Quantification of adaptive immune cell genomes in a complex mixture of cells

摘要

Compositions and methods are described for highly sensitive quantification of the relative representation of DNA from adaptive immune cells (e.g., T and/or B lymphocytes) in DNA extracted from complex mixtures of cells that include cells which are not adaptive immune cells. Included are methods for determining the relative presence in a tumor of tumor infiltrating lymphocytes (TIL), the relative presence of lymphocytes infiltrating a somatic tissue that is the target of an autoimmune disease, and the relative presence of lymphocytes infiltrating a transplanted organ.

主权项

1. A method for determining a relative quantity of tumor-infiltrating lymphocytes in a solid tumor, comprising:
(a) obtaining a sample comprising a solid tumor tissue; (b) amplifying by PCR at least 80% of all rearranged TCR or Ig CDR3-encoding regions present in said sample using a plurality of V-segment oligonucleotide primers comprising sequences selected from the group consisting of SEQ ID NOs: 1-52, 221-238, 255-260, 262-267, 269, 272, 283, 286, 291, 292, 294-297, 301-326, 330, 338, 382, 405, 447-484, 644-695, and 843-879 and a plurality of J-segment oligonucleotide primers comprising sequences selected from the group consisting of 53-63, 65, 215-220, and 247 to produce a plurality of rearranged DNA amplicons; (c) amplifying by PCR a control sequence present in said sample using a pair of control sequence primers, wherein said control sequence primers are capable of amplifying a control sequence that is not an adaptive immune receptor gene and present in all cells in said sample; (d) quantifying a number of adaptive immune receptor sequence reads in said sample generated from high-throughput sequencing (HTS) of said plurality of rearranged DNA amplicons; (e) quantifying a number of control sequence reads in said sample using said amplified control sequence; and (f) comparing said number of adaptive immune receptor sequence reads and said number of control sequence reads to estimate a relative quantity of tumor-infiltrating lymphocytes in said solid tumor.