Patent ID: 8236503

Claim:
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).