Method of measuring adaptive immunity
A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells.
1. 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.
2. The method of claim 1 wherein the universal primer sequence is a GA2 universal primer sequence.
3. The method of claim 2 wherein the V segment primers for TCR amplification comprise SEQ ID NOS: 58-102 and the J segment primers for TCR amplification comprise SEQ ID Nos: 103-113.
4. The method of claim 1 wherein the total diversity of rearranged TCR is greater than 1×10 6 .
5. The method of claim 1 wherein sequencing in step (d) is done by reversible dye termination chemistry.
6. The method of claim 5 wherein the sequencing reads 30-54 base pair intervals.
7. The method of claim 1 wherein the sample comprises genomic DNA.
8. The method of claim 1 wherein the sample comprises cDNA.
9. The method of claim 1 wherein the biological sample is a blood sample.