A method of determining a clonotype profile of recombined nucleic acids encoding a plurality of immune receptor chains in a sample, the method comprising the steps of: (a) attaching sequence tags to recombined nucleic acid molecules of T-cell receptor genes or immunoglobulin genes from a sample from an individual comprising T-cells and/or B-cells and/or cell-free DNA to form tag-nucleic acid conjugates, wherein at least one recombined nucleic acid or copies thereof have different sequence tags attached; (b) amplifying the tag-nucleic acid conjugates; (c) sequencing a sample of the tag-nucleic acid conjugates to provide sequence reads each having an error rate and each comprising a tag sequence and a recombined nucleic acid sequence; (d) aligning sequence reads having like tag sequences to form groups of sequence reads having the same sequence tags; (e) coalescing sequence reads of groups to determine clonotypes, wherein groups of sequence reads are coalesced into different recombined nucleic acid sequences whenever said groups of sequence reads are distinct with a likelihood of at least ninety-five percent; and (f) determining the clonotype profile of the sample by determining levels of the clonotypes; and wherein the steps of attaching and amplifying comprise: (i) combining in a reaction mixture under primer extension conditions a first set of primers with the sample, wherein each primer of the first set has a receptor-specific portion such that the receptor-specific portion anneals to a different recombined nucleic acid at a predetermined location and is extended to form a first extension product, and wherein each primer of the first set has a 5'-non-complementary end containing a first primer binding site and a sequence tag disposed between the receptor-specific portion and the first primer binding site; (ii) removing from the reaction mixture non-extended primers of the first set; (iii) adding to the reaction mixture under primer extension conditions a second set of primers, wherein each primer of the second set has a receptor-specific portion such that the receptor-specific portion anneals to the first extension product at a predetermined location and has a 5'-non-complementary end containing a second primer binding site, and wherein each primer of the second set is extended to form a second extension product, such that each second extension product comprises a first primer binding site, a second primer binding site, at least one sequence tag, and recombined nucleic acid encoding a portion of a T cell receptor chain or a B cell receptor chain; and (iv) performing a polymerase chain reaction in the reaction mixture to form an amplicon, the polymerase chain reaction using forward primers specific for the first primer binding site and reverse primers specific for the second primer binding site. (a) attaching sequence tags to recombined nucleic acid molecules of T-cell receptor genes or immunoglobulin genes from a sample from an individual comprising T-cells and/or B-cells and/or cell-free DNA to form tag-nucleic acid conjugates, wherein at least one recombined nucleic acid or copies thereof have different sequence tags attached; (b) amplifying the tag-nucleic acid conjugates; (c) sequencing a sample of the tag-nucleic acid conjugates to provide sequence reads each having an error rate and each comprising a tag sequence and a recombined nucleic acid sequence; (d) aligning sequence reads having like tag sequences to form groups of sequence reads having the same sequence tags; (e) coalescing sequence reads of groups to determine clonotypes, wherein groups of sequence reads are coalesced into different recombined nucleic acid sequences whenever said groups of sequence reads are distinct with a likelihood of at least ninety-five percent; and (f) determining the clonotype profile of the sample by determining levels of the clonotypes; (i) combining in a reaction mixture under primer extension conditions a first set of primers with the sample, wherein each primer of the first set has a receptor-specific portion such that the receptor-specific portion anneals to a different recombined nucleic acid at a predetermined location and is extended to form a first extension product, and wherein each primer of the first set has a 5'-non-complementary end containing a first primer binding site and a sequence tag disposed between the receptor-specific portion and the first primer binding site; (ii) removing from the reaction mixture non-extended primers of the first set; (iii) adding to the reaction mixture under primer extension conditions a second set of primers, wherein each primer of the second set has a receptor-specific portion such that the receptor-specific portion anneals to the first extension product at a predetermined location and has a 5'-non-complementary end containing a second primer binding site, and wherein each primer of the second set is extended to form a second extension product, such that each second extension product comprises a first primer binding site, a second primer binding site, at least one sequence tag, and recombined nucleic acid encoding a portion of a T cell receptor chain or a B cell receptor chain; and (iv) performing a polymerase chain reaction in the reaction mixture to form an amplicon, the polymerase chain reaction using forward primers specific for the first primer binding site and reverse primers specific for the second primer binding site.