Methods for producing high-fidelity autologous idiotype vaccines
Inventors
Santos, Carlos F. • McCord, Amy M. • HIRSCHEL, Mark
Assignees
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Publication Number
US-9725768-B2
Publication Date
2017-08-08
Expiration Date
Abstract
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.
Core Innovation
The invention provides a method for selecting an idiotype vaccine for treatment of a B-cell derived malignancy in a subject by matching a selected clone’s tumor identifying region to the dominant tumor cell sample reads. The method obtains isolated nucleic acid from a tumor cell sample, amplifies a tumor identifying region characteristic of the tumor cell sample, and sequences the tumor cell sample amplicons to generate tumor cell sample reads representing sequences present in the tumor cell sample.
Potential idiotype-secreting clones are produced from the tumor cell sample, and nucleic acid from one or more of the clones is isolated and amplified to generate a potential idiotype-secreting clone amplicon pool. The amplicon pool is sequenced to produce potential idiotype-secreting clone reads, and a quantity of each sequence read from the tumor cell sample reads is determined.
The potential idiotype-secreting clone reads are aligned with the most abundant tumor cell sample reads, and one or more clones are selected such that the selected clone(s) has the same or substantially similar tumor identifying region as the most abundant tumor cell sample reads. In embodiments described in the document, the tumor identifying region includes immunoglobulin-defined regions such as IgH CDR3 and rearranged VDJ/VJ-like regions, with selection updated over time to account for clonality and tumor identifying region mutants that appear during longitudinal monitoring.
Claims Coverage
The document includes two independent methods for selecting an idiotype vaccine for a B-cell derived malignancy by sequencing and aligning tumor-identifying-region reads, then selecting clones whose tumor identifying region matches the most abundant tumor reads. Across the independent claims, the inventive workflow centers on sequencing tumor cell sample amplicons and comparing clone-derived reads to dominant tumor reads to select same or substantially similar tumor identifying regions.
Sequencing tumor identifying region and selecting matching clone(s) by dominant reads
Obtaining isolated nucleic acid from a tumor cell sample; amplifying at least a portion of a tumor identifying region to produce tumor cell sample amplicons; sequencing the tumor cell sample amplicons to generate tumor cell sample reads representing sequences of the tumor identifying region present in the tumor cell sample; producing a plurality of potential idiotype-secreting clones representing clonal populations harboring the tumor identifying region; isolating nucleic acid from one or more potential idiotype-secreting clones; amplifying the tumor identifying region to produce a potential idiotype-secreting clone amplicon pool; sequencing the amplicon pool to generate potential idiotype-secreting clone reads; determining a quantity of each sequence read from the tumor cell sample reads; aligning the potential idiotype-secreting clone reads with the most abundant tumor cell sample reads; and selecting one or more potential idiotype-secreting clones having the same or substantially similar tumor identifying region as the most abundant tumor cell sample reads.
Aligning clone reads to reference and selecting matching clone(s) by dominant reads
Sequencing amplicons that collectively span a tumor identifying region of a tumor cell sample to produce tumor cell sample reads; aligning the tumor cell sample reads to reference sequences; producing a plurality of potential idiotype-secreting clones representing clonal populations harboring the tumor identifying region; isolating nucleic acid from one or more potential idiotype-secreting clones; amplifying the tumor identifying region of the potential idiotype-secreting clones nucleic acid sample to produce a potential idiotype-secreting clone amplicon pool; sequencing the amplicons to generate potential idiotype-secreting clone reads; determining a quantity of each sequence read from the tumor cell sample reads; aligning the potential idiotype-secreting clone reads with the most abundant tumor cell sample reads; and selecting one or more potential idiotype-secreting clones having the same or substantially similar tumor identifying region as the most abundant tumor cell sample reads.
Both independent claims converge on selecting idiotype-secreting clones by sequencing a tumor identifying region from tumor cell sample amplicons, sequencing corresponding clone-derived amplicons, determining abundance, aligning clone reads to the most abundant tumor cell sample reads, and selecting clones whose tumor identifying region is the same or substantially similar to the dominant tumor reads.
Stated Advantages
Improved disease-free survival is described in the document in the context of an example trial in follicular lymphoma.
Documented Applications
A method is described for selecting and using an autologous idiotype vaccine for treatment of a B-cell derived malignancy, including an example in follicular lymphoma with improved disease-free survival.
Longitudinal monitoring of clonal evolution is described, where updated idiotype vaccines incorporate tumor identifying region mutants and newly appearing sequences.
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