Method of sequence determination using sequence tags

A method of determining clonotypes of an immune repertoire, the method comprising the steps:

• (a) labeling by sampling molecules from T-cells and/or B-cells from a sample comprising T-cells and/or B-cells to form tag-molecule conjugates, wherein each tag has a sequence and each molecule comprises a clonotype comprising a recombined nucleic acid from a T-cell receptor gene or an immunoglobulin gene;
• (b) sequencing by synthesis the tag-molecule conjugates to produce sequence reads comprising at least 1000 clonotypes per run, wherein each sequence read comprises a sequence tag portion and a clonotype portion;
• (c) grouping the sequence reads having like tags to align sequence reads from like clonotypes;
• and
• (d) determining a nucleotide sequence of each clonotype from the aligned sequence reads of like tags.

A method of determining nucleotide sequences of one or more polynucleotides in one or more sequencing-by-synthesis reactions, the method comprising the steps:

• (a) attaching a sequence tag to each of the one or more polynucleotides to form tag-polynucleotide conjugates, wherein substantially every polynucleotide of the tag-polynucleotide conjugates has a unique sequence tag;
• (b) amplifying the tag-polynucleotide conjugates;
• (c) sequencing by synthesis amplified tag-polynucleotide conjugates to produce sequence reads comprising at least 1000 clonotypes per run, wherein sequencing by synthesis comprises exposing templates of amplified tag-polynucleotide conjugates to at least one dNTP flow to produce a sequence of incorporation signals for each template;
• (d) aligning sequences of incorporation signals from like tag-polynucleotide conjugates by their sequence tags;
• and
• (e) determining for each tag-polynucleotide conjugate having the same sequence tag a number of nucleotide incorporations for each dNTP flow as a function of measured incorporation signals for each such dNTP flow.