A method for identifying co-occurrence of nucleic acid segments in a nucleic acid sample from a specimen, the method comprising: obtaining a nucleic acid sample from a specimen, wherein the specimen comprises target immune cells, and wherein the nucleic acid sample comprises a plurality of nucleic acid fragments associated with expression of an antigen receptor molecule in the specimen; determining sequences of first and second nucleic acid segments in the nucleic acid fragments of the sample to generate a first set of sequences corresponding to the first nucleic acid segment and a second set of sequences corresponding to the second nucleic acid in the sample, wherein the first and second nucleic acid segments are coding segments of the antigen receptor molecule; generating a first set of probes from the first set of sequences, wherein each member of the first set of probes comprises an oligonucleotide corresponding to a different one of the first set of sequences linked to a detection moiety; generating a second set of probes from the second set of sequences, wherein each member of the second set of probes comprises an oligonucleotide corresponding to a different one of the second set of sequences linked to a detection moiety; exposing a detection sample obtained from the specimen to a member of the first set of probes and a member of the second set of probes; performing a hybridization analysis to determine whether the member of the first set of probes hybridizes to the detection sample, and to determine whether the member of the second set of probes hybridizes to the detection sample; and determining whether the first and second nucleic acid segments co-occur in a common cell of the target immune cells of the specimen. obtaining a nucleic acid sample from a specimen, wherein the specimen comprises target immune cells, and wherein the nucleic acid sample comprises a plurality of nucleic acid fragments associated with expression of an antigen receptor molecule in the specimen; determining sequences of first and second nucleic acid segments in the nucleic acid fragments of the sample to generate a first set of sequences corresponding to the first nucleic acid segment and a second set of sequences corresponding to the second nucleic acid in the sample, wherein the first and second nucleic acid segments are coding segments of the antigen receptor molecule; generating a first set of probes from the first set of sequences, wherein each member of the first set of probes comprises an oligonucleotide corresponding to a different one of the first set of sequences linked to a detection moiety; generating a second set of probes from the second set of sequences, wherein each member of the second set of probes comprises an oligonucleotide corresponding to a different one of the second set of sequences linked to a detection moiety; exposing a detection sample obtained from the specimen to a member of the first set of probes and a member of the second set of probes; performing a hybridization analysis to determine whether the member of the first set of probes hybridizes to the detection sample, and to determine whether the member of the second set of probes hybridizes to the detection sample; and determining whether the first and second nucleic acid segments co-occur in a common cell of the target immune cells of the specimen.