Adaptive Biotechnologies Corporation

Littelfuse, Inc.

Mark Klinger

Malek Faham

John Matthew Kennedy

Harlan Saul Robins

William Gonzalez

Thomas M Snyder

Tom Novak

Victoria Carlton

Francois Pepin

Peter J R Ebert

Edward J Osborne

Marcos E Milla

Joyce K Hu

Timothy Lee Hayes

Julia Greissl

Jonathan M Carlson

The invention is directed to methods for determining antigen-specific T cells. In some embodiments, methods of the inven-tion may be implemented by the steps of reacting under interaction conditions one or more antigens with T cells in a plurality of subsets of a tissue sample, such as peripheral blood; sorting antigen-interacting T cells from other T cells; separately sequencing for each subset recombined nucleic acid encoding a segment of a TCR chain from a sample of T cells prior to exposure to antigen and from a sample off cells isolated based on their interaction with antigen, thereby form-ing a clonotype profile for the former sample and the latter sample for each subset; and identifying as antigen-specific T cells those T cells associated with a clonotype whose fre-quency increases in the latter sample relative to its frequency in the former sample.

Determining antigen-specific T-cells

Provided are methods for assessing T cell receptor β chain complementary determining region 3 (TCRβ CDR3) sequences. In certain embodiments, the methods comprise assessing TCRβ CDR3 sequences determined from a sample obtained from a subject having or suspected of having a tick bite for the presence or absence of one or more TCRβ CDR3 sequences set forth in the present disclosure. According to some embodiments, at the time of the assessing, the subject is seronegative for Lyme disease and/or has one or more non-specific symptoms consistent with Lyme disease. Also provided are methods comprising administering a Lyme disease therapy to a subject identified as comprising T cells that express a T cell receptor β chain (TCRβ) comprising a TCRβ CDR3 sequence set forth in the present disclosure.

Lyme disease-associated T cell receptor-related methods

Provided are methods of assessing a biological sample obtained from an individual for the presence of a T cell that expresses a T cell receptor (TCR) comprising a TCRβ CDR3 sequence set forth in Table 1. Such methods further comprise identifying the individual as having COVID-19 when the presence of the TCR is detected. The presence of one or more of these TCRs may be of use in prognosticating severity of COVID-19 in the individual and the individual may be treated based on the expected severity of COVID-19. Treatment methods may include administering to the individual a T cell engineered to express the TCR. Such engineered T cells are also disclosed. Also provided are compositions and multimers that find use, e.g., in practicing the methods of the present disclosure.

T cell receptor sequences diagnostic for COVID-19 and related compositions

The invention is directed to methods for determining antigen-specific T cells generally and to T cell receptors which bind an epitope of the Wilms' tumor antigen-1 (WT1) protein specifically. The disclosure also provides polynucleotides encoding the TCRs, engineered cells exogenously expressing the TCRs, and methods of making and using the TCRs and/or cells expressing the TCRs.

Determining WT-1 specific T cells and WT-1 specific T cell receptors (TCRs)

The invention is directed to methods for determining antigen-specific T cells. In some embodiments, methods of the invention may be implemented by the steps of reacting under interaction conditions one or more antigens with T cells in a plurality of subsets of a tissue sample, such as peripheral blood; sorting antigen-interacting T cells from other T cells; separately sequencing for each subset recombined nucleic acid encoding a segment of a TCR chain from a sample of T cells prior to exposure to antigen and from a sample of T cells isolated based on their interaction with antigen, thereby forming a clonotype profile for the former sample and the latter sample for each subset; and identifying as antigen-specific T cells those T cells associated with a clonotype whose frequency increases in the latter sample relative to its frequency in the former sample.

Compositions and methods are disclosed for identifying B-cell receptor sequences that bind to corresponding antigens. The disclosed methods and related embodiments permit the identification paired relationships between rearranged gene segments of B-cell receptors with unique antigens.

Identification of antigen-specific B cell receptors

The invention is directed to methods for determining nucleic acids that encode immune receptor chains originating from the same cell, that is, paired immune receptor chains. Methods of the invention comprise high-throughput sequencing of rearranged nucleic acids encoding immune receptors from one or more samples of lymphocytes. In one aspect, from a plurality of subsets of a sample, nucleic acids encoding separate chains of a pair are separately sequenced, wherein the size of the sample and the number of subsets are selected so that the distribution of lymphocytes approximates a binomial model. Paired chains are determined by identifying pairs that appear together or that are entirely absent in the subsets.

Determining paired immune receptor chains from frequency matched subunits

Determining antigen-specific t-cells

The present invention is drawn to methods for measuring numbers, levels, and/or ratios of cells, such as lymphocytes, infiltrated into a solid tissue, such as a tumor or a tissue affected by an autoimmune disease, and to methods for making patient prognoses based on such measurements. In one aspect, methods of the invention comprise sorting lymphocytes from an accessible tissue, such as peripheral blood, into functional subsets, such as cytotoxic T cells and regulatory T cells, and generating clonotype profiles of each subset. An inaccessible disease-affected tissue is sampled and one or more clonotype profiles are generated. From the latter clonotype profiles, levels lymphocytes in each of the functional subsets are determined in the disease-affected tissue by their clonotypes, which are identified from lymphocytes sorted into subsets from the accessible tissue.

Detection and measurement of tissue-infiltrating lymphocytes

The invention is directed to methods of monitoring B-cell lymphoid proliferative disorders, such as B-cell acute lymphoblastic leukemias, by measuring the presence, absence and/or levels of correlating, or index, clonotypes and related clonotypes that have evolved therefrom, for example, as part of the disease condition. In one aspect, such methods are implemented by generating sequencing-based clonotype profiles and determining frequencies of correlating, or index, clonotypes present, including new clonotypes that have evolved therefrom, particularly, in the case of B-cell ALL, by VH substitution. The invention also includes use of such monitoring information to modify treatment status of a patient.

Monitoring immunoglobulin heavy chain evolution in B-cell acute lymphoblastic leukemia

One embodiment of the present invention provides a fuse having opened-fuse indication, which places two or more coils or conductors in parallel and in thermal contact with an indicating material. The multiple conductors allow a lower level of current to produce sufficient heat or sufficient electrical resistance to transform the indicating material. The multiple conductors can also be made of a reduced diameter, resulting in surge protection at a lower device temperature. The multiple conductor indicator in an embodiment includes a base material. First and second conductors contact the base material. An indicating material thermally couples to the first and second conductors. The indicating material can be on the inside or outside of the fuse body. If on the outside, the body can define a recess, wherein the indicator resides within the recess. The indicator can operate with fuses and other types of circuit protection devices.

Growing community of inventors

Seattle, WA, United States of America

Mark Klinger