Patent Document ID: 20150167080
Application ID: 13196885
Patent Flag: 0

Claim One:
1. A method of determining clonotypes of an immune repertoire, said method comprising the steps: obtaining from a subject a sample comprising T-cells and/or B-cells; spatially isolating on a solid surface individual molecules of recombined nucleic acids encoding T cell receptor molecules or immunoglobulin molecules from said T-cells and/or B-cells of the sample; sequencing by synthesis using reversibly terminated labeled nucleotides said spatially isolated individual molecules of recombined nucleic acids to generate a set of sequence reads, said molecules of recombined nucleic acids each having a V region, an NDN region and a J region, wherein clonotypes are formed from said set of sequence reads by: (a) constructing from sequence reads encompassing at least a portion of an NDN region a sequence tree having leaves representing candidate clonotypes, each leaf and its corresponding candidate clonotype having a frequency; (b) coalescing with a highest frequency candidate clonotype any lesser frequency candidate clonotype whenever a lesser frequency of said lesser frequency candidate clonotype is below a predetermined frequency value and a sequence difference therebetween is below a predetermined difference value to form a clonotype having a sequence of said highest frequency candidate clonotype and having associated sequence reads summed from said highest frequency candidate clonotype and said lesser frequency candidate clonotype; (c) removing leaves corresponding to said coalesced candidate clonotypes from said sequence tree; and (d)repeating steps (b) and (c) until a highest frequency of a lesser frequency candidate clonotype is below a predetermined stopping value, thereby determining clonotypes from said sample.