Method of Measuring Adaptive Immunity

Abstract

A method of measuring immunocompetence is described. This method provides a means for assessing the effects of diseases or conditions that compromise the immune system and of therapies aimed to reconstitute it. This method is based on quantifying T-cell diversity by calculating the number of diverse T-cell receptor (TCR) beta chain variable regions from blood cells.

What is claimed: 
     
         1 . A method for monitoring a disease state of an individual by determining one or more correlating clonotypes of the disease wherein the disease comprises an autoimmune disease, an infectious disease or cancer, the method comprising:
 (a) generating one or more clonotype profiles by sequencing individual, spatially isolated nucleic acid molecules,
 i. wherein each spatially isolated nucleic acid molecule comprises a recombined sequence from a T-cell and/or B-cell from at least one sample from the individual, 
 ii. wherein each of said samples comprises T-cells and/or B-cells and wherein the at least one sample is from a tissue affected by the disease, and 
 iii. wherein each of the one or more clonotype profiles comprises at least 1000 sequence reads of at least 30 base pairs per read; 
   (b) determining one or more correlating clonotypes of the disease in the individual using the one or more clonotype profiles from the tissue affected by the disease;   (c) generating one or more clonotype profiles of one or more blood samples of the individual, wherein each of the one or more clonotype profiles of the one or more blood samples comprises at least 1000 sequence reads of at least 30 base pairs per read; and   (d) monitoring a level of the one or more correlating clonotypes in the one or more blood samples of the individual by comparing the one or more correlating clonotypes identified in step (b) with the one or more clonotype profiles generated in step (c).   
     
     
         2 . The method of  claim 1 , wherein the determining one or more correlating clonotypes of the disease in the individual is achieved by comparing the clonotype profile from the tissue affected by the disease with one or more other clonotype profiles. 
     
     
         3 . The method of  claim 1 , wherein the determining one or more correlating clonotypes of the disease in the individual is achieved by identifying high level clonotypes in the clonotype profile from the tissue affected by the disease. 
     
     
         4 . The method of  claim 1 , wherein said disease is an autoimmune disease and said one or more correlating clonotypes are present in a peak state of the disease, wherein the peak state of the disease is a flare state of the autoimmune disease. 
     
     
         5 . The method of  claim 1 , wherein said T-cells and/or B-cells comprise a subset of T-cells and/or B cells. 
     
     
         6 . The method of  claim 5 , wherein said subset of T-cells and/or B-cells are enriched by interaction with a marker. 
     
     
         7 . The method of  claim 6 , wherein said marker is a cell surface marker on the subset of T-cells and/or B-cells. 
     
     
         8 . The method of  claim 5 , wherein said subset of T-cells and/or B-cells interact with an antigen specifically present in the disease. 
     
     
         9 . The method of  claim 1 , wherein the disease is systemic lupus erythematosus or multiple sclerosis. 
     
     
         10 . The method of  claim 1 , wherein said nucleic acid molecules are amplified. 
     
     
         11 . The method of  claim 10 , wherein each of said samples comprises at least 10,000 B-cells. 
     
     
         12 . The method of  claim 10 , wherein each of said samples comprises at least 10,000 T-cells. 
     
     
         13 . The method of  claim 1 , wherein each of said samples comprises at least 10,000 B-cells and wherein each of said clonotype profiles comprises at least 100,000 sequence reads. 
     
     
         14 . The method of  claim 13 , wherein each of said sequence reads comprises a paired-end read having an error rate of one percent or more. 
     
     
         15 . The method of  claim 1 , wherein each of said samples comprises at least 10,000 T-cells and wherein each of said clonotype profiles comprises at least 100,000 sequence reads. 
     
     
         16 . The method of  claim 15 , wherein each of said sequence reads comprises a paired-end read having an error rate of one percent or more. 
     
     
         17 . A method for monitoring a disease of an individual by quantifying a diversity of an immune receptor repertoire of said individual, wherein said disease comprises an autoimmune disease, an infectious disease, or cancer, said method comprising:
 (a) quantifying diversity of one or more immune receptor repertoires by sequencing by synthesis using an array of spatially isolated, individual DNA molecules,
 (i) wherein each spatially isolated, individual DNA molecule comprises a rearranged sequence from a T-cell and/or a B-cell from at least one sample obtained from said individual, 
 (ii) wherein each of said samples comprises T cells and/or B cells and wherein said at least one sample is obtained from a tissue affected by said disease, and 
 (iii) wherein said diversity of said one or more immune receptor repertoires comprises at least 10 4  unique rearranged sequences of at least 30 base pairs per read; 
   (b) determining one or more measurements of diversity of said one or more immune receptor repertoires of said disease in said individual using said one or more quantified diversities determined from said tissue affected by said disease;   (c) determining one or more measurements of diversity of one or more immune receptor repertoires from blood samples obtained from said individual, wherein each of said measurements of diversity of said blood samples comprises at least 10 4  sequence reads of at least 30 base pairs per read; and   (d) monitoring a change in diversity in said one or more measurements of diversity from said blood samples of said individual by comparing said one or more measurements of diversity determined in step (b) with said one or more measurements of diversity determined in step (c).   
     
     
         18 . The method of  claim 17 , wherein said determining one or more measurements of diversity of said immune receptor repertoire of said disease in said individual comprises comparing a measurement of diversity measured from a sample comprising tissue affected by said disease with one or more other measurements of diversity. 
     
     
         19 . The method of  claim 17 , wherein said disease is an autoimmune disease and wherein said one or more measurements of diversity are measured before a patient undergoes treatment. 
     
     
         20 . The method of  claim 17 , wherein said T-cells and/or B-cells comprise a subset of T-cells and/or B-cells. 
     
     
         21 . The method of  claim 20 , wherein said subset of T-cells and/or B-cells comprise a marker. 
     
     
         22 . The method of  claim 21 , wherein said marker is a cell surface marker on the subset of T-cells and/or B-cells. 
     
     
         23 . The method of  claim 20 , wherein said subset of T-cells and/or B-cells interact with an antigen specifically present in the disease. 
     
     
         24 . The method of  claim 17 , wherein said disease is an autoimmune disease. 
     
     
         25 . The method of  claim 17 , wherein said individual DNA molecules are amplified. 
     
     
         26 . The method of  claim 25 , wherein each of said samples comprises at least 10,000 B cells. 
     
     
         27 . The method of  claim 25 , wherein each of said samples comprises at least 10,000 T cells. 
     
     
         28 . The method of  claim 17 , wherein each of said samples comprises at least 10,000 B cells, and wherein each of said measurements of diversity comprises at least 100,000 sequence reads. 
     
     
         29 . The method of  claim 28 , wherein each of said sequence reads comprise a read having an error rate of one percent or more. 
     
     
         30 . The method of  claim 17 , wherein each of said samples comprises at least 10,000 T-cells and wherein each of said measurements of diversity comprises at least 100,000 sequence reads. 
     
     
         31 . The method of  claim 30 , wherein each of said sequence reads comprise a read having an error rate of one percent or more.