Abstract:
Provided are methods comprising causing relative movement of a first nucleic acid through an opening formed at least in part by an electrolyzed second nucleic acid. Such methods comprise, during the relative movement, detecting a varying conductance along the first nucleic acid, or a varying conductance between the first nucleic acid and an electrode proximate to the first nucleic acid, wherein the varying conductance is indicative of sequential interactions between nucleobases of the first nucleic acid and one or more nucleobases of the electrolyzed second nucleic acid. The varying conductance comprises conductance fingerprints for the different nucleobases in the first nucleic acid. In certain embodiments, the methods comprise determining the identity of one or more nucleotide, optionally determining a sequence, of the first nucleic acid based on the varying conductance. Computer-readable media and systems that find use, e.g., in practicing the methods of the present disclosure, are also provided.
Abstract:
Methods of monitoring and measuring dynamic adaptive immune cell responses are provided. High-throughput sequencing of T cell receptor and immunoglobulin loci is used to characterize the breadth of an effector cell response to a stimulus, such as a vaccine or infection. Unique responding effector cell clones and abundance thereof can be determined. Additionally, methods for determining the contribution of responding effector cells to the immunological memory compartment are provided.
Abstract:
Methods are provided for correction of amplification bias and quantitation of adaptive immune cells in a sample using synthetic templates that include random oligonucleotide sequences.
Abstract:
Provided are methods for assessing T cell receptor β chain complementary determining region 3 (TCRβ CDR3) sequences. In certain embodiments, prior to the assessing, the subject has been identified as having, or is suspected of having, inflammatory bowel disease (IBD). According to some embodiments, at the time of the assessing, the subject has one or more non-specific symptoms consistent with Crohn's disease. Also provided are methods comprising administering a Crohn's 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. Computer readable media and systems for assessing TCRβ CDR3 sequences are also provided.
Abstract:
Methods are provided for predicting and determining a subject's immune response to allograft. Methods include assessing immune response to an allograft by characterizing the diversity and distribution of clones of the adaptive immune repertoire. Methods are also provided for characterizing the adaptive immune response of a subject to an allograft using a mixed lymphocyte reaction culture.