the sample with a label probe system, wherein the LPS comprises a plurality of label amplifiers (LMs) and a plurality of label probes (LPs), wherein each LM comprises a segment that can bind to a label amplifier anchor segment of the COM and a plurality of label probe anchor segments, wherein each LP comprises a detectable label and a segment that hybridizes to the label probe anchor segment of LM, wherein the aforesaid hybridizations form a signal generating complex comprising a target nucleic acid with the nucleotide variation, an SP, an NP, an SPM, an NPM, a plurality of COMs, a plurality of LMs, and a plurality of LPs; and detecting in situ signal from the SGC on the sample. contacting the sample with a nucleotide variation probe and a neighbor probe, wherein the SP comprises a target anchor segment (SPAT) that can specifically hybridize to a region of the target nucleic acid comprising the nucleotide variation and a pre-amplifier anchor segment (SPAP), and wherein the NP comprises a target anchor segment (NPAT) that can hybridize to a region of the target nucleic acid adjacent to the binding site of the SP and a pre-amplifier anchor segment (NPAP); contacting the sample with an SP pre-amplifier and an NP pre-amplifier, wherein the SPM comprises a segment that can bind to the SP and comprises two or more SP collaboration anchors (SPCAs), and wherein the NPM comprises a segment that can bind to the NP and comprises two or more NP collaboration anchors (NPCAs); contacting the sample with a collaboration amplifier, wherein the COM comprises a first segment complementary to the SPCA, a second segment complementary to the NPCA, and a third segment comprising a plurality of label amplifier anchor segments; contacting the sample with a label probe system, wherein the LPS comprises a plurality of label amplifiers (LMs) and a plurality of label probes (LPs), wherein each LM comprises a segment that can bind to a label amplifier anchor segment of the COM and a plurality of label probe anchor segments, wherein each LP comprises a detectable label and a segment that hybridizes to the label probe anchor segment of LM, wherein the aforesaid hybridizations form a signal generating complex comprising a target nucleic acid with the nucleotide variation, an SP, an NP, an SPM, an NPM, a plurality of COMs, a plurality of LMs, and a plurality of LPs; and detecting in situ signal from the SGC on the sample.