Methods of monitoring conditions by sequence analysis

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.