Monitoring health and disease status using clonotype profiles
First Claim
1. A method of determining antigen-specific T cells in a tissue sample, comprising the steps of:
- dividing the tissue sample into a first subset and a second subset;
identifying clonotypes from the first subset by sequencing recombined nucleic acids encoding a T-cell receptor chain or a portion thereof from the first subset to provide sequence reads from which clonotypes are identified;
exposing the second subset to an antigen;
separating T cells from the second subset that interact with the antigen to obtain an enriched T cell sample;
identifying clonotypes from the enriched T cell sample by sequencing recombined nucleic acids encoding a T-cell receptor chain or a portion thereof from the enriched T cell sample to provide sequence reads from which clonotypes are identified; and
identifying antigen-specific T cells in the tissue sample as T cells whose clonotype frequencies increase in the enriched T cell sample relative to the frequencies of the same clonotype in the first subset.
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Accused Products
Abstract
There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.
299 Citations
18 Claims
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1. A method of determining antigen-specific T cells in a tissue sample, comprising the steps of:
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dividing the tissue sample into a first subset and a second subset; identifying clonotypes from the first subset by sequencing recombined nucleic acids encoding a T-cell receptor chain or a portion thereof from the first subset to provide sequence reads from which clonotypes are identified; exposing the second subset to an antigen; separating T cells from the second subset that interact with the antigen to obtain an enriched T cell sample; identifying clonotypes from the enriched T cell sample by sequencing recombined nucleic acids encoding a T-cell receptor chain or a portion thereof from the enriched T cell sample to provide sequence reads from which clonotypes are identified; and identifying antigen-specific T cells in the tissue sample as T cells whose clonotype frequencies increase in the enriched T cell sample relative to the frequencies of the same clonotype in the first subset. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9)
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10. A method of determining antigen-specific T cells in a tissue sample, comprising the steps of:
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exposing the tissue sample to an antigen; separating T cells that interact with the antigen from T cells that do not interact with the antigen to obtain an enriched T cell sample and an unenriched T cell sample, respectively; identifying clonotypes from the enriched T cell sample by sequencing recombined nucleic acids encoding a T-cell receptor chain or a portion thereof from the enriched T cell sample to provide sequence reads from which clonotypes are identified; identifying clonotypes from the unenriched T cell sample by sequencing recombined nucleic acids encoding a T-cell receptor chain or a portion thereof from the unenriched T cell sample to provide sequence reads from which clonotypes are identified; and identifying antigen-specific T cells in the tissue sample as T cells whose clonotype frequencies increase in the enriched T cell sample relative to the frequencies of the same clonotype in the unenriched T cell sample. - View Dependent Claims (11, 12, 13, 14, 15, 16, 17, 18)
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Specification