Method of measuring adaptive immunity

A method for generating a clonotype profile of rearranged T cell receptor (TCR) and/or immunoglobulins (Ig) in a biological sample comprising:

• (a) combining a plurality of V segment primers and a plurality of J segment primers with DNA from a biological sample comprising T cells and/or B cells wherein the V segment primers for TCR amplification comprise the primers of SEQ ID Nos:
• 1-45, the J segment primers for TCR amplification comprise the primers of SEQ ID Nos:
• 46-57, the V segment primers for Ig amplification comprise the primers of SEQ ID Nos:443-451 and the J segment primers for amplification of Ig comprise the primers of SEQ ID Nos:
• 452-467, wherein the terminal “n” position in SEQ ID NO:
• 1-45 and SEQ ID Nos:
• 46-57 comprises a universal primer sequence, and wherein SEQ ID Nos:443-451 and SEQ ID Nos:
• 452-467 comprise a universal primer sequence;
• (b) amplifying rearranged TCR and/or Ig using the plurality of V segment primers and J segment primers in a multiplex polymerase chain reaction (PCR) to produce amplified rearranged TCR and/or Ig DNA molecules;
• (c) immobilizing said amplified rearranged TCR and/or Ig DNA molecules on a solid surface and performing solid phase PCR to form template clusters on the solid surface;
• and
• (d) sequencing the TCR and/or Ig DNA molecules in the template clusters to produce sequence reads that encompasses a CDR3 encoding region of the TCR and/or Ig thereby generating a clonotype profile TCRs and/or Igs in the biological sample.