Patent US10266901

a) amplifying said recombined TCR and/or IG DNA sequences in the sample by polymerase chain reaction (PCR) using a set of amplification primers, wherein said amplification primers comprise a generic primer sequence;

b) spatially isolating individual molecules of amplified recombined TCR and/or IG DNA comprising generic primer sequences;

c) amplifying the spatially isolated individual molecules of amplified recombined TCR and/or IG DNA by PCR using primers specific for the generic primer sequences wherein said primers specific for the generic primer sequence comprise a sequencing adaptor sequence;

d) sequencing said recombined TCR and/or IG DNA sequences by synthesis using reversible terminated labeled nucleotides to provide at least 1000 sequence reads each having an error rate and each comprising at least 30 base pairs so that different clonotypes of said sample are determined from sequence reads with a confidence of at least 99.9 percent based on the error rate; and

e) determining the levels of different clonotypes in the sample to generate a profile of clonotypes of recombined DNA sequences.