METHODS FOR PRODUCING HIGH-FIDELITY AUTOLOGOUS IDIOTYPE VACCINES

摘要

The present invention concerns methods for selecting and producing idiotype vaccines, and in particular methods for selecting and producing an idiotype vaccine for treatment of a B-cell derived malignancy in a subject based on the clonal profile (clonotype) of the malignancy; a method for producing an updated idiotype vaccine matched to a B-cell derived malignancy exhibiting a shifting clonal profile; and the high-fidelity idiotype vaccines produced using the methods. The invention also includes idiotype vaccines produced using the described methods and methods of treating B-cell derived malignancies using the produced vaccines.

主权项

1. A method for selecting an idiotype vaccine for treatment of a B-cell derived malignancy in a subject, comprising:
(a) obtaining isolated nucleic acid from a cell sample comprising one or more cells of the B-cell derived malignancy (the “tumor cell sample”); (b) amplifying at least a portion of the genomic region of the one or more cells that is characteristic of the tumor cell sample (the “tumor identifying region”), resulting in amplicons that collectively span the tumor identifying region (the “tumor cell sample amplicons”); (c) sequencing the tumor cell sample amplicons, resulting in reads (the “tumor cell sample reads”) that are a quantity of sequences representative of the nucleic acid sequences of the tumor identifying region present in the tumor cell sample; (d) optionally, aligning the tumor cell sample reads to reference sequences (or to the potential idiotype-secreting clones (e.g., hybridoma) if using VDJ spanning primers); (e) producing a plurality of clones from the tumor cell sample (“potential idiotype-secreting clones”), wherein each clone is representative of one clonal population of B-cells harboring the tumor identifying region common to one clonal population of B-cells; (f) isolating nucleic acid from one or more of the potential idiotype-secreting clones (“potential idiotype secreting clones nucleic acid sample”); (g) amplifying at least a portion of the tumor identifying region of the potential idiotype secreting clones nucleic acid sample, resulting in amplicons that collectively span the tumor identifying region (“the potential idiotype secreting clone amplicon pool”); (h) sequencing the amplicons of the potential idiotype secreting clone amplicon pool, wherein the resulting reads (“potential idiotype secreting clone reads”) are a quantity of sequences representative of the nucleic acid sequences of the tumor identifying region present in the tumor cell sample; (i) optionally, aligning the tumor cell sample reads to reference sequences; (j) determining a quantity of each sequence read from the tumor cell sample reads; (k) aligning the potential idiotype secreting clone reads with the most abundant tumor cell sample reads (the number of unique sequences which comprise, e.g., greater than about 10% of the tumor cell sample reads); and (l) selecting one or more potential idiotype secreting clones from the plurality of potential idiotype secreting clones, wherein the selected clone(s) has the same or substantially similar tumor identifying region (e.g., greater than about 80% sequence identity) as the most abundant tumor cell sample reads.