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US20160002731A1 - Immunocompetence assessment by adaptive immune receptor diversity and clonality characterization - Google Patents

Immunocompetence assessment by adaptive immune receptor diversity and clonality characterization Download PDF

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US20160002731A1
US20160002731A1 US14/432,738 US201314432738A US2016002731A1 US 20160002731 A1 US20160002731 A1 US 20160002731A1 US 201314432738 A US201314432738 A US 201314432738A US 2016002731 A1 US2016002731 A1 US 2016002731A1
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immunotherapy
air
tcr
polypeptide
test subject
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Harlan S. Robins
Julie Rubinstein
Ryan Emerson
Jianda Yuan
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Memorial Sloan Kettering Cancer Center
Adaptive Biotechnologies Corp
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Memorial Sloan Kettering Cancer Center
Adaptive Biotechnologies Corp
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Assigned to MEMORIAL SLOAN-KETTERING CANCER CENTER reassignment MEMORIAL SLOAN-KETTERING CANCER CENTER ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: YUAN, Jianda
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    • G—PHYSICS
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    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • G06F19/22—
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
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    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays
    • G06F19/12—
    • G—PHYSICS
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    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search

Definitions

  • the present disclosure relates generally to assessment of immunocompetence of a subject's adaptive immune system by highly sensitive, high throughput DNA sequence-based quantification of the diversity and frequency of occurrence (e.g., clonal expansion) of adaptive immune cells having a particular rearranged T cell receptor (TCR) or immunoglobulin (IG or Ig) encoding gene sequence.
  • Information about the immunological status of a subject or a population of subjects can be used, for example, to characterize an individual or to stratify a patient population with respect to ability to mount an immune response or likelihood of responding to immunotherapy or the likelihood of developing an immune-mediated side effect in response to said therapy, or to otherwise inform a course of clinical immunotherapy management.
  • the adaptive immune system protects higher organisms against infections and other pathological events that can be attributable to foreign substances, using adaptive immune receptors, the antigen-specific recognition proteins that are expressed by hematopoietic cells of the lymphoid lineage and that are capable of distinguishing self from non-self molecules in the host.
  • lymphocytes can be found in the circulation and tissues of a host, and their recirculation between blood and the lymphatics has been described, including their extravasation via lymph node high endothelial venules, as well as at sites of infection, inflammation, tissue injury and other clinical insults.
  • the dynamic nature of movement by lymphocytes throughout a host organism is reflected in changes in the qualitative (e.g., antigen-specificity of the clonally expressed adaptive immune receptor (immunoglobulin or T cell receptor), T cell versus B cell, T helper (T h ) cell versus T regulatory (T reg ) cell, effector T cell versus memory T cell, etc.) and quantitative distribution of lymphocytes among tissues, as a function of changes in host immune status.
  • T cell receptor immunoglobulin or T cell receptor
  • T cell versus B cell T helper (T h ) cell versus T regulatory (T reg ) cell
  • T reg T regulatory
  • effector T cell versus memory T cell etc.
  • the adaptive immune system employs several strategies to generate a repertoire of T- and B-cell antigen receptors with sufficient diversity to recognize the universe of potential pathogens.
  • B lymphocytes mature to express antibodies (immunoglobulins, Igs) that occur as heterodimers of a heavy (H) and light (L) chain polypeptide, while T lymphocytes express heterodimeric T cell receptors (TCR).
  • TCR T cell antigen receptor
  • TCR T cell antigen receptor
  • the proteins that make up these chains are encoded by DNA that employs a unique mechanism for generating the tremendous diversity of the TCR.
  • This multi-subunit immune recognition receptor associates with the CD3 complex and binds to peptides presented by the major histocompatibility complex (MHC) class I and II proteins on the surface of antigen-presenting cells (APCs). Binding of TCR to the antigenic peptide on the APC is a central event in T cell activation, which occurs at an immunological synapse at the point of contact between the T cell and the APC.
  • MHC major histocompatibility complex
  • APCs antigen-presenting cells
  • Each TCR peptide contains variable complementarity determining regions (CDRs), as well as framework regions (FRs) and a constant region.
  • CDRs variable complementarity determining regions
  • FRs framework regions
  • the sequence diversity of ⁇ T cells is largely determined by the amino acid sequence of the third complementarity-determining region (CDR3) loops of the ⁇ and ⁇ chain variable domains, which diversity is a result of recombination between variable (V ⁇ ), diversity (D ⁇ ), and joining (J ⁇ ) gene segments in the ⁇ chain locus, and between analogous V ⁇ and J ⁇ gene segments in the a chain locus, respectively.
  • V ⁇ variable
  • D ⁇ diversity
  • J ⁇ joining
  • CDR3 sequence diversity is further increased by deletion and template-independent addition of nucleotides at the V ⁇ -D ⁇ , D ⁇ -J ⁇ , and V ⁇ -J ⁇ junctions during the process of TCR gene rearrangement.
  • immunocompetence is reflected in the diversity of TCRs.
  • the ⁇ TCR is distinctive from the ⁇ TCR in that it encodes a receptor that interacts closely with the innate immune system.
  • TCR ⁇ is expressed early in development, has specialized anatomical distribution, has unique pathogen and small-molecule specificities, and has a broad spectrum of innate and adaptive cellular interactions.
  • a biased pattern of TCR ⁇ V and J segment expression is established early in ontogeny as the restricted subsets of TCR ⁇ cells populate the mouth, skin, gut, vagina, and lungs prenatally. Consequently, the diverse TCR ⁇ repertoire in adult tissues is the result of extensive peripheral expansion following stimulation by environmental exposure to pathogens and toxic molecules.
  • Igs expressed by B cells are proteins consisting of four polypeptide chains, two heavy chains (H chains) and two light chains (L chains), forming an H 2 L 2 structure.
  • Each pair of H and L chains contains a hypervariable domain, consisting of a V L and a V H region, and a constant domain.
  • the H chains of Igs are of several types, ⁇ , ⁇ , ⁇ , and ⁇ .
  • the diversity of Igs within an individual is mainly determined by the hypervariable domain.
  • the V domain of H chains is created by the combinatorial joining of the V H , D H , and J H gene segments.
  • Hypervariable domain sequence diversity is further increased by deletion and template-independent addition of nucleotides at the V H -D H , D H -J H , and V H -J H junctions during the process of Ig gene rearrangement. In this respect, immunocompetence is reflected in the diversity of Igs.
  • adaptive immune cells Quantitative characterization of adaptive immune cells based on the presence in such cells of functionally rearranged Ig and TCR encoding genes that direct productive expression of adaptive immune receptors has been achieved using biological samples from which adaptive immune cells can be readily isolated in significant numbers, such as blood, lymph or other biological fluids. In these samples, adaptive immune cells occur as particles in fluid suspension. See, e.g., US 2010/0330571; see also, e.g., Murphy, Janeway's Immunobiology (8 th Ed.), 2011 Garland Science, NY, Appendix I, pp. 717-762.
  • the adaptive immune system has long been implicated as having a role in the recognition of cancer cells, and in the ensuing generation of an immune response to eliminate tumors (e.g., Murphy, Janeway's Immunobiology (8 th Ed.), 2011 Garland Science, NY, pp. 682-697; Pandolfi et al., 2011 Clin. Dev. Immunol. Article ID894704; Draghiciu et al., 2011 Clin. Dev. Immunol. Article ID439053).
  • cancer immunotherapy by which efforts are made to induce, recruit, enhance or otherwise potentiate the adaptive immune response, in this context, by encouraging anti-tumor immunity.
  • Such immunotherapeutic approaches represent preferable alternatives to conventional cancer therapies, that can be non-cancer cell-specific and can involve harsh cytotoxic regimens such as radiation and chemotherapy.
  • Cancer immunotherapy is sometimes administered to patients who also receive chemotherapy and/or radiation therapy, but because chemotherapy and radiation are particularly cytotoxic toward dividing cells, whilst immunocyte proliferation can be a cardinal feature of many immune responses, such approaches can counterproductively compromise the adaptive immune system and thus can be accompanied by difficulties in arriving at effective therapeutic regimens.
  • a method for determining an immunological status of a test subject comprising obtaining nucleic acid sequence information generated from one or more samples comprising nucleic acids from lymphoid cells of said test subject, wherein said nucleic acid sequence information comprising sequences for a plurality of unique rearranged nucleic acid sequences, each of said plurality of unique rearranged nucleic acid sequences encoding an AIR polypeptide, said one or more samples obtained from said test subject at one or more time points for said one or more samples, using said nucleic acid sequence information, determining a total number of observed rearranged sequences in said sample; determining a total number of unique rearranged DNA sequences in said sample; quantifying an AIR sequence diversity score for said one or more samples based on said total number of unique rearranged DNA sequences; quantifying an AIR sequence distribution score for said one or more samples by calculating a frequency of occurrence of each unique rearranged DNA sequence as a percentage of said total number of observed
  • the method includes comparing said test subject rating scores for said one or more samples to a second set of control subject rating scores obtained from samples from a control subject and determining said immunological status of said test subject at said one or more time points, wherein said test subject is determined to have a immunological status at said one or more time points that is different from an immunological status of said control subject, if a difference between said test subject rating score and said control subject rating score is statistically significant and wherein said test subject is determined to have the same immunological status of said control subject if there is no statistically significant difference between said test subject rating score and said control subject rating score.
  • the nucleic acids comprise genomic DNA. In other embodiments, the nucleic acids comprise cDNA. In some embodiments, the nucleic acids comprise messenger RNA.
  • the methods of the invention also include steps for quantifying an AIR sequence distribution score for said subject comprising determining a number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 50% of the total number of observed rearranged sequences in said sample; and characterizing a AIR sequence distribution score as a low score if the number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 50% of the total number of observed rearranged sequences in said sample is less than or equal to a predetermined threshold.
  • the method includes quantifying an AIR sequence distribution score for said subject comprising determining a number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 40% of the total number of observed rearranged sequences in said sample; and characterizing a AIR sequence distribution score as a low score if the number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 40% of the total number of observed rearranged sequences in said sample is less than or equal to a predetermined threshold.
  • the method includes quantifying an AIR sequence distribution score for said subject comprising determining a number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 30% of the total number of observed rearranged sequences in said sample; and characterizing a AIR sequence distribution score as a low score if the number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 30% of the total number of observed rearranged sequences in said sample is less than or equal to a predetermined threshold.
  • the method includes quantifying an AIR sequence distribution score for said subject comprising determining a number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 20% of the total number of observed rearranged sequences in said sample; and characterizing a AIR sequence distribution score as a low score if the number of unique rearranged AIR sequences that have a combined frequency of occurrence of up to 20% of the total number of observed rearranged sequences in said sample is less than or equal to a predetermined threshold.
  • the method comprises quantifying an AIR sequence distribution score comprising selecting at least one unique rearranged sequence having the highest frequency of occurrence at each time point compared with the frequency of occurrences for each of the remaining unique rearranged sequences in said sample and determining a profile of AIR sequence distribution for said at least one unique rearranged sequence over time in said test subject.
  • the method comprises selecting a plurality of the most abundant unique AIR rearranged sequence having a frequency of occurrence at each time point that is statistically significantly higher than an average frequency of occurrence for the total number of unique rearranged DNA sequences and determining a profile of AIR sequence distribution for each of said most abundant unique rearranged sequences over time in said test subject.
  • the method includes quantifying said AIR sequence diversity score comprises determining a total number of unique clones in said sample.
  • control subject has a known immunological status. In one embodiment, the control subject is a healthy subject and has an uncompromised immunological status. In another embodiment, the control subject has a compromised immunological status.
  • control subject has a known outcome of response to immunotherapy.
  • response is a positive response to immunotherapy.
  • response is a poor response to immunotherapy.
  • test subject is predicted to have the same outcome of response to immunotherapy as compared to the control subject. In yet another embodiment, test subject is predicted to have a different outcome of response to immunotherapy as compared to the control subject.
  • the control subject has a known outcome of response to a stem cell transplant.
  • the response can be a positive response to the stem cell transplant.
  • the response is a poor response to the stem cell transplant.
  • the test subject is predicted to have the same outcome of response to the stem cell transplant as compared to the control subject. In other embodiments, the test subject is predicted to have a different outcome of response to the stem cell transplant as compared to the control subject.
  • control subject has a known outcome of response to a treatment.
  • the treatment comprises an immunotherapeutic antibody, a cytokine, a hematopoietic cell transplant, an immunosuppressive agent, or a vaccine.
  • the one or more samples comprise solid tissue samples obtained from the test subject.
  • the one or more samples comprise blood samples obtained from the test subject.
  • a low AIR sequence diversity score and a low AIR sequence distribution score are characterized as a low test subject rating score and are indicative of a high TCR clonality in said test subject.
  • a low test subject rating score is predictive of a poor response to immunotherapy in said test subject.
  • a high AIR sequence diversity score and a high AIR sequence distribution score are characterized as a high test subject rating score and are indicative of a low TCR clonality.
  • a high test subject rating score is predictive of a positive response to immunotherapy in said test subject.
  • the test subject has been treated with immunotherapy.
  • the immunotherapy comprises administration of an inhibitor of a negative regulator of the immune system.
  • the negative regulator is selected from a group consisting of CTLA-4 and PD-1.
  • the negative regulator is CTLA-4.
  • the negative regulator is PD-1.
  • the inhibitor is an anti-CTLA-4 antibody.
  • the inhibitor is an anti-PD-1 antibody.
  • the one or more samples comprise solid tumor samples obtained from the test subject.
  • a high AIR sequence diversity score and a high AIR sequence distribution score are characterized as a low test subject rating score and are indicative of a low TCR clonality in said test subject.
  • a low test subject rating score is predictive of a poor response to immunotherapy.
  • a low AIR sequence diversity score and a low AIR sequence distribution score are characterized as a high test subject rating score and are indicative of a high TCR clonality.
  • a high test subject rating score is predictive of a positive response to immunotherapy in said subject.
  • the test subject has been treated with immunotherapy.
  • the immunotherapy comprises administration of an inhibitor of a negative regulator of the immune system.
  • the negative regulator is selected from a group consisting of CTLA-4 and PD-1.
  • the negative regulator can be CTLA-4.
  • the negative regulator can be PD-1.
  • the inhibitor is an anti-CTLA-4 antibody.
  • the inhibitor is an anti-PD-1 antibody.
  • the method also includes determining a side effect of an immunotherapy treatment for said test subject indicated by a clonal expansion of at least one clone that has a frequency of occurrence that is statistically significantly different from a mean frequency of occurrence of a set of remaining clones in a sample obtained after said immunotherapy treatment.
  • the set of remaining clones comprise clones each having a frequency of occurrence that is in the top 50% of the total clones in said sample.
  • the set of remaining clones comprise clones each having a frequency of occurrence that is in the top 40% of the total clones in said sample.
  • the set of remaining clones comprise clones each having a frequency of occurrence that is in the top 30% of the total clones in said sample. In other embodiments, the set of remaining clones comprise clones each having a frequency of occurrence that is in the top 20% of the total clones in said sample. In one embodiment, the set of remaining clones comprise clones each having a frequency of occurrence that is in the top 10% of the total clones in said sample. In one aspect, the at least one clone has a frequency of occurrence that is statistically significantly different from clones each having a frequency of occurrence that is in the top quartile of frequency of occurrences in said sample. In other aspects, the clonal expansion of said at least one clone is indicative of a poor response of said test subject to said immunotherapy treatment.
  • the method also includes amplifying nucleic acid sequences obtained from at least one of said samples comprising lymphoid cells of a test subject in a multiplexed polymerase chain reaction (PCR) assay using (1) a plurality of AIR V-segment oligonucleotide primers and (2) either a plurality of AIR J-segment oligonucleotide primers or a plurality of AIR C-segment oligonucleotide primers.
  • PCR polymerase chain reaction
  • the plurality of AIR V-segment oligonucleotide primers are each independently capable of specifically hybridizing to at least one polynucleotide encoding a mammalian AIR V-region polypeptide, wherein each AIR V-segment oligonucleotide primer comprises a nucleotide sequence of at least 15 contiguous nucleotides that is complementary to at least one functional AIR-encoding gene segment, wherein said plurality of AIR V-segment oligonucleotide primers specifically hybridize to substantially all functional AIR V-encoding gene segments that are present in said sample.
  • the plurality of J-segment oligonucleotide primers are each independently capable of specifically hybridizing to at least one polynucleotide encoding a mammalian AIR J-region polypeptide, wherein each J-segment primer comprises a nucleotide sequence of at least 15 contiguous nucleotides that is complementary to at least one functional AIR J-encoding gene segment, wherein said plurality of J-segment primers specifically hybridize to substantially all functional AIR J-encoding gene segments that are present in the sample.
  • the plurality of C-segment oligonucleotide primers are each independently capable of specifically hybridizing to at least one polynucleotide encoding a mammalian AIR C-region polypeptide, wherein each C-segment primer comprises a nucleotide sequence of at least 15 contiguous nucleotides that is complementary to at least one functional AIR C-encoding gene segment, wherein the plurality of C-segment primers specifically hybridize to substantially all functional AIR C-encoding or gene segments that are present in the sample.
  • the plurality of AIR V-segment oligonucleotide primers, and (2) either said plurality of AIR J-segment oligonucleotide primers and said plurality of AIR C-segment oligonucleotide primers are capable of promoting amplification in said multiplex PCR of substantially all rearranged AIR CDR3-encoding regions in said sample to produce a plurality of amplified rearranged DNA molecules from a population of adaptive immune cells in said sample, said plurality of amplified rearranged DNA molecules being sufficient to quantify the full diversity of said AIR CDR3-encoding region in said at least one sample.
  • each functional AIR V-encoding gene segment comprises a V gene recombination signal sequence (RSS) and each functional AIR J-encoding gene segment comprises a J gene RSS, wherein each amplified rearranged DNA molecule comprises (i) at least 10, 20, 30 or 40 contiguous nucleotides of a sense strand of said AIR V-encoding gene segment, wherein said at least 10, 20, 30 or 40 contiguous nucleotides are situated 5′ to said V gene RSS and (ii) at least 10, 20 or 30 contiguous nucleotides of a sense strand of said AIR J-encoding gene segment, wherein said at least 10, 20 or 30 contiguous nucleotides are situated 3′ to said J gene RSS.
  • RSS V gene recombination signal sequence
  • each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 1500 nucleotides in length. In another embodiment, each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 1000 nucleotides in length. In yet another embodiment, each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 600 nucleotides in length. In other embodiments, each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 500 nucleotides in length.
  • each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 400 nucleotides in length. In another aspect, each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 300 nucleotides in length. In yet another aspect, each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 200 nucleotides in length. In some embodiments, each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is less than 100 nucleotides in length. In a preferred embodiment, each amplified rearranged DNA molecule in said plurality of amplified rearranged DNA molecules is between 50-600 nucleotides in length.
  • the method includes selecting a set of unique rearranged sequences in one of said samples having a frequency of occurrence that is statistically significantly higher compared with other unique rearranged sequences in said sample.
  • the high frequency of occurrence is determined by a pre-determined threshold percentage.
  • the selected number of unique rearranged sequences in said set is determined by a pre-determined number.
  • the method includes determining from said set whether one of said high frequency unique rearranged sequences is persistent or transient, wherein a persistent unique rearranged sequence is present across two or more samples obtained from said test subject over subsequent periods of time, and wherein a transient unique rearranged sequence is present in only one sample obtained at one timepoint from said subject.
  • the method also includes determining a course of immunotherapy for said subject based on the presence of one or more persistent unique rearranged sequences in said two or more samples of said test subject, wherein the presence of persistent unique rearranged sequences indicates an increased likelihood that said subject has a healthy immune status.
  • the presence of said one or more persistent unique rearranged sequences in said subject is predictive of a positive response to immunotherapy treatment by said subject.
  • the method of the invention includes determining a course of immunotherapy for said subject based on a presence of one or more transient unique rearranged sequences in said one or more samples of said test subject, wherein said presence of said one or more transient unique rearranged sequences indicates an increased likelihood that said subject has a compromised immune status.
  • the presence of said one or more transient unique rearranged sequences in said subject is predictive of a poor response to immunotherapy treatment by said subject.
  • the method of the invention provides steps for categorizing a test subject having a low test subject rating score in said one or more samples as having a lower relative likelihood of responding to immunotherapy in comparison to a second subject having a higher rating score; and stratifying a patient population of test subjects according to relative likelihood of responding to immunotherapy.
  • the method includes determining said test subject rating score comprises extrapolating based on a mathematical model a total AIR repertoire diversity of said test subject by sequencing said nucleic acid sequences from one of said samples and determining a test subject rating score from said total AIR repertoire diversity.
  • the mathematical model is an unseen species model.
  • determining said test subject rating score comprises calculating a Shannon entropy score and a clonality score and determining a test subject rating score based on said Shannon entropy score and said clonality score.
  • the clonality score is a transform of the Shannon entropy score.
  • the adaptive immune receptor (AIR) polypeptide is a mammalian AIR polypeptide and is selected from a T cell receptor-gamma (TCRG) polypeptide, a T cell receptor-beta (TCRB) polypeptide, a T cell receptor-alpha (TCRA) polypeptide, a T cell receptor-delta (TCRD) polypeptide, an immunoglobulin heavy-chain (IGH) polypeptide, and an immunoglobulin light-chain (IGL) polypeptide.
  • the IGH polypeptide is selected from an IgM, an IgA polypeptide, an IgG polypeptide, an IgD polypeptide and an IgE polypeptide.
  • the IGL polypeptide can be selected from an IGL-lambda polypeptide and an IGL-kappa polypeptide.
  • the mammalian AIR polypeptide is a human AIR polypeptide.
  • the mammalian AIR polypeptide is selected from a non-human primate AIR polypeptide, a rodent AIR polypeptide, a canine AIR polypeptide, a feline AIR polypeptide and an ungulate AIR polypeptide.
  • the test subject is selected from: a subject having or suspected of having a malignant condition, a subject who has received a hematopoietic cell transplant, a subject who has received a solid organ transplant, and subject having a microbial infection.
  • the malignant condition is selected from a hematologic malignancy, a melanoma, a sarcoma and a carcinoma.
  • the malignant condition can be selected from malignant melanoma, small cell lung cancer, non-small cell lung cancer, renal cell carcinoma, pancreatic cancer, breast cancer, ovarian cancer and prostate cancer.
  • the hematopoietic cell transplant is selected from a cord blood transplant, an autologous hematopoietic cell transplant, an allogeneic hematopoietic cell transplant, and a bone marrow transplant.
  • the hematopoietic cell transplant comprises an autologous T cell transplant.
  • the plurality of time points comprise timepoints during or after immunotherapy. In another aspect, the plurality of time points comprise timepoints prior to immunotherapy.
  • the method includes steps for managing a treatment of said test subject who is undergoing immunotherapy based on a determination of said immunological status of said test subject.
  • the immunotherapy comprises a treatment with an immunotherapy agent that is selected from an immunotherapeutic antibody, a cytokine, a hematopoietic cell transplant, an immunosuppressive agent, and a vaccine.
  • the immunotherapy comprises a treatment with an inhibitor of a negative regulator of an immune response.
  • the negative regulator of an immune response is selected from CTLA4/CD152, LAG3/CD223, and PD-1/CD279.
  • the negative regulator of an immune response can be CTLA-4/CD152 and said inhibitor of said negative regulator of an immune response can be an anti-CTLA-4 antibody.
  • the anti-CTLA-4 antibody is selected from ipilimumab and tremelimumab.
  • the negative regulator of an immune response is PD-1/CD279 and said inhibitor of the negative regulator of an immune response is an anti-PD-1 antibody.
  • the immunotherapy comprises a treatment with an agent that targets a potentiator of an immune response.
  • the potentiator of an immune response is selected from 41BB/CD137, OX40/CD134 and CD40.
  • the immunotherapy comprises a treatment of an inflammatory condition or an autoimmune disease with an inhibitor of an inflammatory pathway.
  • the inflammatory condition or said autoimmune disease is selected from rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, Crohn's disease and juvenile idiopathic arthritis.
  • the inflammatory pathway comprises at least one of tumor necrosis factor-alpha (TNF ⁇ ), interferon-gamma (IFN ⁇ ), interleukin-1 (IL-1), interleukin-6 (IL-6), interleukin-8 (IL-8).
  • TNF ⁇ tumor necrosis factor-alpha
  • IFN ⁇ interferon-gamma
  • IL-1 interleukin-1
  • IL-6 interleukin-6
  • IL-8 interleukin-8
  • the inflammatory pathway comprises TNF ⁇ and said inhibitor of the inflammatory pathway is an agent that specifically binds to TNF ⁇ .
  • the agent that specifically binds to TNF ⁇ is selected from an anti-TNF ⁇ antibody and an artificial soluble TNF ⁇ receptor.
  • the anti-TNF ⁇ antibody is selected from adalimumab and infliximab and said artificial soluble TNF ⁇ receptor is etanercept.
  • a computer-implemented method for determining an immunological status of a test subject, comprising: storing data for a control subject obtained from a plurality of samples at various timepoints, said data comprising for each sample, nucleic acid sequence information for a plurality of unique rearranged nucleic acid sequences in said sample, an AIR sequence diversity score for said sample, a frequency of occurrence of each unique rearranged nucleic acid sequence in said sample, and a determined immunological status for said subject; determining rules by a processor for assessing an immunological status of a test subject based on said data of said control subject; inputting data for a test subject for a plurality of samples obtained at various timepoints before and after immunotherapy, said data comprising for each sample, nucleic acid sequence information for a plurality of unique rearranged nucleic acid sequences in said sample, an AIR sequence diversity score for said sample, and a frequency of occurrence of each unique rearranged nucleic acid sequence in said sample; and receiving a
  • the method includes determining a predicted response to immunotherapy of said test subject.
  • the data for said control subject comprises nucleic acid sequence information obtained from said control subject at a timepoint prior to immunotherapy treatment.
  • the data for said control subject comprises nucleic acid sequence information obtained from said control subject at a timepoint after immunotherapy treatment.
  • FIG. 1 illustrates TCR clones that remained over time after myeloablative treatment. Shown is the range of values for the proportion of each patient's repertoire represented by clones that were held over after stem cell transplant. The bottom quartile ranged to zero. The proportion of holdover clones was calculated as the proportion of total TCR sequencing reads corresponding to clones observed (at any level) before transplant. Values indicated some persistence of pre-transplant clones in these patients' TCR repertoires.
  • FIG. 2 shows the number of transient TCR clones observed in patients during early immune reconstitution, at 28, 56, 100 and 180 days post-transplant, as compared with healthy controls. For each sample, each of the top 10 TCR clones by frequency was classified as either persistent (observed again in the same patient at a later time point) or transient (not observed again at any level in subsequent samples from the same patient). The number of transient clones was highly variable among patients, ranging from 0 to 9, but the median number of transient clones decreased with time. Four healthy controls were also analyzed, and the number of transient TCR clones ranged from 0 to 2 with a median of 0.
  • FIG. 3 illustrates TCR repertoire reconstitution after stem cell transplant, shown in TCR repertoire size across all patients following hematopoietic stem cell transplant. Samples were taken before transplant and five times after transplant (at days 28, 56, 100, 180 and 365). TCR repertoire size for each patient was estimated using high-throughput sequencing of TCR rearrangements, and the geometric mean of estimated TCR repertoire size is shown. After transplant, patients had a vastly reduced TCR repertoire that reached its minimum 56 days post-transplant, before beginning a slow recovery.
  • FIG. 4 shows an estimated TCR repertoire size comparison based on high-throughput sequencing of TCR ⁇ rearrangements for all patients with and without eventual non-relapse mortality (NRM). TCR repertoire size values are shown as quartiles for both populations. Significance was assessed using a one-tailed Mann-Whitney U test. Patients who went on to suffer from non-relapse mortality had significantly lower estimated repertoire sizes at 56 and 100 days post-transplant.
  • FIG. 5 shows a comparison of CD3+ counts and estimated TCR repertoire size.
  • CD3+ counts (number of cells/mL) were compared to estimated TCR repertoire size for samples from all surviving patients from days 28, 56 and 100 for which both metrics were available.
  • There was a weak correlation between CD3+ counts and repertoire size (r 0.06), indicating that an estimate on the lower bound of TCR ⁇ diversity obtained through sequencing revealed information independent of the total density of circulating T cells.
  • FIG. 6 shows TCR repertoire clonality in blood samples.
  • low TCR repertoire clonality was a predictor of immunotherapy (treatment with ipilimumab (an anti-CTLA-4 mAb)) responder status and high TCR repertoire clonality was a predictor of immunotherapy non-responder status.
  • FIG. 7 shows results from quantitative sequencing of TCR encoding DNA from tumor tissue samples.
  • the results show an increase in TCR clonality in lymphocytes present in solid tumor tissue samples obtained after administration of immunotherapy (treatment with ipilimumab (an anti-CTLA-4 mAb)) (DT) relative to the level of TCR clonality detected in tumor samples obtained prior to immunotherapy (AT).
  • immunotherapy treatment with ipilimumab (an anti-CTLA-4 mAb)
  • AT immunotherapy
  • FIG. 8 shows dynamics in the relative representations of individual TCR clonal populations over time in blood samples and in solid tumor samples obtained prior to immunotherapy (treatment with ipilimumab (an anti-CTLA-4 mAb)) and post immunotherapy.
  • Timepoints A, B, and C are timepoints taken from blood samples. Timepoint A is before immunotherapy, and timepoints B and C are two timepoints after starting the immunotherapy regimen.
  • Timepoints AT, BT, CT are paired tumor samples (AT is before immunotherapy, and timepoints BT and CT are two timepoints after starting the immunotherapy regimen).
  • the arrow indicates a single clone that has increased in preponderance post-therapy to account for 10% of the repertoire at timepoint CT.
  • FIG. 9 shows TCR sequence diversity and distribution entropies determined in peripheral blood samples obtained prior to (timepoint A) and after (timepoints B and C) initiation of immunotherapy (treatment with ipilimumab (an anti-CTLA-4 mAb)) shows dynamics of individual TCR clonal representations over time, pre-therapy (timepoint A) and post-therapy (timepoints B and C). Arrow indicates a single clone that has increased in preponderance post-therapy to account for greater than 10% of the repertoire at timepoint C.
  • FIG. 10A shows measurements of TCR repertoire clonality from tissue samples from melanoma lesions obtained from late-stage metastatic melanoma patients before, during and after immunotherapy with anti-PD-1 antibody.
  • FIG. 11B shows the mean and standard deviation of T cell infiltration (measured as T cell receptor rearrangements per diploid genome) according to response to immunotherapy in cohort 1 (plain square), cohort 2 (slanted stripe square) and in the combined data (straight stripe square).
  • FIG. 11C shows a comparison of each patient's rank (in descending rank, out of 25 patients total) for level of T cell infiltration and TCR repertoire clonality.
  • T cells were obtained from tissue samples of melanoma lesions. Immunotherapy was treatment with an anti-PD-1 antibody. Compared to responders (diamond), non-responders (circle) simultaneously tend toward low TCR repertoire clonality and low levels of infiltrating T lymphocytes.
  • FIG. 12 is a high-level block diagram illustrating an example of a computer, according to one embodiment of the invention.
  • the present invention provides, in certain embodiments and as described herein, unexpectedly advantageous methods for determining the immunological status of a subject or of a plurality of subjects, including by qualitatively (e.g., by T cell receptor or immunoglobulin sequence diversity) and quantitatively (e.g., by TCR or IG sequence distribution) characterizing adaptive immune cell (e.g., T cell or B cell) clonality, from which immunocompetence of an individual's adaptive immune system can be assessed.
  • adaptive immune cell e.g., T cell or B cell
  • the present embodiments thus provide novel methods for assessing the immunocompetence of an individual and for stratifying a population according to immune system status, where determination of both the sequence diversity of TCR and/or IG expressed by lymphoid cells in an individual, and the relative degree of T cell and/or B cell clonality in the individual, are of relevance to prognosis, diagnosis, and outcome, including likelihood of developing immune-related side effects, in a variety of clinical contexts.
  • the present embodiments for the first time permit high resolution, large-scale, high throughput assessment of immunocompetence by characterization at the DNA sequence level of (i) TCR and IG repertoire diversity, and (ii) TCR and IG repertoire distribution.
  • the invention includes compositions and methods for quantitative detection of sequences of substantially all possible TCR and IG gene rearrangements that can be present in a sample containing lymphoid cell DNA.
  • a sample containing lymphoid cell DNA (genomic DNA, cDNA or alternatively, messenger RNA) from a subject is used as a template for multiplexed PCR amplification using a primer set that is specifically designed to be capable of amplifying substantially all possible DNA rearrangements encoding a particular TCR or IG chain.
  • the multiplex PCR amplification products are amenable to rapid, high throughput, high quality quantitative DNA sequencing.
  • Structural TCR or IG repertoire diversity in the sample is determined by identifying a plurality of unique rearranged DNA sequences from the DNA sequence information, and therefrom determining the total number of unique sequences in the sample.
  • a blood sample can be obtained as the source of lymphoid cells from which lymphoid cell DNA and/or RNA can be extracted to provide PCR templates.
  • the methods described herein are used to quantify the diversity and distribution of the adaptive immune receptor (AIR) repertoire within each individual subject's adaptive immune system.
  • the methods described herein are also used to stratify a patient population according to the patient's immunocompetence status or the relative likelihood of individuals to respond to an immunotherapy or develop immune-related side effects.
  • AIR adaptive immune receptor
  • Quantification of AIR sequence diversity e.g., the number of different unique AIR encoding sequences, identified by obtaining distinctive nucleotide sequence information for all rearranged DNA encoding a particular AIR polypeptide in a sample
  • AIR sequence distribution e.g., frequency of occurrence of each unique rearranged AIR encoding DNA sequence
  • this sequence distribution can represent the degree of T cell or B cell clonality in each sample from a patient (e.g., quantitative degree of representation, or relative abundance).
  • Any of a number of known computational tools for processing this distribution parameter can be used to generate distribution values (e.g., the frequency of occurrence of each unique sequence) and diversity values (e.g., the total number of different unique sequences).
  • the distribution and diversity values can be used in a rating step to rate individual samples and compare them to a control sample and/or to one another.
  • a relatively low degree of TCR repertoire diversity in patients following the cord blood transplant was shown to be a predictor of the relative likelihood of susceptibility to infection and of the immunological inability to clear the infection (e.g., poor response).
  • a relatively high degree of TCR repertoire diversity in human patients following cord blood transplant to treat hematologic malignancies was shown to be a predictor of the relative likelihood of resistance to infection and of immunocompetence, i.e., the immunological ability to clear the infection.
  • a high TCR sequence diversity and low clonality in the blood of the patient correlated with positive clinical outcomes.
  • a TCR repertoire that was characterized by a low TCR sequence diversity (high clonality) and a lower entropy of TCR sequence distribution was associated with poorer clinical outcomes that were attributable to compromised adaptive immune capability.
  • solid tumor samples obtained from patients before and after immunotherapy with an inhibitor of a negative regulator of immune response e.g., anti-PD-1 antibody
  • a high level of infiltrating T cell presence and high clonality i.e., evidence of T cell migration to the tumor and clonal proliferation within the tumor
  • a minimal infiltrating T cell repertoire and low clonality in solid tumors i.e., evidence of a restricted and non-specific T cell response within the tumor
  • the presently-disclosed embodiments will find a wide range of uses by profiling a subject's immunocompetence at a given point in time, for example, as a prognostic or diagnostic or to inform a therapeutic strategy, and for other purposes.
  • adaptive immune receptor refers to an immune cell receptor, such as a T cell receptor (TCR) or an Immunoglobulin (Ig) receptor found in mammalian cells.
  • TCR T cell receptor
  • Ig Immunoglobulin
  • primer refers to an oligonucleotide capable of acting as a point of initiation of DNA synthesis under suitable conditions. Such conditions include those in which synthesis of a primer extension product complementary to a nucleic acid strand is induced in the presence of four different nucleoside triphosphates and an agent for extension (e.g., a DNA polymerase or reverse transcriptase) in an appropriate buffer and at a suitable temperature.
  • agent for extension e.g., a DNA polymerase or reverse transcriptase
  • percent “identity,” in the context of two or more nucleic acid or polypeptide sequences, refer to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLASTP and BLASTN or other algorithms available to persons of skill) or by visual inspection.
  • sequence comparison algorithms e.g., BLASTP and BLASTN or other algorithms available to persons of skill
  • the percent “identity” can exist over a region of the sequence being compared, e.g., over a functional domain, or, alternatively, exist over the full length of the two sequences to be compared.
  • sequence comparison typically one sequence acts as a reference sequence to which test sequences are compared.
  • test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
  • sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
  • Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see Ausubel et al., infra).
  • BLAST algorithm One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly-available through the National Center for Biotechnology Information website (www.ncbi.nlm.nih.gov).
  • sufficient amount means an amount sufficient to produce a desired effect, e.g., an amount sufficient to modulate immune response in a cell.
  • therapeutically effective amount is an amount that is effective to ameliorate a symptom of a disease.
  • a therapeutically effective amount can be a “prophylactically effective amount” as prophylaxis can be considered therapy.
  • the singular forms “a,” “an” and “the” include plural references unless the content clearly dictates otherwise.
  • the terms “about” or “approximately” when preceding a numerical value indicates the value plus or minus a range of 5%, 6%, 7%, 8% or 9%, etc.
  • the terms “about” or “approximately” when preceding a numerical value indicates the value plus or minus a range of 10%, 11%, 12%, 13% or 14%, etc.
  • the terms “about” or “approximately” when preceding a numerical value indicates the value plus or minus a range of 15%, 16%, 17%, 18%, 19% or 20%, etc.
  • the immunocompetence is assessed by measuring the subject's adaptive immune receptor (AIR) sequence diversity and AIR sequence distribution.
  • AIR adaptive immune receptor
  • Diversity of unique rearranged TCR or IG encoding DNA sequences in lymphoid cells in a sample reflects the number of different T or B cell clones in a sample from a subject. Sequence diversity can be determined as the number of clones in a sample of a particular size, such as by direct counting or weighted counting in a sample.
  • a sample can be a blood sample or a tissue sample (solid tumor sample), for example.
  • the number of different clones in a subject can be estimated based on the number of clones in a subsample.
  • an arbitrary cutoff value can be assigned to estimate the number of different “effective” clones, such as counting toward diversity only those clones that account for greater than 0.01% of all T or all B cells in the sample.
  • Other models for weighted or extrapolated diversity determinations are contemplated for use in certain related embodiments, such as entropy models, the “unseen species model” (see, e.g., Efron et al., 1976 Biometrika 63:435; Fisher et al., 1943 J. Anim. Ecol. 12:42) or other suitable models as will be known to those familiar with the art.
  • AIR diversity can be measured by quantitative sequencing of the total AIR observed sequences in a particular sample.
  • Compositions and methods for quantitative sequencing of rearranged adaptive immune receptor gene sequences and for adaptive immune receptor clonotype determination are described, for example, in Robins et al., 2009 Blood 114, 4099; Robins et al., 2010 Sci. Translat. Med. 2:47ra64; Robins et al., 2011 J. Immunol. Meth. doi:10.1016/j.jim.2011.09. 001; Sherwood et al. 2011 Sci. Translat. Med. 3:90ra61; U.S. application Ser. No. 13/217,126, U.S. application Ser. No.
  • a sequencing program such as Raw HiSeqTM can be used to preprocess sequence data to remove errors in the primary sequence of each read, and to compress the sequence data.
  • a nearest neighbor algorithm can be used to collapse the data into unique sequences by merging closely related sequences, to remove both PCR and sequencing errors.
  • the diversity score or rating can be determined to be low when there are a small number of unique rearranged AIR sequences in the repertoire as compared to the total number of observed rearranged AIR sequences in a sample.
  • the diversity score or rating can be higher when there is a large number of unique rearranged AIR sequences in the repertoire as compared to the total number of observed rearranged AIR sequences in a sample.
  • the determination of a low or high diversity score or rating can be based on pre-determined thresholds or calculations of statistical significance, as can be determined by one of skill in the art.
  • a predetermined threshold for classifying a diversity score or rating as “low” can be, in some embodiments, a score that is not higher (with statistical significance) than that obtained from blood samples of a subject population, wherein the population can be a population determined to experience a poor outcome in response to an immunotherapeutic intervention.
  • the predetermined threshold is determined based on calculation of the top or highest 50%, 25%, 10% or 5% of diversity or rating scores determined from rearranged AIR sequences from the sample.
  • the rating system can be varied or adjusted in view of a number of factors, including but not limited to, the sample size, method of diversity quantification (e.g., whether by direct sequencing, or by extrapolation, “hidden species,” etc.), clinical signs and symptoms of the patient population from whom samples are obtained, etc.
  • methods of diversity quantification e.g., whether by direct sequencing, or by extrapolation, “hidden species,” etc.
  • members of a patient population can be categorized on the basis of relative diversity and/or distribution ratings, and in certain embodiments, arbitrary segmentation of the population can be practiced.
  • the patient population can be stratified according to (i) the degree of sequence diversity or distribution by quartile, quintile, decile, etc., or (ii) by rating relative AIR sequence diversity and distribution entropy in 50, 40, 30, 20 or 10 percent of the total number of sequences as a correlate of clonality, or (iii) by selecting the 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 most abundant unique AIR sequences at each of a succession of timepoints.
  • the categorization provides a set of parameters by which immunocompetence can be assessed.
  • the AIR sequence distribution can be used to determine and assess a subject's immunological status (e.g., immunocompetence).
  • AIR sequence distribution such as TCR or IG sequence distribution, refers to the variation among the number of different T cell or B cell clones in a sample, e.g., the number of cells that express an identical TCR or IG.
  • AIR sequence distribution can be determined by quantifying the frequency of occurrence of each unique rearranged AIR encoding DNA sequence, as a percentage of the total number of observed rearranged AIR encoding DNA sequences.
  • the quantified distribution of AIR sequences can be used, optionally along with AIR sequence diversity, to rate or rank the immunocompetence of a subject, according to certain presently-contemplated embodiments for determining immunological status.
  • an AIR sequence distribution can be determined by, but not limited to, the following methods: (i) identifying and quantifying at least 1-20 of the most abundant unique rearranged (clonal) AIR sequences in a subject over a time interval, or (ii) by identifying and quantifying the number of unique rearranged (clonal) AIR sequences that are needed to account for a given percentage (e.g., up to 10, 20, 30, 40 or 50%) of the total number of observed rearranged sequences in a sample from a subject.
  • a given percentage e.g., up to 10, 20, 30, 40 or 50%
  • entropy i.e., Shannon entropy as typically defined in information theory, which can be normalized to the range [0-1] by dividing by the logarithm of the number of elements in the sample set
  • modes of distribution e.g., mean, skewness, kurtosis, etc.
  • a method for determining immunological status of a test subject includes steps for identifying, quantifying, rating, comparing and categorizing the immunological status of the test subject.
  • identifying DNA sequence information for each of a plurality of unique rearranged DNA sequences that encode an adaptive immune receptor (AIR) polypeptide in one or more samples containing lymphoid cell DNA obtained from a test subject at each of one or a plurality of timepoints, and determining a total number of unique rearranged AIR polypeptide encoding DNA sequences in the test subject at each of the one or a plurality of timepoints to quantify AIR sequence diversity in the subject can be performed as described above and in Robins et al., 2009 Blood 114, 4099; Robins et al., 2010 Sci. Translat. Med. 2:47ra64; Robins et al., 2011 J. Immunol. Meth.
  • the frequency of occurrence of each unique rearranged DNA sequence can be quantified as a percentage of the total number of observed rearranged AIR polypeptide encoding DNA sequences. For example, if an AIR sequence diversity value is determined from a count of actual sequence data, that value can be used to determine AIR sequence distribution. In another example, if AIR sequence diversity data are estimated, such as by extrapolation of a subsample to the subject's full adaptive immune system, or using the “unseen species model,” or by any other estimation method, then any of widely known method for capturing properties of a distribution can be employed.
  • AIR sequence diversity and AIR sequence distribution values for each sample can be used to rate the immunological status of samples. Any of a wide variety of simple, weighted and/or sophisticated rating systems can be employed, as can depend on the diversity and distribution estimation methods that are used.
  • a low rating is assigned to a test subject's sample in which a small number of unique rearranged sequences in reference to a predetermined threshold have a combined frequency of occurrence of no more than 50 percent of the total number of observed rearranged sequences.
  • a higher test subject rating is assigned to a sample in which a higher number of unique rearranged sequences in reference to a predetermined threshold have a combined frequency of occurrence of no more than 50 percent of the total number of observed rearranged sequences.
  • the rating is lower where a smaller number of different clones accounts for 50 percent of the total number of observed rearranged sequences, as would be the case where one or a few dominant clones or oligoclonality are present.
  • a lower test subject rating is assigned to a sample in which a lower number of unique rearranged sequences have a combined frequency of occurrence of no more than 40, 30, 20 or 10 percent of the total number of observed rearranged sequences
  • a higher test subject rating is assigned to a sample in which a higher number of unique rearranged sequences have, respectively, a combined frequency of occurrence of no more than 40, 30, 20 or 10 percent of the total number of observed rearranged sequences in the sample.
  • the assigned ratings that can then be compared to control subject ratings generated from control lymphoid cell DNA samples obtained from a second subject with a known immunological status In certain embodiments, the second subject has a known, compromised immunological status, as defined by one of skill in the art. In other embodiments, the second subject can be a healthy control individual with a known, uncompromised immunological status according to art-established criteria (e.g., Rich et al., Clinical Immunology: Principles and Practice, 3 rd Ed., Mosby, St. Louis).
  • the test subject can be categorized as having a compromised immunological status at each of said timepoints at which the test subject rating is lower, in a statistically significant manner, than the control subject rating, such that the immunological status of the test subject is thereby determined.
  • a “control subject” can refer to a population of control subjects each sharing a relevant clinical phenotype.
  • a test subject can be categorized as having a compromised immunological status and/or an unhealthy immune status when a TCR or IG sequence diversity score for a sample from the test subject is, with statistical significance, two standard deviations below that of a sample from a control subject, wherein said control subject is known to have an uncompromised immunological status or a healthy immune status.
  • a test subject can be regarded as having a compromised immunological status and/or an unhealthy immune status when a TCR or IG sequence distribution (entropy) score for a sample from the test subject is, with statistical significance, two standard deviations below that of a sample from a control subject, wherein said control subject is known to have an uncompromised immunological status or a healthy immune status.
  • Status categorization can then inform diagnosis, prognosis and/or treatment strategies.
  • age-related decline in adaptive immune system capabilities can be detected according to the herein described methods, such that elderly patients can be immunologically profiled for purposes of predicting whether or not they would be likely to respond immunologically to a vaccine.
  • hematopoietic cell transplant recipients can be tested periodically post-transplant to determine whether or when adaptive immunity has been reconstituted by transplanted cells, so that prophylactic anti-infective (e.g., antibiotic, anti-viral, etc.) and/or immunosuppressive therapies (e.g., to treat graft-versus-host disease (GVHD)) can be adjusted on the basis of each patient's adaptive immune system status instead of on the basis of a fixed regimen.
  • prophylactic anti-infective e.g., antibiotic, anti-viral, etc.
  • immunosuppressive therapies e.g., to treat graft-versus-host disease (GVHD)
  • the immune repertoire and immunocompetence of solid organ transplant recipients can be tested periodically to determine whether and to what extent the host adaptive immune system can be involved in graft rejection. From such test results, the clinician can adjust immunosuppressive therapies as needed, for example, to palliate rejection or to reduce or avoid potentially deleterious side-effects of excessive immunosuppressive therapy.
  • immunocompetence can be assessed as described herein in candidate immunotherapy recipients such as oncology patients, in order to predict which patients can be likely to respond positively to immunotherapy and which are unlikely to do so.
  • responders have many more infiltrating T cells than non-responders (i.e., there are more total infiltrating T cells present), but that those T cells are distributed quite unevenly (i.e., high clonality).
  • the method includes amplifying DNA extracted from or generated from the sample in a multiplexed PCR using (1) a plurality of AIR V-segment oligonucleotide primers and (2) either a plurality of AIR J-segment oligonucleotide primers or a plurality of AIR C-segment oligonucleotide primers.
  • a plurality of AIR V-segment oligonucleotide primers and (2) either a plurality of AIR J-segment oligonucleotide primers or a plurality of AIR C-segment oligonucleotide primers.
  • the plurality of V-segment oligonucleotide primers are each independently capable of specifically hybridizing to at least one polynucleotide encoding a mammalian AIR V-region polypeptide, wherein each V-segment primer comprises a nucleotide sequence of at least 15 contiguous nucleotides that is complementary to at least one functional AIR-encoding gene segment and wherein the plurality of V-segment primers specifically hybridize to substantially all functional AIR V-encoding gene segments that are present in the sample.
  • the plurality of J-segment oligonucleotide primers are each independently capable of specifically hybridizing to at least one polynucleotide encoding a mammalian AIR J-region polypeptide, wherein each J-segment primer comprises a nucleotide sequence of at least 15 contiguous nucleotides that is complementary to at least one functional AIR J-encoding gene segment and wherein the plurality of J-segment primers specifically hybridize to substantially all functional AIR J-encoding or gene segments that are present in the sample.
  • the plurality of C-segment oligonucleotide primers are each independently capable of specifically hybridizing to at least one polynucleotide encoding a mammalian AIR C-region polypeptide, wherein each C-segment primer comprises a nucleotide sequence of at least 15 contiguous nucleotides that is complementary to at least one functional AIR C-encoding gene segment and wherein the plurality of C-segment primers specifically hybridize to substantially all functional AIR C-encoding or gene segments that are present in the sample.
  • the V-segment and J- or C-segment primers are capable of promoting amplification in said multiplex polymerase chain reaction (PCR) of substantially all rearranged AIR CDR3-encoding regions in the sample to produce said plurality of amplified rearranged DNA molecules from a population of adaptive immune cells in the sample, said plurality of amplified rearranged DNA molecules being sufficient to quantify diversity of the AIR CDR3-encoding region in the population of T cells.
  • the method can simply involve sequence analysis of the aforementioned amplified DNA sequence data sufficient to characterize the sample with respect to the absolute and/or relative number of distinct clones present in the sample.
  • a functional AIR-encoding gene segment refers to a TCR or IG encoding gene segment that has undergone rearrangement in the DNA of a lymphoid cell and that is productively expressed, for instance, such that in preferred embodiments rearrangements that involve pseudogenes are not included, nor are rearrangements that result in an out-of-frame or prematurely terminated AIR polypeptide.
  • a method for stratifying a patient population according to relative likelihood of responding to immunotherapy comprising the following steps:
  • the at least one sample is a solid tumor sample.
  • a method for determining immunological status to manage treatment of a test subject undergoing immunotherapy comprising the following steps:
  • Immunocompetence can be usefully understood to include the capacity or potential of an individual's adaptive immune system to mount an effective immune response, such as an immune response that is directed to a particular tumor or to a pathogen (e.g., an infective bacteria, virus, fungus or other microbial or disease-causing agent) such that the tumor or pathogen is eradicated or neutralized.
  • a pathogen e.g., an infective bacteria, virus, fungus or other microbial or disease-causing agent
  • methods for assessing immunocompetence which methods can be predictive of an individual's likelihood of responding in a clinically beneficial manner to immunotherapy.
  • an immunocompetent adaptive immune system such as that of a clinically healthy, normal individual, or population of individuals, known by clinical criteria to be free of any risk or presence of disease or immunological disorder, will be characterized by a relatively high degree of AIR sequence diversity and high entropy of AIR sequence distribution in samples obtained from the subject's blood.
  • an immunoincompetent adaptive immune system e.g., relatively poor capacity of an adaptive immune system to mount an immune response
  • AIR sequence diversity and entropy of AIR sequence distribution are herein shown to be dynamic over time, and can tend to decline over time as a correlate of increasing age, increasing susceptibility to disease, decreasing likelihood of responding robustly to vaccines or to other immunotherapies, and/or other clinically relevant criteria.
  • solid tumor samples obtained from patients before and after immunotherapy with an inhibitor of a negative regulator of immune response a high level of infiltrating T cells and high clonality were associated with a positive response to immunotherapy.
  • a low level of infiltrating T cells and low clonality in solid tumors were associated with failure to respond to treatment.
  • Immunotherapy can include any of a variety of interventions by which the activity levels of one or more cells of the adaptive immune system are altered (e.g., up- or down-regulated in a statistically significant manner).
  • the intervention can induce, recruit, enhance or otherwise potentiate an adaptive immune response, which in preferred embodiments will be an antigen-specific immune response.
  • immunotherapy can comprise administration of one or more specific antibodies that recognize adaptive immune system cells to alter the immunological activity of such cells.
  • immunotherapeutic approaches include the use of cytokines that similarly can directly or indirectly alter immunocyte activity; vaccines that elicit adaptive immune responses such as antigen-specific responses to tumor-associated antigens; hematopoietic cell transplants which include bone marrow transplants, cord blood transplants and autologous hematopoietic cell transplants including autologous T cell transplants (e.g., Blume and Thomas, 2000 Biol. Blood Marrow Transpl. 6(1):1-12); inhibitors of negative regulators of adaptive immune responses such as inhibitors of CTLA4/CD152 (e.g., ipilimumab, tremelimumab; Callahan et al., 2010 Sem. Oncol.
  • cytokines that similarly can directly or indirectly alter immunocyte activity
  • vaccines that elicit adaptive immune responses such as antigen-specific responses to tumor-associated antigens
  • hematopoietic cell transplants which include bone marrow transplants, cord blood transplants and autologous
  • immunosuppressive agents e.g., Goodman & Gilman's The Pharmacological Basis of Therapeutics, (12 th Ed., Brunton et al., Eds., McGraw Hill, NY, 2011, pages 909-1099; 1891-1990; Murphy, Janeway's Immunobiology (8 th Ed.), 2011 Garland Science, NY, pp. 669-716).
  • immunotherapy can comprise treatment with an immunotherapy agent, such as an immunotherapeutic antibody, a cytokine, a hematopoietic cell transplant, an immunosuppressive agent, or a vaccine.
  • immunotherapy comprises treatment with an inhibitor of a negative regulator of an immune response.
  • the negative regulator of an immune response can be one or more of CTLA4/CD152, LAG3/CD223, and PD-1/CD279.
  • the negative regulator of an immune response can be CTLA-4/CD152 and the inhibitor of the negative regulator of an immune response is an anti-CTLA-4 antibody, such as ipilimumab (e.g., Lyseng-Williamson et al., 2012 Am. J. Clin.
  • the negative regulator of an immune response can be PD-1/CD279, and the inhibitor of the negative regulator of an immune response is an anti-PD-1 antibody.
  • immunotherapy can comprise treatment with an agent that targets a potentiator of an immune response.
  • the potentiator of an immune response can be 41BB/CD137 (Kwon et al., 1989 Proc. Nat. Acad. Sci. USA 86:1963), OX40/CD134 (GenBank Acc. No. AJ277151) or CD40 (Banchereau et al., 1994 Ann. Rev. Immunol. 12:881).
  • immunotherapy can comprise treatment of an inflammatory condition or an autoimmune disease with an inhibitor of an inflammatory pathway.
  • Contemplated inflammatory conditions or autoimmune diseases include rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, Crohn's disease and juvenile idiopathic arthritis.
  • the inflammatory pathway comprises at least one of tumor necrosis factor-alpha (TNF ⁇ ), interferon-gamma (IFN ⁇ ), interleukin-1 (IL-1), interleukin-6 (IL-6), interleukin-8 (IL-8).
  • TNF ⁇ tumor necrosis factor-alpha
  • IFN ⁇ interferon-gamma
  • IL-1 interleukin-1
  • IL-6 interleukin-6
  • IL-8 interleukin-8
  • TNF ⁇ inflammatory pathway that include TNF ⁇
  • inhibitors of the inflammatory pathway that specifically bind to TNF ⁇ such as anti-TNF ⁇ antibodies (e.g., adalimumab, infliximab) and artificial soluble TNF ⁇ receptors (e.g., etanercept).
  • anti-TNF ⁇ antibodies e.g., adalimumab, infliximab
  • artificial soluble TNF ⁇ receptors e.g., etanercept
  • the ability to quantify the immunocompetency of a patient's adaptive immune system (as defined as either diversity in the blood or clonality in a tumor tissue, in the case of solid tumors) prior to treatment with an immunomodulatory drug or treatment regimen is predictive of response to treatment and correlative to overall survival.
  • targets in the immune cascade that can be targeted as potential treatments to cancer and other therapeutic areas. Some are expressed on the surface of T cells and are negative regulators of the immune response, and some are expressed on the surface of antigen presenting cells and are thought to upregulate the immune cascade.
  • targets in immunotherapy that are or have been used in the clinic (anti-CTLA, ipilimumab) or in active clinical trials, and are currently in use by multiple pharmaceutical manufacturers after reporting successful early data in patients. These targets and inhibitors or regulators thereof can be used in immunotherapy or treatment measures, in accordance with methods of the invention described herein.
  • CTLA-4 cytotoxic T-lymphocyte antigen 4
  • CD28 provides positive modulatory signals in the early stages of an immune response
  • CTLA-4 signaling inhibits T-cell activation, particularly during strong T-cell responses.
  • CTLA-4 blockade using anti-CTLA-4 monoclonal antibody therapy has great appeal because suppression of inhibitory signals results in the generation of an antitumor T-cell response.
  • Both clinical and preclinical data indicate that CTLA-4 blockade results in direct activation of CD4+ and CD8+ effector cells, and anti-CTLA-4 monoclonal antibody therapy has shown promise in a number of cancers, particularly melanoma.
  • PD-1 Programmed death 1
  • PD-L1 and PD-L2 deliver inhibitory signals that regulate the balance between T cell activation, tolerance, and immunopathology.
  • Immune responses to foreign and self-antigens require specific and balanced responses to clear pathogens and tumors and yet maintain tolerance to self-antigens.
  • Induction and maintenance of T cell tolerance requires PD-1, and its ligand PD-L1 on nonhematopoietic cells can limit effector T cell responses and protect tissues from immune-mediated tissue damage.
  • the PD-1:PD-L pathway also has been usurped by microorganisms and tumors to attenuate antimicrobial or tumor immunity and facilitate chronic infection and tumor survival.
  • 4-1BB 4-1BB (CD137), a member of the TNF receptor superfamily, is an activation-induced T-cell costimulatory molecule. Signaling via 4-1BB upregulates survival genes, enhances cell division, induces cytokine production, and prevents activation-induced cell death in T cells. The importance of the 4-1BB pathway has been underscored in a number of diseases, including cancer. Growing evidence indicates that anti-4-1BB monoclonal antibodies possess strong antitumor properties, which in turn are the result of their powerful CD8+ T-cell activating, IFN- ⁇ producing, and cytolytic marker-inducing capabilities.
  • CD40 is a costimulatory protein found on antigen presenting cells and is required for their activation.
  • the binding of CD154 (CD40L) on T H cells to CD40 activates antigen presenting cells and induces a variety of downstream effects.
  • the protein receptor encoded by this gene is a member of the TNF-receptor superfamily. This receptor has been found to be essential in mediating a broad variety of immune and inflammatory responses including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation.
  • Entrez Gene CD40 molecule, TNF receptor superfamily member 5; En.wikipedia.org/wiki/CD40_(protein).
  • Exemplary CD40 compounds include, but are not limited to, the following developed by Seattle Genetics/Genentech (dacetuzumab) and Novartis (lucatumumab).
  • LAG-3 (CD223) is a cell surface molecule expressed on activated T cells (Huard et al. Immunogenetics 39:213-217, 1994), NK cells (Triebel et al. J Exp Med 171:1393-1405, 1990), B cells (Kisielow et al. Eur J Immunol 35:2081-2088, 2005), and plasmacytoid dendritic cells (Workman et al. J Immunol 182:1885-1891, 2009) that plays an important but incompletely understood role in the function of these lymphocyte subsets.
  • LAG-3 is being developed as a target, by companies such as BMS.
  • Immune modulation can also be categorized by compound family (versus specific target) into either a member of the immunoglobulin family or the TNF family. See Nature Reviews Drug Discovery 12, 130-146 (February 2013) (doi:10.1038/nrd3877). This categorization is useful to highlight the breadth of therapeutic categories outside of cancer that these targets can hit, and for which a measure of immunocompetence can be equally as relevant.
  • GITR-specific GITR-GITRL T cell activation Solid tumours I humanized IgG1 Atacicept ZymoGenetics/ TACI and human TACI, BCMA B cell activation and SLE, rheumatoid II/III EMD Serano IgG1 fusion protein and BAFFR antibody production arthritis, multiple sclerosis and optic neuritis CP-870,893 Plizer CD40-specific CD40 APC activation and Multiple cancers I human IgG1 B cell maturation Lucatumumab Novartis CD40-specific CD40 APC activation and Lymphoma and I/II human IgG1 B cell maturation leukaemia Dacetuzumab Seattle Genetics CD40-specific CD40 APC activation and Lymphoma and II humanized IgG1 B cell maturation multiple myaloma ADCC, antibody dependent cell-mediated cytotoxicity; APC, antigen presenting cell; B7H1, B7 homolog 1; BAFFR, B cell activation factor receptor
  • the subject or biological source from which a test biological sample can be obtained, can be a human or non-human animal, or a transgenic or cloned or tissue-engineered (including through the use of stem cells) organism.
  • the subject or biological source can be known to have, or can be suspected of having or being at risk for having, cancer or another malignant condition, or an autoimmune disease, or an inflammatory condition, or a bacterial, viral, fungal or other microbial infection, or the subject or biological source can be a solid organ transplant recipient (e.g., recipient of all or a portion of a transplanted liver, lung, kidney, pancreas, intestine, heart, or skin).
  • the subject or biological source can be a hematopoietic cell transplant recipient (e.g., recipient of a bone marrow transplant, cord blood transplant, autologous T cell transplant, etc.).
  • the subject or biological source can be known to be free of a risk or presence of such disease.
  • the test biological sample can be obtained from the subject or biological source at one or a plurality of timepoints, for example, at one or a plurality of timepoints prior to administration of treatment or therapy (e.g., immunotherapy) to the subject or biological source, and also at one or a plurality of timepoints during or after administration of treatment or therapy (e.g., immunotherapy) to the subject or biological source.
  • treatment or therapy e.g., immunotherapy
  • Certain preferred embodiments contemplate a subject or biological source that is a human subject such as a patient that has been diagnosed as having or being at risk for developing or acquiring cancer according to art-accepted clinical diagnostic criteria, such as those of the U.S. National Cancer Institute (Bethesda, Md., USA) or as described in DeVita, Hellman, and Rosenberg's Cancer: Principles and Practice of Oncology (2008, Lippincott, Williams and Wilkins, Philadelphia/Ovid, N.Y.); Pizzo and Poplack, Principles and Practice of Pediatric Oncology (Fourth edition, 2001, Lippincott, Williams and Wilkins, Philadelphia/Ovid, N.Y.); Vogelstein and Kinzler, The Genetic Basis of Human Cancer (Second edition, 2002, McGraw Hill Professional, New York); Dancey et al.
  • Certain embodiments contemplate a human subject that is known to be free of a risk for having, developing or acquiring cancer by such criteria.
  • malignant conditions that are contemplated according to certain present embodiments can include solid tumors such as melanoma, sarcoma, and carcinoma.
  • Others can also include, for example, malignant melanoma, small cell lung cancer, non-small cell lung cancer, renal cell carcinoma, pancreatic cancer, breast cancer, ovarian cancer and prostate cancer.
  • non-human subject or biological source for example a non-human primate such as a macaque, chimpanzee, gorilla, vervet, orangutan, baboon or other non-human primate, including such non-human subjects that can be known to the art as preclinical models, including preclinical models for solid tumors and/or other cancers.
  • a non-human primate such as a macaque, chimpanzee, gorilla, vervet, orangutan, baboon or other non-human primate
  • preclinical models including preclinical models for solid tumors and/or other cancers.
  • Certain other embodiments contemplate a non-human subject that is a mammal, for example, a mouse, rat, rabbit, pig, sheep, horse, bovine, goat, gerbil, hamster, guinea pig or other mammal; many such mammals can be subjects that are known to the art as preclinical models for certain diseases or disorders, including lymphoid hematopoietic malignancies and/or other cancers (e.g., Li et al., 2011 Dis. Model. Mech. 4:311; von Euler et al., 2011 Vet. Comp. Oncol. 9:1; Goldstein et al., 2010 Expert Rev. Hematol. 3:301; Diamond et al., 2009 J. Bone Min. Res.
  • a mammal for example, a mouse, rat, rabbit, pig, sheep, horse, bovine, goat, gerbil, hamster, guinea pig or other mammal
  • the subject or biological source can be a non-mammalian vertebrate, for example, another higher vertebrate, or an avian, amphibian or reptilian species, or another subject or biological source.
  • Biological samples can be provided by obtaining a blood sample, biopsy specimen, excised tumor specimen such as a solid tumor specimen, tissue explant, organ culture, biological fluid or any other tissue or cell preparation from a subject or a biological source.
  • B cells and T cells can thus be obtained from a biological sample, such as from a variety of tissue and biological fluid samples including bone marrow, thymus, lymph glands, lymph nodes, peripheral tissues and blood, and also from tumor tissues (e.g., tumor-infiltrating lymphocytes), but peripheral blood is most easily accessed. Any peripheral tissue can be sampled for the presence of B and T cells and is therefore contemplated for use in the methods described herein.
  • Tissues and biological fluids from which adaptive immune cells can be obtained include, but are not limited to skin, epithelial tissues, colon, spleen, a mucosal secretion, oral mucosa, intestinal mucosa, vaginal mucosa or a vaginal secretion, cervical tissue, ganglia, saliva, cerebrospinal fluid (CSF), bone marrow, cord blood, serum, serosal fluid, plasma, lymph, urine, ascites fluid, pleural fluid, pericardial fluid, peritoneal fluid, abdominal fluid, culture medium, conditioned culture medium or lavage fluid.
  • CSF cerebrospinal fluid
  • adaptive immune cells e.g., hematopoietic cells of lymphoid lineage such as T cells and B cells
  • hematopoietic cells of lymphoid lineage such as T cells and B cells
  • Peripheral blood samples can be obtained by phlebotomy from subjects.
  • Peripheral blood mononuclear cells PBMC are isolated by techniques known to those of skill in the art, e.g., by Ficoll-Hypaque® density gradient separation. In certain embodiments, whole PBMCs are used for analysis.
  • preparations that comprise predominantly lymphocytes (e.g., T and B cells) or that comprise predominantly T cells or predominantly B cells can be prepared for use as a biological sample as provided herein, according to established, art-accepted methodologies.
  • specific subpopulations of T or B cells can be isolated prior to analysis using the methods described herein.
  • kits for isolating different subpopulations of T and B cells include, but are not limited to, subset selection immunomagnetic bead separation or flow immunocytometric cell sorting using antibodies specific for one or more of any of a variety of known T and B cell surface markers.
  • Illustrative markers include, but are not limited to, one or a combination of CD2, CD3, CD4, CD8, CD14, CD19, CD20, CD25, CD28, CD45RO, CD45RA, CD54, CD62, CD62L, CDw137 (41BB), CD154, GITR, FoxP3, CD54, and CD28.
  • cell surface markers such as CD2, CD3, CD4, CD8, CD 14, CD19, CD20, CD45RA, and CD45RO can be used to determine T, B, and monocyte lineages and subpopulations in flow cytometry.
  • forward light-scatter, side-scatter, and/or cell surface markers such as CD25, CD62L, CD54, CD137, CD154 can be used to determine activation state and functional properties of cells.
  • Illustrative combinations useful in certain of the methods described herein can include CD8 + CD45RO + (memory cytotoxic T cells), CD4 + CD45RO + (memory T helper), CD8 + CD45RO ⁇ (CD8 + CD62L + CD45RA + (na ⁇ ve-like cytotoxic T cells); CD4 + CD25 + CD62L hi GITR + FoxP3 ⁇ (regulatory T cells).
  • Illustrative antibodies for use in immunomagnetic cell separations or flow immunocytometric cell sorting include fluorescently labeled anti-human antibodies, e.g., CD4 FITC (clone M-T466, Miltenyi Biotec), CD8 PE (clone RPA-T8, BD Biosciences), CD45RO ECD (clone UCHL-1, Beckman Coulter), and CD45RO APC (clone UCHL-1, BD Biosciences). Staining of total PBMCs can be done with the appropriate combination of antibodies, followed by washing cells before analysis.
  • fluorescently labeled anti-human antibodies e.g., CD4 FITC (clone M-T466, Miltenyi Biotec), CD8 PE (clone RPA-T8, BD Biosciences), CD45RO ECD (clone UCHL-1, Beckman Coulter), and CD45RO APC (clone UCHL-1, BD Biosciences).
  • Lymphocyte subsets can be isolated by fluorescence activated cell sorting (FACS), e.g., by a BD FACSAriaTM cell-sorting system (BD Biosciences) and by analyzing results with FlowJoTM software (Treestar Inc.), and also by conceptually similar methods involving specific antibodies immobilized to surfaces or beads.
  • FACS fluorescence activated cell sorting
  • BD Biosciences BD Biosciences
  • FlowJoTM software Telestar Inc.
  • total genomic DNA can be extracted from cells using methods known in the art and/or commercially available kits, e.g., by using the QIAamp® DNA blood Mini Kit (QIAGEN®).
  • the approximate mass of a single haploid genome is 3 pg.
  • at least 25,000 to 250,000 cells for example, at least 50,000 to 125,000 cells, or at least 75,000 to 150,000 cells, or at least 100,000 to 200,000 cells, are used for analysis, i.e., about 0.15 to 1.5 ⁇ g, or for instance, 0.6 to 1.2 ⁇ g DNA from diploid T or B cells.
  • T or B cells present in a sample can vary considerably when the sample is obtained from a patient having a lymphoid hematological malignancy such as acute T-cell lymphoblastic leukemia (T-ALL).
  • T-ALL acute T-cell lymphoblastic leukemia
  • PBMCs peripheral blood mononuclear cells
  • the number of T cells can vary and can be estimated to be about 30% of total cells
  • the number of B cells can vary and can be estimated to be about 5-15% of total cells in a PBMC preparation.
  • the native TCR is a heterodimeric cell surface protein of the immunoglobulin superfamily which is associated with invariant proteins of the CD3 complex involved in mediating signal transduction.
  • TCRs exist in ⁇ and ⁇ forms, which are structurally similar but have quite distinct anatomical locations and probably functions.
  • the MHC class I and class II ligands, which bind to the TCR, are also immunoglobulin superfamily proteins but are specialized for antigen presentation, with a highly polymorphic peptide binding site which enables them to present a diverse array of short peptide fragments at the APC cell surface.
  • the extracellular portions of native heterodimeric ⁇ and ⁇ TCRs consist of two polypeptides each of which has a membrane-proximal constant domain, and a membrane-distal variable domain. Each of the constant and variable domains includes an intra-chain disulfide bond.
  • the variable domains contain the highly polymorphic loops analogous to the complementarity determining regions (CDRs) of antibodies. CDR3 of ⁇ TCRs interact with the peptide presented by MHC, and CDRs 1 and 2 of ⁇ TCRs interact with the peptide and the MHC.
  • the diversity of TCR sequences is generated via somatic rearrangement of linked variable (V), diversity (D), joining (J), and constant genes.
  • Ig and TCR gene loci contain many different variable (V), diversity (D), and joining (J) gene segments, which are subjected to rearrangement processes during early lymphoid differentiation.
  • V variable
  • D diversity
  • J joining
  • the V-D-J rearrangements are mediated via a recombinase enzyme complex in which the RAG1 and RAG2 proteins play a key role by recognizing and cutting the DNA at the recombination signal sequences (RSS), which are located downstream of the V gene segments, at both sides of the D gene segments, and upstream of the J gene segments. Inappropriate RSS reduce or even completely prevent rearrangement.
  • the recombination signal sequence (RSS) consists of two conserved sequences (heptamer, 5′-CACAGTG-3′, and nonamer, 5′-ACAAAAACC-3′), separated by a spacer of either 12+/ ⁇ 1 by (“12-signal”) or 23+/ ⁇ 1 by (“23-signal”).
  • a number of nucleotide positions have been identified as important for recombination including the CA dinucleotide at position one and two of the heptamer, and a C at heptamer position three has also been shown to be strongly preferred as well as an A nucleotide at positions 5, 6, 7 of the nonamer.
  • the rearrangement process generally starts with a D to J rearrangement followed by a V to D-J rearrangement in the case of Ig heavy chain (IgH), TCR beta (TCRB), and TCR delta (TCRD) genes or concerns direct V to J rearrangements in case of Ig kappa (IgK), Ig lambda (IgL), TCR alpha (TCRA), and TCR gamma (TCRG) genes.
  • the sequences between rearranging gene segments are generally deleted in the form of a circular excision product, also called TCR excision circle (TREC) or B cell receptor excision circle (BREC).
  • V, D, and J gene segments represent the so-called combinatorial repertoire, which is estimated to be ⁇ 2 ⁇ 10 6 for Ig molecules, ⁇ 3 ⁇ 10 6 for TCR ⁇ and ⁇ 5 ⁇ 10 3 for TCR ⁇ molecules.
  • deletion and random insertion of nucleotides occurs during the rearrangement process, resulting in highly diverse junctional regions, which significantly contribute to the total repertoire of Ig and TCR molecules, estimated to be >10 12 .
  • Mature B-lymphocytes further extend their Ig repertoire upon antigen recognition in follicle centers via somatic hypermutation, a process, leading to affinity maturation of the Ig molecules.
  • the somatic hypermutation process focuses on the V- (D-) J exon of IgH and Ig light chain genes and concerns single nucleotide mutations and sometimes also insertions or deletions of nucleotides. Somatically-mutated Ig genes are also found in mature B-cell malignancies of follicular or post-follicular origin.
  • V-segment and J-segment primers can be employed in a PCR reaction to amplify rearranged TCR or Ig CDR3-encoding DNA regions in a test biological sample, wherein each functional TCR or Ig V-encoding gene segment comprises a V gene recombination signal sequence (RSS) and each functional TCR or Ig J-encoding gene segment comprises a J gene RSS.
  • RSS V gene recombination signal sequence
  • each amplified rearranged DNA molecule can comprise (i) at least about 10, 20, 30 or 40 contiguous nucleotides of a sense strand of the TCR or Ig V-encoding gene segment, with the at least about 10, 20, 30 or 40 contiguous nucleotides being situated 5′ to the V gene RSS and/or each amplified rearranged DNA molecule can comprise (ii) at least about 10, 20 or 30 contiguous nucleotides of a sense strand of the TCR or Ig J-encoding gene segment, with the at least about 10, 20 or 30 contiguous nucleotides being situated 3′ to the J gene RSS.
  • each amplified TCR or Ig CDR3-encoding region is present in an amplified rearranged DNA molecule that is less than 600 nucleotides in length.
  • these design features for amplifying CDR3-encoding V-J junctional regions permit V-segment primer hybridization to substantially all functional TCR or Ig V-encoding gene segments, and also permit J-segment primer hybridization to substantially all functional TCR or Ig J-encoding segments, and also permit amplification of CDR3-encoding regions that are amenable to sequencing by the herein described high-throughput sequencing (HTS) platforms while including adequate sequence information to identify all possible V-D-J and V-J combinations.
  • HTS high-throughput sequencing
  • the present methods involve a multiplex PCR method using a set of forward primers that specifically hybridize to the V segments and a set of reverse primers that specifically hybridize to the J segments where the multiplex PCR reaction allows amplification of all the possible VJ (and VDJ) combinations within a given population of T or B cells.
  • DNA or RNA can be extracted from cells in a sample, such as a sample of blood or lymph or other sample from a subject known to contain lymphoid cells, using standard methods or commercially available kits known in the art.
  • genomic DNA is used.
  • cDNA is transcribed from mRNA obtained from the cells and then used for multiplex PCR.
  • a multiplex PCR system can be used to amplify rearranged adaptive immune cell receptor loci from genomic DNA, preferably from a CDR3 region.
  • the CDR3 region is amplified from a TCR ⁇ , TCR ⁇ , TCR ⁇ or TCR ⁇ CDR3 region or similarly from an IgH or IgL (lambda or kappa) locus.
  • compositions comprise a plurality of V-segment and J-segment primers that are capable of promoting amplification in a multiplex polymerase chain reaction (PCR) of substantially all productively rearranged adaptive immune receptor CDR3-encoding regions in the sample for a given class of such receptors (e.g., TCR ⁇ , TCRI ⁇ , IgH, etc.), to produce a multiplicity of amplified rearranged DNA molecules from a population of T cells (for TCR) or B cells (for Ig) in the sample.
  • PCR polymerase chain reaction
  • primers are designed so that each amplified rearranged DNA molecule in the multiplicity of amplified rearranged DNA molecules is less than 600 nucleotides in length, thereby excluding amplification products from non-rearranged adaptive immune receptor loci.
  • compositions and methods relate to substantially all (e.g., greater than 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%) of these known and readily detectable adaptive immune receptor V-, D- and J-region encoding gene segments.
  • the TCR and Ig genes can generate millions of distinct proteins via somatic mutation. Because of this diversity-generating mechanism, the hypervariable complementarity determining regions (CDRs) of these genes can encode sequences that can interact with millions of ligands, and these regions are linked to a constant region that can transmit a signal to the cell indicating binding of the protein's cognate ligand.
  • the adaptive immune system employs several strategies to generate a repertoire of T- and B-cell antigen receptors with sufficient diversity to recognize the universe of potential pathogens.
  • CDR3 complementarity-determining region
  • the assay technology uses two pools of primers to provide for a highly multiplexed PCR reaction.
  • the first, “forward” pool e.g., by way of illustration and not limitation, V-segment oligonucleotide primers described herein can in certain preferred embodiments be used as “forward” primers when J-segment oligonucleotide primers are used as “reverse” primers according to commonly used PCR terminology, but the skilled person will appreciate that in certain other embodiments J-segment primers can be regarded as “forward” primers when used with V-segment “reverse” primers) includes an oligonucleotide primer that is specific to (e.g., having a nucleotide sequence complementary to a unique sequence region of) each V-region encoding segment (“V segment) in the respective TCR or Ig gene locus.
  • primers targeting a highly conserved region are used, to simultaneously capture many V segments, thereby reducing the number of primers required in the multiplex PCR.
  • the “reverse” pool primers anneal to a conserved sequence in the joining (“J”) segment.
  • Each primer can be designed so that a respective amplified DNA segment is obtained that includes a sequence portion of sufficient length to identify each J segment unambiguously based on sequence differences amongst known J-region encoding gene segments in the human genome database, and also to include a sequence portion to which a J-segment-specific primer can anneal for resequencing.
  • This design of V- and J-segment-specific primers enables direct observation of a large fraction of the somatic rearrangements present in the adaptive immune receptor gene repertoire within an individual.
  • This feature in turn enables rapid comparison of the TCR and/or Ig repertoires (i) in individuals having a particular disease, disorder, condition or other indication of interest (e.g., cancer, an autoimmune disease, an inflammatory disorder or other condition) with (ii) the TCR and/or Ig repertoires of control subjects who are free of such diseases, disorders conditions or indications.
  • a particular disease, disorder, condition or other indication of interest e.g., cancer, an autoimmune disease, an inflammatory disorder or other condition
  • the term “gene” refers to the segment of DNA involved in producing a polypeptide chain such as all or a portion of a TCR or Ig polypeptide (e.g., a CDR3-containing polypeptide); it includes regions preceding and following the coding region “leader and trailer” as well as intervening sequences (introns) between individual coding segments (exons), and can also include regulatory elements (e.g., promoters, enhancers, repressor binding sites and the like), and can also include recombination signal sequences (RSSs) as described herein.
  • RLSs recombination signal sequences
  • the nucleic acids of the present embodiments can be in the form of RNA or in the form of DNA, which DNA includes cDNA, genomic DNA, and synthetic DNA.
  • the DNA can be double-stranded or single-stranded, and if single stranded can be the coding strand or non-coding (anti-sense) strand.
  • a coding sequence which encodes a TCR or an immunoglobulin or a region thereof for use according to the present embodiments can be identical to the coding sequence known in the art for any given TCR or immunoglobulin gene regions or polypeptide domains (e.g., V-region domains, CDR3 domains, etc.), or can be a different coding sequence, which, as a result of the redundancy or degeneracy of the genetic code, encodes the same TCR or immunoglobulin region or polypeptide.
  • the present disclosure provides a plurality of V segment primers and a plurality of J segment primers, wherein the plurality of V segment primers and the plurality of J segment primers amplify substantially all combinations of the V and J segments of a rearranged immune receptor locus.
  • the method provides amplification of substantially all of the rearranged AIR sequences in a lymphoid cell, and capable of quantifying the diversity of the TCR or IG repertoire of at least 10 6 , 10 5 , 10 4 , or 10 3 unique rearranged AIR sequences in a sample.
  • “Substantially all combinations” refers to at least 95%, 96%, 97%, 98%, 99% or more of all the combinations of the V and J segments of a rearranged immune receptor locus.
  • the plurality of V segment primers and the plurality of J segment primers amplify all of the combinations of the V and J segments of a rearranged immune receptor locus.
  • a multiplex PCR system can use at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25, and in certain embodiments, at least 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, or 39, and in other embodiments 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 65, 70, 75, 80, 85, or more forward primers, in which each forward primer specifically hybridizes to or is complementary to a sequence corresponding to one or more V region segments.
  • the multiplex PCR system also uses at least 3, 4, 5, 6, or 7, and in certain embodiments, 8, 9, 10, 11, 12 or 13 reverse primers, in which each reverse primer specifically hybridizes to or is complementary to a sequence corresponding to one or more J region segments.
  • V and J segment primers can be used to amplify the full diversity of TCR and IG sequences in a repertoire.
  • primer oligonucleotide sequences for amplifying TCR and IG sequences see, e.g., Robins et al., 2009 Blood 114, 4099; Robins et al., 2010 Sci. Translat. Med. 2:47ra64; Robins et al., 2011 J. Immunol. Meth.
  • Oligonucleotides or polynucleotides that are capable of specifically hybridizing or annealing to a target nucleic acid sequence by nucleotide base complementarity can do so under moderate to high stringency conditions.
  • suitable moderate to high stringency conditions for specific PCR amplification of a target nucleic acid sequence would be between 25 and 80 PCR cycles, with each cycle consisting of a denaturation step (e.g., about 10-30 seconds (s) at greater than about 95° C.), an annealing step (e.g., about 10-30 s at about 60-68° C.), and an extension step (e.g., about 10-60 s at about 60-72° C.), optionally according to certain embodiments with the annealing and extension steps being combined to provide a two-step PCR.
  • a denaturation step e.g., about 10-30 seconds (s) at greater than about 95° C.
  • an annealing step e.g., about 10-30 s at about
  • PCR reagents can be added or changed in the PCR reaction to increase specificity of primer annealing and amplification, such as altering the magnesium concentration, optionally adding DMSO, and/or the use of blocked primers, modified nucleotides, peptide-nucleic acids, and the like.
  • nucleic acid hybridization techniques can be used to assess hybridization specificity of the primers described herein.
  • Hybridization techniques are well known in the art of molecular biology.
  • suitable moderately stringent conditions for testing the hybridization of a polynucleotide as provided herein with other polynucleotides include prewashing in a solution of 5 ⁇ SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50° C.-60° C., 5 ⁇ SSC, overnight; followed by washing twice at 65° C. for 20 minutes with each of 2 ⁇ , 0.5 ⁇ and 0.2 ⁇ SSC containing 0.1% SDS.
  • stringency of hybridization can be readily manipulated, such as by altering the salt content of the hybridization solution and/or the temperature at which the hybridization is performed.
  • suitable highly stringent hybridization conditions include those described above, with the exception that the temperature of hybridization is increased, e.g., to 60° C.-65° C. or 65° C.-70° C.
  • the primers are designed not to cross an intron/exon boundary.
  • the forward primers in certain embodiments anneal to the V segments in a region of relatively strong sequence conservation between V segments so as to maximize the conservation of sequence among these primers. Accordingly, this minimizes the potential for differential annealing properties of each primer, and so that the amplified region between V and J primers contains sufficient TCR or Ig V sequence information to identify the specific V gene segment used.
  • the J segment primers hybridize with a conserved element of the J segment, and have similar annealing strength.
  • the J segment primers anneal to the same conserved framework region motif
  • Oligonucleotides can be prepared by any suitable method, including direct chemical synthesis by a method such as the phosphotriester method of Narang et al., 1979, Meth. Enzymol. 68:90-99; the phosphodiester method of Brown et al., 1979, Meth. Enzymol. 68:109-151; the diethylphosphoramidite method of Beaucage et al., 1981, Tetrahedron Lett. 22:1859-1862; and the solid support method of U.S. Pat. No. 4,458,066, each incorporated herein by reference.
  • a review of synthesis methods of conjugates of oligonucleotides and modified nucleotides is provided in Goodchild, 1990, Bioconjugate Chemistry 1(3): 165-187, incorporated herein by reference.
  • a primer is preferably a single-stranded DNA.
  • the appropriate length of a primer depends on the intended use of the primer but typically ranges from 6 to 50 nucleotides, or in certain embodiments, from 15-35 nucleotides. Short primer molecules generally require cooler temperatures to form sufficiently stable hybrid complexes with the template.
  • a primer need not reflect the exact sequence of the template nucleic acid, but must be sufficiently complementary to hybridize with the template. The design of suitable primers for the amplification of a given target sequence is well known in the art and described in the literature cited herein.
  • primers can incorporate additional features which allow for the detection or immobilization of the primer but do not alter the basic property of the primer, that of acting as a point of initiation of DNA synthesis.
  • primers can contain an additional nucleic acid sequence at the 5′ end which does not hybridize to the target nucleic acid, but which facilitates cloning, detection, or sequencing of the amplified product.
  • the region of the primer which is sufficiently complementary to the template to hybridize is referred to herein as the hybridizing region.
  • a primer is “specific” for a target sequence if, when used in an amplification reaction under sufficiently stringent conditions, the primer hybridizes primarily to the target nucleic acid.
  • a primer is specific for a target sequence if the primer-target duplex stability is greater than the stability of a duplex formed between the primer and any other sequence found in the sample.
  • salt conditions such as salt conditions as well as base composition of the primer and the location of the mismatches, will affect the specificity of the primer, and that routine experimental confirmation of the primer specificity will be needed in many cases.
  • Hybridization conditions can be chosen under which the primer can form stable duplexes only with a target sequence.
  • the use of target-specific primers under suitably stringent amplification conditions enables the selective amplification of those target sequences which contain the target primer binding sites.
  • primers for use in the methods described herein comprise or consist of a nucleic acid of at least about 15 nucleotides long that has the same sequence as, or is substantially complementary to, a contiguous nucleic acid sequence of the target V or J segment.
  • Longer primers e.g., those of about 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, or 50 nucleotides long that have the same sequence as, or sequence complementary to, a contiguous sequence of the target V or J segment, will also be of use in certain embodiments.
  • primers can have additional sequence added (e.g., nucleotides that cannot be the same as or complementary to the target V or J segment), such as restriction enzyme recognition sites, adaptor sequences for sequencing, bar code sequences, and the like (see e.g., primer sequences provided herein and in the sequence listing).
  • the length of the primers can be longer, such as 55, 56, 57, 58, 59, 60, 65, 70, 75, or 80 nucleotides in length or more, depending on the specific use or need.
  • the forward and reverse primers are both modified at the 5′ end with the universal forward primer sequence compatible with a DNA sequencing nucleic acid sequence.
  • adaptive immune receptor V-segment or J-segment oligonucleotide primer variants that can share a high degree of sequence identity to the oligonucleotide primers.
  • adaptive immune receptor V-segment or J-segment oligonucleotide primer variants can have substantial identity to the adaptive immune receptor V-segment or J-segment oligonucleotide primer sequences disclosed herein, for example, such oligonucleotide primer variants can comprise at least 70% sequence identity, preferably at least 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or higher sequence identity compared to a reference polynucleotide sequence such as the oligonucleotide primer sequences disclosed herein, using the methods described herein (e.g., BLAST analysis using standard parameters).
  • oligonucleotide primer variants will contain one or more substitutions, additions, deletions and/or insertions, preferably such that the annealing ability of the variant oligonucleotide is not substantially diminished relative to that of an adaptive immune receptor V-segment or J-segment oligonucleotide primer sequence that is specifically set forth herein.
  • adaptive immune receptor V-segment and J-segment oligonucleotide primers are designed to be capable of amplifying a rearranged TCR or IGH sequence that includes the coding region for CDR3.
  • the primers for use in the multiplex PCR methods of the present disclosure can be functionally blocked to prevent non-specific priming of non-T or B cell sequences.
  • the primers can be blocked with chemical modifications as described in U.S. patent application publication US2010/0167353.
  • the use of such blocked primers in the present multiplex PCR reactions involves primers that can have an inactive configuration wherein DNA replication (i.e., primer extension) is blocked, and an activated configuration wherein DNA replication proceeds.
  • the inactive configuration of the primer is present when the primer is either single-stranded, or when the primer is specifically hybridized to the target DNA sequence of interest but primer extension remains blocked by a chemical moiety that is linked at or near to the 3′ end of the primer.
  • the activated configuration of the primer is present when the primer is hybridized to the target nucleic acid sequence of interest and is subsequently acted upon by RNase H or another cleaving agent to remove the 3′ blocking group, thereby allowing an enzyme (e.g., a DNA polymerase) to catalyze primer extension in an amplification reaction.
  • an enzyme e.g., a DNA polymerase
  • the kinetics of the hybridization of such primers are akin to a second order reaction, and are therefore a function of the T cell or B cell gene sequence concentration in the mixture.
  • Blocked primers minimize non-specific reactions by requiring hybridization to the target followed by cleavage before primer extension can proceed.
  • a primer hybridizes incorrectly to a sequence that is related to the desired target sequence but which differs by having one or more non-complementary nucleotides that result in base-pairing mismatches, cleavage of the primer is inhibited, especially when there is a mismatch that lies at or near the cleavage site.
  • This strategy to improve the fidelity of amplification reduces the frequency of false priming at such locations, and thereby increases the specificity of the reaction.
  • reaction conditions can be optimized to maximize the difference in cleavage efficiencies between highly efficient cleavage of the primer when it is correctly hybridized to its true target sequence, and poor cleavage of the primer when there is a mismatch between the primer and the template sequence to which it can be incompletely annealed.
  • a number of blocking groups are known in the art that can be placed at or near the 3′ end of the oligonucleotide (e.g., a primer) to prevent extension.
  • a primer or other oligonucleotide can be modified at the 3′-terminal nucleotide to prevent or inhibit initiation of DNA synthesis by, for example, the addition of a 3′ deoxyribonucleotide residue (e.g., cordycepin), a 2′,3′-dideoxyribonucleotide residue, non-nucleotide linkages or alkane-diol modifications (U.S. Pat. No. 5,554,516).
  • a 3′ deoxyribonucleotide residue e.g., cordycepin
  • 2′,3′-dideoxyribonucleotide residue e.g., non-nucleotide linkages or alkane-diol modifications
  • blocking groups include 3′ hydroxyl substitutions (e.g., 3′-phosphate, 3′-triphosphate or 3′-phosphate diesters with alcohols such as 3-hydroxypropyl), 2′,3′-cyclic phosphate, 2′ hydroxyl substitutions of a terminal RNA base (e.g., phosphate or sterically bulky groups such as triisopropyl silyl (TIPS) or tert-butyl dimethyl silyl (TBDMS)).
  • 2′-alkyl silyl groups such as TIPS and TBDMS substituted at the 3′-end of an oligonucleotide are described by Laikhter et al., U.S. patent application Ser. No. 11/686,894, which is incorporated herein by reference.
  • Bulky substituents can also be incorporated on the base of the 3′-terminal residue of the oligonucleotide to block primer extension.
  • the oligonucleotide can comprise a cleavage domain that is located upstream (e.g., 5′ to) of the blocking group used to inhibit primer extension.
  • the cleavage domain can be an RNase H cleavage domain, or the cleavage domain can be an RNase H2 cleavage domain comprising a single RNA residue, or the oligonucleotide can comprise replacement of the RNA base with one or more alternative nucleosides. Additional illustrative cleavage domains are described in US 2010/0167353, which is incorporated by reference in its entirety.
  • a multiplex PCR system can use 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, or more forward primers, wherein each forward primer is complementary to a single functional TCR or Ig V segment or a small family of functional TCR or Ig V segments, e.g., a TCR V ⁇ segment, or (see e.g., the TCR primers as set forth in the Sequence Listing), and, for example, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more reverse primers, each specific to a TCR or Ig J segment, such as TCR J ⁇ segment (see e.g., Sequence Listing).
  • a multiplex PCR reaction can use four forward primers each specific to one or more functional TCR ⁇ V segment and four reverse primers each specific for one or more TCR ⁇ J segments.
  • a multiplex PCR reaction can use 84 forward primers each specific to one or more functional V segments and six reverse primers each specific for one or more J segments. Accordingly, various combinations of V and J primers can be used in a multiplex PCR reaction.
  • the V and J segment primers are used to produce a plurality of amplicons from the multiplex PCR reaction.
  • the amplicons range in size from 10, 20, 30, 40, 50, 75, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500 to 1600 nucleotides in length.
  • the amplicons have a size between 50-600 nucleotides in length.
  • these embodiments exploit current understanding in the art (also described above) that once an adaptive immune cell (e.g., a T or B lymphocyte) has rearranged its adaptive immune receptor-encoding (e.g., TCR or Ig) genes, its progeny cells possess the same adaptive immune receptor-encoding gene rearrangement, thus giving rise to a clonal population that can be uniquely identified by the presence therein of rearranged (e.g., CDR3-encoding) V- and J-gene segments that can be amplified by a specific pairwise combination of V- and J-specific oligonucleotide primers as herein disclosed.
  • an adaptive immune cell e.g., a T or B lymphocyte
  • its adaptive immune receptor-encoding e.g., TCR or Ig
  • FIG. 12 is a high-level block diagram illustrating an example of a computer 1200 for use in analyzing molecular analytes, in accordance with one embodiment. Illustrated are at least one processor 1202 coupled to a chipset 1204 .
  • the chipset 1204 includes a memory controller hub 1220 and an input/output (I/O) controller hub 1222 .
  • a memory 1206 and a graphics adapter 1212 are coupled to the memory controller hub 1220 , and a display device 1218 is coupled to the graphics adapter 1212 .
  • a storage device 1208 , keyboard 1210 , pointing device 1214 , and network adapter 1216 are coupled to the I/O controller hub 122 .
  • Other embodiments of the computer 1200 have different architectures.
  • the memory 1206 is directly coupled to the processor 1202 in some embodiments.
  • the storage device 1208 is a non-transitory computer-readable storage medium such as a hard drive, compact disk read-only memory (CD-ROM), DVD, or a solid-state memory device.
  • the memory 1206 holds instructions and data used by the processor 1202 .
  • the pointing device 1214 is used in combination with the keyboard 1210 to input data into the computer system 1200 .
  • the graphics adapter 1212 displays images and other information on the display device 1218 .
  • the display device 1218 includes a touch screen capability for receiving user input and selections.
  • the network adapter 1216 couples the computer system 1200 to the network.
  • Some embodiments of the computer 1020 have different and/or other components than those shown in FIG. 12 .
  • the server can be formed of multiple blade servers and lack a display device, keyboard, and other components.
  • the computer 1200 is adapted to execute computer program modules for providing functionality described herein.
  • module refers to computer program instructions and other logic used to provide the specified functionality.
  • a module can be implemented in hardware, firmware, and/or software.
  • program modules formed of executable computer program instructions are stored on the storage device 1208 , loaded into the memory 1206 , and executed by the processor 1202 .
  • the computer 1200 is designed to execute a machine learning algorithm for predicting an immune response of a test subject.
  • the system 1200 enables software to carry out actions for a computer-implemented method for determining an immunological status of a test subject.
  • the computer-implemented method includes steps for storing data for a control subject obtained from a plurality of samples at various timepoints, said data comprising for each sample, nucleic acid sequence information for a plurality of unique rearranged nucleic acid sequences in said sample, an AIR sequence diversity score for said sample, a frequency of occurrence of each unique rearranged nucleic acid sequence in said sample, and a determined immunological status for said subject.
  • the computer-implemented method includes steps for determining rules by a processor for assessing an immunological status of a test subject based on said data of said control subject; inputting data for a test subject for a plurality of samples obtained at various timepoints before and after immunotherapy, said data comprising for each sample, nucleic acid sequence information for a plurality of unique rearranged nucleic acid sequences in said sample, an AIR sequence diversity score for said sample, and a frequency of occurrence of each unique rearranged nucleic acid sequence in said sample; and receiving a determination of an immunological status of said test subject.
  • the computer-implemented method comprises determining a predicted response to immunotherapy of said test subject.
  • the data for said control subject comprises nucleic acid sequence information obtained from said control subject at a timepoint prior to immunotherapy treatment.
  • the data for said control subject comprises nucleic acid sequence information obtained from said control subject at a timepoint after immunotherapy treatment.
  • This example describes a clinical study in which 34 patients with high risk hematological malignancies were myeloablated and then transplanted with double umbilical cord blood (CB) units. Blood samples were collected at 0, 28, 56, 100, 180, and 360 days post transplant. At each time point, ImmunoseqTM high-throughput T cell receptor (TCR) sequencing assay (Adaptive Biotechnologies Corp., Seattle, Wash.) was applied to all samples. The ImmunoseqTM data were used to assay the adaptive immune system at unprecedented depth, so that T cell clonal expansion and contraction of hundreds of thousands of T cell clones were tracked over time and TCR repertoire diversity was directly measured.
  • TCR T cell receptor
  • the adaptive immune system reconstitution was shown to oscillate wildly with an almost entirely new repertoire appearing at least monthly after CB transplant.
  • the largest clones from the prior blood draw dropped to below detectable levels within weeks, contrasting with the control data where the top clones in healthy patients were not only all observed at the following time point, but remained the highest frequency clones.
  • CBT cord blood transplant
  • This Example demonstrates the ability to more accurately measure functional immune reconstitution in patients undergoing HCT and thus determine the consequent risk of mortality from infectious complications, which will positively impact direct medical decision-making aimed at reducing this risk, especially in the setting of immunosuppressive therapy for the prevention and treatment of GVHD.
  • an individual T cell In the blood of a healthy adult, an individual T cell primarily expresses one of millions of different TCRs, and a clone is the set of T cells expressing the same TCR 1,2 . Diversity of the TCR repertoire is known to be necessary for adequate protection against foreign pathogens. This is evident in humans with primary or acquired immunodeficiency diseases (e.g., SCIDS, CVID, and HIV), in aging, and following hematopoietic cell transplantation where loss of TCR diversity has been implicated in the increase in morbidity and mortality from infection that is observed in these patients.
  • primary or acquired immunodeficiency diseases e.g., SCIDS, CVID, and HIV
  • T cell repertoire diversity provides a direct measurement of immune reconstitution after myeloablative CBT.
  • TCR diversity was measured in CBT recipients at time points 28, 56, and 100 days post transplant, and shown to be predictive of non-relapse mortality (NRM). Additionally, to better understand the dynamics of immune reconstitution, quantitative TCR sequence diversity and distribution data were obtained at each time point and used to track the expansion and contraction of hundreds of thousands of T cell clones simultaneously.
  • Patients, Treatment Regimens and Post-Transplant Supportive Care Patients with hematologic malignancy, aged ⁇ 45 years old, received a myeloablative CBT if they lacked a suitably HLA-matched related or unrelated donor. The patients' underlying disease was categorized as standard or high-risk based upon previously described criteria [17]. Patients received a single or double CB graft as determined by institutional priority criteria. All CB units were HLA-typed at the intermediate resolution level for HLA-A and HLA-B and allele-level (high resolution) for HLA-DRB 1, and all CB units were required to be matched to the recipient at ⁇ 4 of the 6 HLA loci. Patients without pre-transplant blood samples stored for TCR analysis or who died before day 28 were excluded.
  • Myeloablative conditioning consisted of either cyclophosphamide (Cy) (total 120 mg/kg), hyperfractionated total body irradiation (TBI) over 4 days (total of 13.2 Gy), and fludarabine (Flu) (total 75 mg/m 2 ), or Treosulfan (Treo) (total 42 gm/m 2 ), Flu (total 150 mg/m 2 ), and a single fraction of 2 Gy TBI. All patients received GVHD immunoprophylaxis with cyclosporine-A (CSA) and mycophenolate mofetil (MMF) beginning on day-3.
  • CSA cyclosporine-A
  • MMF mycophenolate mofetil
  • the TCR ⁇ CDR3 region was defined according to the IMGT collaboration 3 , beginning with the second conserved cysteine encoded by the 3′ portion of the V ⁇ gene segment and ending with the conserved phenylalanine encoded by the 5′ portion of the J ⁇ gene segment. The number of nucleotides between these codons determined the length and therefore the frame of the CDR3 region. TCR ⁇ CDR3 regions were amplified and sequenced using previously described protocols (Robins et al., 2009 Blood 114, 4099; Robins et al., 2010 Sci. Translat. Med. 2:47ra64; Robins et al., 2011 J. Immunol. Meth. doi:10.1016/j.jim.2011.09.
  • Sequence reads of length 60 bp were obtained using the Illumina HiSeqTM System (Illumina, Inc., San Diego, Calif.). Raw HiSeqTM sequence data were preprocessed to remove errors in the primary sequence of each read, and to compress the data. A nearest neighbor algorithm was used to collapse the data into unique sequences by merging closely related sequences, to remove both PCR and sequencing errors.
  • ⁇ Fludarabine 75 mg/m 2 , Cytoxan 120 mg/kg, TBI 1320 cGy.
  • ⁇ Treosulfan 42 gm/m 2 , Fludarabine 150 mg/m 2 , TBI 200 cGy.
  • ⁇ HLA matching reflects the lowest HLA-match of the 2 units.
  • FIG. 1 shows the proportion of TCR repertoire carried over after transplant across patients and time points.
  • Analysis of clones using the ImmunoseqTM high throughput TCR sequencing assay yielded different results than microchimerism as measured by previous methods.
  • TCR clones post transplant In order to assess the stability of the reconstituting adaptive immune system over time, the persistence of TCR clones found at early time-points was investigated in later samples. Using only patients with samples collected and sequenced at 28, 56, 100, 180 and 365 days post-transplant, the top 10 TCR clones were determined by frequency in each patient at the 28, 56, 100 and 180 day time-points and the sequences of each of these clones was classified as either persistent or transient. A top-ten TCR clone that was observed (at any frequency) at a later time-point was considered persistent, and clones that were never again observed in samples from the same patient were considered transient.
  • FIG. 2 shows the median number of transient TCR clones in the top 10, at each time-point post-transplant.
  • dynamic and highly unstable TCR repertoires were observed in which many TCR clones that were present at high frequency in an early sample were never again observed subsequently.
  • this pattern began to subside and patients' TCR repertoires became more stable.
  • PBMC samples were sequenced from four healthy control subjects over the same length of time.
  • the median number of transient TCR clones in the top 10 was 0 for these healthy controls at each time-point, confirming the assumption that the high prevalence of transient TCR clones following transplant was indicative of an unusually unstable TCR repertoire.
  • T cell clonal diversity post transplant Changes in T cell clonal diversity post transplant.
  • the distribution of T cell clones was used to estimate the lower bound on the diversity in the full blood using an unseen species analysis (Robins et al., 2009 Blood 114, 4099). The diversity estimate was computed for each time point.
  • FIG. 3 presents a summary of immune reconstitution as measured by TCR repertoire during the first year post-transplant in this cohort.
  • the geometric mean of the diversity metric is shown at each time point and is illustrative of the general course of reconstitution.
  • Myeloablative conditioning regimens resulted in a large drop in TCR diversity from pre-transplant values.
  • Diversity decreased from pre-transplant values to day 28, which was close to the mean time to engraftment for most patients (engraftment time ranged from 7 to 45 days with a mean of 24).
  • TCR diversity reached its lowest value at 56 days post-transplant before beginning a slow recovery to a substantial increase in TCR repertoire diversity by one year post-transplant.
  • patient TCR repertoires still had a much lower diversity than healthy repertoires by the end of the one-year study.
  • TCR diversity can be explained by variations in absolute T cell counts.
  • the TCR diversity of such a patient was limited.
  • several of the patients had very low CD3 counts and, therefore, low diversity.
  • there were patients in this cohort who had higher absolute CD3 counts but little diversity, secondary to highly oligoclonal TCR repertoire (a small number of highly expanded clones).
  • TCR Diversity as a predictor of mortality from infection. Of the 34 patients in the present study, 15 died in the first year post transplant. The sole cause of death in 6 of these patients was relapsed disease, with death primarily from infectious causes in the remaining nine patients. Infectious complications post transplant were not unexpected or uncommon. However, prior to the present disclosure, there was no concrete measurement having strong predictive value to assess which patients were at increased risk of dying from life threatening infections post transplant. Such predictive capability can change the medical management of patients post stem cell transplant. Therefore, the present direct measurement of TCR diversity was analyzed for its potential as an informative predictor of the ability of the adaptive immune system to fight infection. The diversity of the T cell repertoire at early time points post transplant (Day 56 and Day 100) was indeed a strong predictor of mortality from non-relapse causes.
  • Table 3 summarizes the results obtained when analyzing CD3+ counts alongside the TCR diversity metric, using data from day 56 and 100 post-transplant.
  • each sample was assigned to a high (at or above median) or low (below median) group for both metrics, and the number of eventual deaths from NRM falling into each category were compared (out of the six that survived until day 56).
  • Table 3 presents the results of a one-tailed p-value for a Mann-Whitney U test of the hypothesis that patients dying from NRM tended to have lower values of absolute CD3+ counts or TCR diversity.
  • the TCR diversity metric was a predictor of clinical outcome as early as day 56 post transplant while absolute CD3+ counts were uninformative at that time.
  • This study used a direct TCR sequence-based measure of immune reconstitution that correlated with adverse clinical outcomes, particularly the increased risk of infectious complications in patients undergoing myeloablative cord blood transplantation.
  • Recipients of CBT were at increased risk of delayed hematopoietic and immune recovery, and improvement in overall survival for these patients was dependent on strategies that can enhance the kinetics of neutrophil and immune system recovery.
  • Direct measures of hematopoietic recovery are simple and well established by obtaining complete blood counts.
  • a direct measure of immune system recovery especially with respect to T cell function as opposed to T cell numbers, has been lacking prior to the present disclosure. Thus, there are standards of care regarding medications for the prevention and treatment of GVHD.
  • TCR diversity is a highly useful measure with which to stratify patients soon after transplant based on the risk of future infectious complications.
  • a patient has not met a threshold level of TCR diversity by two to three months post-transplant, that patient can benefit by coming off IST more rapidly as tolerated, and/or can be treated more aggressively with anti-microbial prophylaxis, and/or can be kept under observation for a longer period until immune reconstitution has reached adequate levels.
  • this measure should allow ample time for such prophylactic measures.
  • the presently described robust measurement of immune reconstitution can also help determine when patients have achieved sufficient immune reconstitution to discontinue prophylactic treatment, rather than administering a regimen of the same duration to each patient.
  • T cell receptor diversity and distribution were determined as described above in blood and solid tumor samples, obtained prior to and after initiation of immunotherapy, from cancer patients who were candidates to receive either a CTLA-4 inhibitor or a PD-1 inhibitor.
  • the efficacy of each immunotherapy agent was independently assessed by standard oncology clinical criteria (categorizing subjects as responders or non-responders) and the relative ability of each patient's adaptive immune system to respond beneficially to the immunotherapy was shown to be predicted by a modified entropy calculation of the distribution of the TCR repertoire prior to immunotherapy.
  • responders Before the initiation of immunotherapy (anti-CTLA-4 mAb), responders exhibited relatively higher TCR sequence diversity in lymphocytes present in blood and tumor samples, and higher TCR sequence distribution entropy, observed as a flatter TCR distribution profile, relative to non-responders.
  • FIG. 6 the results of quantitatively sequencing TCR encoding DNA from blood samples show that low TCR repertoire clonality, indicative of higher TCR sequence diversity and higher TCR sequence distribution entropy, was a predictor of immunotherapy (anti-CTLA-4 mAb) responder status.
  • FIG. 6 also shows that high TCR repertoire clonality, indicative of lower TCR sequence diversity and lower TCR sequence distribution entropy, was a predictor of immunotherapy non-responder status.
  • FIG. 7 shows the results from quantitative sequencing of TCR encoding DNA from tumor tissue samples.
  • FIG. 7 illustrates an increase in TCR clonality in lymphocytes present in solid tumor tissue samples obtained after administration of immunotherapy (anti-CTLA-4 mAb) (DT) relative to the level of TCR clonality detected in tumor samples obtained prior to immunotherapy (AT). The sample was obtained from a responder subject.
  • FIG. 7 demonstrates that the immunotherapy treatment had a noticeable impact on the subject's T cell repertoire.
  • Timepoints A, B, and C are timepoints taken from blood samples. Timepoint A is before immunotherapy, and timepoints B and C are two timepoints after starting the immunotherapy regimen. Timepoints AT, BT, CT are paired tumor samples (AT is before immunotherapy, and timepoints BT and CT are two timepoints after starting the immunotherapy regimen). Each line of datapoints follows a single clone.
  • the arrow at timepoint CT indicates a single clone that was unremarkable in its relative abundance prior to therapy, but that increased in relative frequency in tumor samples post-therapy, to account for 10% of the repertoire at timepoint CT.
  • the three most numerous clones in tumor samples at timepoint A decreased significantly in their subsequent relative representation, as determined at later timepoints.
  • TCR sequence diversity and distribution entropies were determined in blood samples obtained prior to (timepoint A) and after (timepoints B and C) initiation of immunotherapy.
  • the results are summarized in FIG. 9 , which shows dynamics of individual TCR clonal representations over time.
  • the arrow indicates a single clone that was not highly represented prior to immunotherapy but that increased in preponderance post-therapy to account for greater than 10% of the repertoire at timepoint C.
  • a side effect of an immunotherapy treatment can be a proliferation of a single or few clones in the blood of a subject, such that the frequency of occurrence of the single or few clones is statistically significantly greater than the frequencies of occurrence of the other clones in the repertoire.
  • the frequency of occurrence of a single clone is determined to be greater than a predetermined threshold, such as greater than the top quartile of frequencies of occurrence of the clones in the repertoire.
  • the single clone that accounts for greater than 10% of the repertoire after immunotherapy treatment is statistically significantly different and is an indicator of poor response by the subject.
  • a clone frequency that is less than 1% in frequency of occurrence before immunotherapy and spikes in frequency to greater than 1% of frequency of occurrence in the repertoire is an indicator of poor outcome in the subject.
  • TCRB sequencing was performed using high-throughput sequencing of the TCRB gene locus to characterize the repertoire of tumor-infiltrating lymphocytes (TILs) in late-stage metastatic melanoma patients undergoing immunotherapy (treatment with an anti-PD-1 antibody).
  • the goal of the study was to determine whether characterization of the intratumoral T cell repertoire by high-throughput sequencing is sufficient to predict clinical outcome (i.e., drug response) using immunological profiling (by TCRB sequencing) of a pre-treatment tumor biopsy.
  • PD-1 Programmed cell death protein 1
  • PD-1 is a type 1 membrane protein, a member of the immunoglobulin superfamily, and thought to play a role in B cell differentiation.
  • the efficacy of the immunotherapy treatment was independently assessed by standard oncology clinical criteria. Subjects were characterized as follows: responders (separated into “partial response” indicating a reduction in patient tumor burden and “stable disease” indicating lack of progression without decreased tumor burden) or non-responders (continued disease progression).
  • responders separated into “partial response” indicating a reduction in patient tumor burden and “stable disease” indicating lack of progression without decreased tumor burden
  • non-responders continuous disease progression.
  • the relative ability of each patient's adaptive immune system to respond beneficially to the immunotherapy was shown to be predicted by a modified entropy calculation of the distribution of the TCR repertoire prior to immunotherapy.
  • clonality was used in which each tumor sample's TCR sequence distribution entropy was normalized to the range (0-1) by accounting for the number of unique TCR rearrangements observed in that tumor sample and inverted so that a high normalized entropy becomes a low clonality and vice versa.
  • clonality was used in which each tumor sample's TCR sequence distribution entropy was normalized to the range (0-1) by accounting for the number of unique TCR rearrangements observed in that tumor sample and inverted so that a high normalized entropy becomes a low clonality and vice versa.
  • tissue samples from malignant lesion biopsies were prepared for 12 patients before administration of an anti-PD-1 antibody (administered as an immunotherapeutic agent for patients with metastatic melanoma).
  • Tissue samples biopsies from melanoma lesions
  • genomic DNA was extracted from these tissue samples.
  • the repertoire of TILs in each sample was characterized to determine (1) the extent of intratumoral lymphocyte infiltration, and (2) the clonal structure of the intratumoral lympochyte repertoire.
  • FIG. 10A shows that high intratumoral TCR repertoire clonality, indicative of a TCR repertoire characterized by a small number of highly-expanded T cell clones (low AIR sequence diversity), was a statistically-significant predictor of immunotherapy responder status in this retrospective study of a 12-patient cohort.
  • the mean and standard deviation of TCR repertoire clonality (a modified metric based on TCR sequence distribution entropy normalized to the range (0-1) by accounting for the number of unique TCR sequences present in each sample) are presented according to response to immunotherapy.
  • T cell infiltration was assessed in the cohort of 12 patients.
  • the mean and standard deviation of T cell infiltration are presented according to response to immunotherapy.
  • TCR repertoire clonality and response to immunotherapy were assessed for cohorts 1, 2 and the combined cohort.
  • the mean and standard deviation of TCR repertoire clonality (a modified metric based on TCR sequence distribution entropy normalized to the range (0-1) by accounting for the number of unique TCR sequences present in each sample) is shown according to response to immunotherapy in cohort 1 (plain square), cohort 2 (slant striped square) and in the combined data (straight striped square).
  • T cell infiltration was assessed in the patient groups.
  • the mean and standard deviation of T cell infiltration (measured as T cell receptor rearrangements per diploid genome) is shown according to response to immunotherapy in cohort 1 (plain square), cohort 2 (slanted stripe square) and in the combined data (straight stripe square).
  • FIG. 11C shows a comparison of each patient's rank (out of 25 patients total) for level of T cell infiltration and TCR repertoire clonality. Compared to responders (diamond), non-responders (circle) simultaneously tend toward low TCR repertoire clonality and low levels of infiltrating T lymphocytes.

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