Method of measuring adaptive immunity

A method for quantifying TCRγ CDR3-encoding region diversity in a population of T cells, comprising:

• (a) amplifying DNA extracted from a biological sample that comprises T cells, in a multiplex polymerase chain reaction (PCR) that comprises:
• (i) a plurality of V-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human T cell receptor (TCR) 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 TCR Vγ-encoding gene segment and wherein the plurality of V-segment primers specifically hybridize to substantially all functional TCR Vγ-encoding gene segments that are present in the sample, and
• (ii) a plurality of J-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human T cell receptor (TCR) 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 TCR Jγ-encoding gene segment and wherein the plurality of J-segment primers specifically hybridize to substantially all functional TCR Jγ-encoding gene segments that are present in the sample,
• wherein the V-segment and J-segment primers are capable of promoting amplification in said multiplex polymerase chain reaction (PCR) of substantially all rearranged TCRγ CDR3-encoding regions in the sample to produce a multiplicity of amplified rearranged DNA molecules from a population of T cells in the sample, said multiplicity of amplified rearranged DNA molecules being sufficient to quantify diversity of the TCRγ CDR3-encoding region in the population of T cells;
• and
• (b) determining a relative frequency of occurrence for each unique rearranged DNA molecule in said multiplicity of amplified rearranged DNA molecules, and thereby quantifying TCRγ CDR3-encoding region diversity.

A composition comprising:

• (a) a plurality of V-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human immunoglobulin heavy chain (IGH) 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 IGH VH-encoding gene segment and wherein the plurality of V-segment primers specifically hybridize to substantially all functional IGH VH-encoding gene segments that are present in a sample that comprises B cells from a human subject;
• and
• (b) a plurality of J-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human immunoglobulin heavy chain (IGH) 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 TCR JH-encoding gene segment and wherein the plurality of J-segment primers specifically hybridize to substantially all functional IGH JH-encoding gene segments that are present in the sample that comprises B cells from the human subject;
• wherein the V-segment and J-segment primers are capable of promoting amplification in a multiplex polymerase chain reaction (PCR) of substantially all rearranged IGH CDR3-encoding regions in the sample to produce a multiplicity of amplified rearranged DNA molecules from a population of B cells in the sample, said multiplicity of amplified rearranged DNA molecules being sufficient to quantify diversity of the IGH CDR3-encoding region in the population of B cells.

A method for quantifying IGH CDR3-encoding region diversity in a population of B cells, comprising:

• (a) amplifying DNA extracted from a biological sample that comprises B cells, in a multiplex polymerase chain reaction (PCR) that comprises:
• (i) a plurality of variable (V)-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human immunoglobulin heavy chain (IGH) 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 IGH V-encoding gene segment and wherein the plurality of V-segment primers specifically hybridize to substantially all functional IGH V-encoding gene segments that are present in the sample, and
• (ii) a plurality of J-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human immunoglobulin heavy chain (IGH) 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 IGH J-encoding gene segment and wherein the plurality of J-segment primers specifically hybridize to substantially all functional IGH J-encoding gene segments that are present in the sample,
• wherein the V-segment and J-segment primers are capable of promoting amplification in said multiplex polymerase chain reaction (PCR) of substantially all rearranged IGH CDR3-encoding regions in the sample to produce a multiplicity of amplified rearranged DNA molecules from a population of B cells in the sample, said multiplicity of amplified rearranged DNA molecules being sufficient to quantify diversity of the IGH CDR3-encoding region in the population of B cells;
• and
• (b) determining a relative frequency of occurrence for each unique rearranged DNA molecule in said multiplicity of amplified rearranged DNA molecules, and thereby quantifying IGH CDR3-encoding region diversity.

A composition comprising:

• (a) a plurality of V-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human T cell receptor (TCR) 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 TCR Vβ-encoding gene segment and wherein the plurality of V-segment primers specifically hybridize to substantially all functional TCR Vβ-encoding gene segments that are present in a sample that comprises T cells from a human subject;
• and
• (b) a plurality of J-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human T cell receptor (TCR) 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 TCR Jβ-encoding gene segment and wherein the plurality of J-segment primers specifically hybridize to substantially all functional TCR Jβ-encoding gene segments that are present in the sample that comprises T cells from the human subject;
• wherein the V-segment and J-segment primers are capable of promoting amplification in a multiplex polymerase chain reaction (PCR) of substantially all rearranged TCRβ CDR3-encoding regions in the sample to produce a multiplicity of amplified rearranged DNA molecules from a population of T cells in the sample, said multiplicity of amplified rearranged DNA molecules being sufficient to quantify diversity of the TCRβ CDR3-encoding region in the population of T cells.

A method for quantifying TCRβ CDR3-encoding region diversity in a population of T cells, comprising:

• (a) amplifying DNA extracted from a biological sample that comprises T cells, in a multiplex polymerase chain reaction (PCR) that comprises:
• (i) a plurality of V-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human T cell receptor (TCR) 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 TCR Vβ-encoding gene segment and wherein the plurality of V-segment primers specifically hybridize to substantially all functional TCR Vβ-encoding gene segments that are present in the sample, and
• (ii) a plurality of J-segment oligonucleotide primers that are each independently capable of specifically hybridizing to at least one polynucleotide encoding a human T cell receptor (TCR) 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 TCR Jβ-encoding gene segment and wherein the plurality of J-segment primers specifically hybridize to substantially all functional TCR Jβ-encoding gene segments that are present in the sample,
• wherein the V-segment and J-segment primers are capable of promoting amplification in said multiplex polymerase chain reaction (PCR) of substantially all rearranged TCRβ CDR3-encoding regions in the sample to produce a multiplicity of amplified rearranged DNA molecules from a population of T cells in the sample, said multiplicity of amplified rearranged DNA molecules being sufficient to quantify diversity of the TCRβ CDR3-encoding region in the population of T cells;
• and
• (b) determining a relative frequency of occurrence for each unique rearranged DNA molecule in said multiplicity of amplified rearranged DNA molecules, and thereby quantifying TCRβ CDR3-encoding region diversity.