Methods of monitoring conditions by sequence analysis
AssigneeSequenta, Inc.
InventorsMalek Faham, Thomas Willis
Life of this patent
Estimating the term…
Abstract
There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.
Claims20
A method for determining a profile of clonotypes of recombined DNA sequences in T-cells and/or B-cells comprising:
- (a) obtaining a sample from a subject comprising T-cells and/or B-cells;
- (b) spatially isolating individual molecules of recombined DNA sequences from said cells on a solid surface;
- (c) sequencing said spatially isolated individual molecules of recombined DNA sequences to provide at least 1000 sequence reads each comprising at least 30 bp so that different clonotypes of said sample are determined from such sequence reads with a confidence of at least 99.9 percent;
- and
- (d) determining levels of different clonotypes from said sample to generate said profile of clonotypes of recombined DNA sequences.
A method for determining a profile of clonotypes of recombined DNA sequences in T-cells and/or B-cells comprising:
- (a) obtaining a sample from a subject comprising T-cells and/or B-cells;
- (b) spatially isolating individual molecules of recombined DNA sequences from said cells on a solid surface;
- (c) sequencing said spatially isolated individual molecules of recombined DNA sequences to provide at least 1000 sequence reads each comprising at least 30 bp, wherein different clonotypes of said sample are determined from such sequence reads with a confidence of at least 99.9 percent and wherein said sequencing does not comprise pyrosequencing;
- and
- (d) determining levels of different clonotypes from said sample to generate said profile of clonotypes of recombined DNA sequences.
A method for determining a profile of clonotypes of recombined T-cell receptor gene and/or immunoglobulin gene DNA sequences in T-cells and/or B-cells comprising:
- (a) obtaining a sample from a subject comprising T-cells and/or B-cells;
- (b) spatially isolating individual molecules of genomic DNA from said cells on a solid surface;
- (c) sequencing said spatially isolated individual molecules of genomic DNA to provide at least 1000 sequence reads each comprising at least 30 bp so that different clonotypes of said sample are determined from such sequence reads with a confidence of at least 99.9 percent;
- and
- (d) determining levels of different clonotypes from said sample to generate said profile of clonotypes of recombined T-cell receptor gene and/or immunoglobulin gene DNA sequences.
Dependencies are inferred from the claim text.