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US 12,606,870 B2Granted
Methods of monitoring conditions by sequence analysis
AssigneeAdaptive Biotechnologies Corporation
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.
Claims21
A method comprising:
- (a) amplifying recombined nucleic acids comprising complementary determining region 3 (CDR3) sequences from T cell receptor (TCR) genes or immunoglobulin genes from at least one sample of nucleic acids from T cells and/or B cells obtained from an individual having an autoimmune disease, wherein the at least one sample is a blood sample;
- (b) spatially isolating individual molecules of the amplified recombined nucleic acids;
- (c) generating one or more clonotype profiles by sequencing the spatially isolated amplified recombined nucleic acids, wherein each of the one or more clonotype profiles comprises at least 10,000 sequence reads of at least 30 base pairs per read;
- (d) determining one or more correlating clonotypes of the autoimmune disease in the individual using the one or more clonotype profiles;
- (e) identifying the individual as having a level of the one or more correlating clonotypes indicative of an active episode of the autoimmune disease;
- and
- (f) administering an autoimmune disease therapy to the individual to treat the autoimmune disease.
4 more elements
A method comprising:
- (a) amplifying recombined nucleic acids comprising complementary determining region 3 (CDR3) sequences from T cell receptor (TCR) genes or immunoglobulin genes from at least one sample of nucleic acids from T cells and/or B cells obtained from an individual suspected of having an autoimmune disease, wherein the at least one sample is a blood sample;
- (b) spatially isolating individual molecules of the amplified recombined nucleic acids;
- (c) generating one or more clonotype profiles by sequencing the spatially isolated amplified recombined nucleic acids, wherein each of the one or more clonotype profiles comprises at least 10,000 sequence reads of at least 30 base pairs per read;
- (d) determining presence of one or more correlating clonotypes of the autoimmune disease in the individual using the one or more clonotype profiles;
- (e) identifying the individual as having the autoimmune disease based on the presence of the one or more correlating clonotypes of the autoimmune disease;
- and
- (f) administering an autoimmune disease therapy to the individual to treat the autoimmune disease.
4 more elements
Dependencies are inferred from the claim text.