Patent ID: 9181590
Filing Date: 2015-11-10
Classification: C12Q

Abstract:
1. A method for assessing the prognosis of a subject receiving therapeutic treatment for a solid tumor based on the relative quantity of and/or degree of clonality of tumor infiltrating lymphocytes in said solid tumor comprising: a) obtaining a first sample from a solid tumor from a subject at a time point prior to therapeutic treatment and a second sample from the solid tumor from a subject at a time point after to therapeutic treatment; b) extracting DNA from said first and second samples; c) amplifying in a multiplex PCR reaction substantially all rearranged TCR or Ig CDR3 encoding regions present in said sample samples 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, 843-879 and a plurality of said J segment oligonucleotide primers comprising sequences selected from the group consisting of 53-63, 65, 215-220, 247, 638-639, 696-697 and 699-701 to produce a plurality of rearranged DNA amplicons; d) sequencing said plurality of rearranged DNA amplicons using high throughput single molecule sequencing to produce a plurality of sequence reads; and, e) determining the relative quantity of and/or degree of clonality of said plurality of sequence reads in step (d) thereby determining the relative quantity of and/or degree of clonality of tumor infiltrating lymphocytes in the first sample and the second sample wherein the relative quantity number of and/or degree of clonality of tumor infiltrating lymphocytes is an assessment of prognosis of a subject receiving therapeutic treatment for a solid tumor.