Characterization of adaptive immune response to vaccination or infection using immunosequencing

A method of measuring T cell response to a vaccine in a subject, comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from a first biological sample of the subject at a first time point post vaccination;
• sorting activated T cells from a subset of the first biological sample using flow cytometry to generate a set of activated T cells;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from the set of activated T cells;
• and
• identifying activated T cell clones in the set having CDR3 regions of significantly higher proportional abundance in the activated T cell population in comparison to the first biological sample, thereby identifying vaccine-induced responsive clones.

A method for determining the effectiveness of a vaccine comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from a first biological sample of the subject at a first time point prior to vaccination;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from a second biological sample of the subject at a second time point post vaccination;
• identifying T cell clones having CDR3 regions of significantly higher proportional abundance in the second biological sample in comparison to the first biological sample, thereby identifying vaccine-induced responsive clones;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from a third biological sample of the subject at a third time point post vaccination;
• identifying newly recruited memory T cell clones corresponding to the vaccine-induced responsive clones that have been recruited to a memory T cell population post vaccination;
• and
• comparing a degree of recruitment of vaccine-induced responsive clones to immunological memory to a reference degree of recruitment, wherein the vaccine is effective when the degree of recruitment is greater than or equal to the reference degree of recruitment.

A method of measuring a T cell response to an infection in a subject, comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from a first biological sample of the subject at a first time point prior to infection;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from a second biological sample of the subject at a second time point after infection;
• and
• identifying T cell clones having CDR3 regions of significantly higher proportional abundance in the second biological sample in comparison to the first biological sample, thereby identifying infection-induced responsive clones.

A method of measuring a T cell response to an infection in a subject, comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from a first biological sample of the subject at a first time point post infection;
• sorting activated T cells from a subset of the first biological sample using flow cytometry to generate a set of activated T cells;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of TCR loci obtained from the set of activated T cells;
• and
• identifying activated T cell clones in the set having CDR3 regions of significantly higher proportional abundance in the activated T cell population in comparison to the first biological sample, thereby identifying infection-induced responsive clones.

A method for measuring B cell response to a vaccine in a subject, comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of immunoglobulin (Ig) loci obtained from a first biological sample of the subject at a first time point prior to vaccination;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from a second biological sample of the subject at a second time point post vaccination;
• clustering groups of CDR3 sequences of common descent comprising clones having undergone somatic hypermutation, wherein said clustering employs a clustering algorithm using a string distance metric;
• and
• identifying B cell clones having CDR3 sequence clusters of significantly higher proportional abundance in the second biological sample in comparison to the first biological sample, thereby identifying vaccine-induced responsive clones.

A method of measuring B cell response to a vaccine in a subject, comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from a first biological sample of the subject at a first time point post vaccination;
• sorting activated B cells from a subset of the first biological sample using flow cytometry to generate a set of activated B cells;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from the set of activated B cells;
• clustering groups of CDR3 sequences of common descent comprising clones having undergone somatic hypermutation, wherein said clustering employs a clustering algorithm using a string distance metric;
• and
• identifying activated B cell clones in the set having CDR3 sequence clusters of significantly higher proportional abundance in the activated B cell population in comparison to the first biological sample, thereby identifying vaccine-induced responsive clones.

A method for determining the effectiveness of a vaccine comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of immunoglobulin (Ig) loci obtained from a first biological sample of the subject at a first time point prior to vaccination;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from a second biological sample of the subject at a second time point post vaccination;
• clustering groups of CDR3 sequences of common descent comprising clones having undergone somatic hypermutation, wherein said clustering employs a clustering algorithm using a string distance metric;
• and
• identifying B cell clones having CDR3 sequence clusters of significantly higher proportional abundance in the second biological sample in comparison to the first biological sample, thereby identifying vaccine-induced responsive clones;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from a third biological sample of the subject at a third time point post vaccination;
• identifying newly recruited memory B cell clones corresponding to the vaccine-induced responsive clones that are not present in the first biological sample and have been recruited to a memory B cell population post vaccination;
• and
• comparing a degree of recruitment of vaccine-induced responsive clones to immunological memory to a reference degree of recruitment, wherein the vaccine is effective when the degree of recruitment is greater than or equal to the reference degree of recruitment.

A method of measuring a B cell response to an infection in a subject, comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of immunoglobulin (Ig) loci obtained from a first biological sample of the subject at a first time point prior to infection;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from a second biological sample of the subject at a second time point post infection;
• clustering groups of CDR3 sequences of common descent comprising clones having undergone somatic hypermutation, wherein said clustering employs a clustering algorithm using a string distance metric;
• and
• identifying B cell clones having CDR3 sequence clusters of significantly higher proportional abundance in the second biological sample in comparison to the first biological sample, thereby identifying vaccine-induced responsive clones.

A method of measuring B cell response to an acute viral infection in a subject, comprising:

• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from a first biological sample of the subject at a first time point post infection;
• sorting activated B cells from a subset of the first biological sample using flow cytometry to generate a set of activated B cells;
• performing high-throughput sequencing of nucleic acid molecules comprising rearranged CDR3 regions of Ig loci obtained from the set of activated B cells;
• clustering groups of CDR3 sequences of common descent comprising clones having undergone somatic hypermutation, wherein said clustering employs a clustering algorithm using a string distance metric;
• and
• identifying activated B cell clones having CDR3 sequence clusters of significantly higher proportional abundance in the activated B cell population in comparison to the first biological sample, thereby identifying infection-induced responsive clones.