Genetics Institute, Inc.

The General Hospital Corporation

The Broad Institute, Inc.

Dana-farber-cancer Institute Inc.

Allied Corporation

Other

Edward F Fritsch

Mary Collins

Nir Hacohen

Jon I Williams

Marian S Ellwood

Kenneth A Jacobs

Steven E Diamond

Catherine Ju-Ying Wu

Catherine J Wu

Joseph G Brewen

Brian Seed

Joseph P Dougherty

Kaliappanadar Nellaiappan

Ute E Burkhardt

Lin Sun

Elena Getmanova

Michael Steven Rooney

Indu Javeri

John J Toole, Jr

Sachet Ashok Shukla

D Randall Steinbrink

H William Taeusch

David S Phelps

Joanna Floros

Alexander Kovtun

Jing Sun

Pavan Bachireddy

The present disclosure relates to methods for profiling subject specific and personalized T cell receptor (TCR) repertoires using a single-cell sequencing method. More particularly, disclosed are methods for determining binding of T cell receptors to subject specific neoantigens. In addition, the techniques herein may identify the antigenic targets of T cell receptors in the context of tumor neoantigens. Moreover, the present disclosure enables the discovery of T cell targets in numerous diseases, with implications for understanding the basic mechanisms of the mammalian immune response and for developing antigen-specific diagnostic markers and therapies. Finally, cloned TCRs can be used to formulate personalized immunotherapies for those inflicted with a disease, such as cancer.

Methods for profiling the T-cell-receptor repertoire

In one aspect, the invention features a combination of oligonucleotides comprising a forward primer oligonucleotide and a blocking oligonucleotide. The forward primer oligonucleotide has a 3' end region, where the 3&#x2032; end region includes a portion complementary to a mutation positioned in a region within a polynucleotide. The blocking oligonucleotide contains a blocking moiety and has a 5&#x2032; end region, where the 5&#x2032; end region includes a portion complementary to a wild-type sequence of the region corresponding to the position of the mutation. In other aspects, the invention provides kits including the combination of primer oligonucleotides and methods of using the oligonucleotides to detect a mutation in a polynucleotide.

Compositions and methods for detecting a mutant variant of a polynucleotide

The present invention relates to neoplasia vaccine or immunogenic composition administered in combination with other agents, such as checkpoint blockade inhibitors for the treatment or prevention of neoplasia in a subject.

Combination therapy with neoantigen vaccine

Methods for profiling the t cell repertoire

Disclosed herein in one aspect is a pharmaceutical composition comprising a plurality of neoantigenic peptides and a pharmaceutically acceptable carrier, each neoantigenic peptide comprising a tumor-specific neoepitope capable of binding to an HLA protein in a subject, each tumor-specific neoepitope comprising a tumor-specific mutation present in a tumor, wherein (a) the composition comprises neoantigenic peptides comprising tumor-specific mutations present in at least 1% of subjects in a population of subjects suffering from cancer; (b) the composition comprises neoantigenic peptides comprising tumor-specific neoepitopes which bind to HLA proteins present in at least 5% of subjects in the population; and (c) the composition comprises at least one neoantigenic peptide capable of eliciting an immune response against a tumor present in at least 5% of the subjects in the population of subjects suffering from cancer.

Shared neoantigens

Disclosed herein are methods and compositions related to engineered fragments of the human transglutaminase-related protein family, described herein as engineered transglutaminase barrel proteins (ETBPs), that have utility as high affinity, high selectivity target-binding proteins offering advantages as antibody equivalents for therapeutic, analytical, manufacturing and research purposes. ETBPs differ from naturally occurring human transglutaminase fragments by the addition, deletion, replacement and/or substitution of the naturally occurring amino acid sequence. ETBPs can be easily expressed in prokaryotic cells and in many cases can be purified by a simple solubilization and precipitation method.

Engineered transglutaminase barrel proteins

Process and nucleic acid construct for producing reagent complexes

This invention relates to novel proteins useful for enhancing pulmonary surfactant activity, methods for obtaining said proteins and compositions containing one or more of the proteins. The proteins of this invention include the following:

Pulmonary surfactant proteins

A diagnostic reagent is disclosed which is capable of binding to a target nucleotide sequence which is bound to a labeled polynucleotide in a target binding region which is at least partially co-extensive with the target binding region in the probe polynucleotide which is capable of binding to the target nucleotide sequence. A method is disclosed in which the reagent is contacted with a sample and with a capturing polynucleotide under conditions such that target nucleotide which may be present in the sample binds to the probe polynucleotide and displaces labeled polynucleotide from the reagent complex, and the capturing polynucleotide binds selectively to the displaced labeled polynucleotide in the region of the labeled polynucleotide that had been bound to the probe polynucleotide. Determination of the displaced nucleotide gives a value which is a function of the presence and concentration of target nucleotide in the sample.

Method and kit involving displacement and rehybridization of labeled

A diagnostic reagent is disclosed containing a complex of a probe polynucleotide (P) bound via purine/pyrimidine hydrogen bonding to a labeled polynucleotide (L). The probe (P) contains a target binding region (TBR) capable of binding to a target nucleotide sequence (G) of a biological sample. A method is disclosed in which contact with a sample containing the target nucleotide sequence (G) causes binding, initially between G and a single-stranded portion (IBR) of the target binding region (TBR). Thereafter the labeled polynucleotide (L) is displaced from the complex by branch migration of (G) into the (P)/(L) binding region. A volume excluding polymeric agent such as poly(ethylene oxide) (PEO or PEG) or other polyethers enhances the rate of appearance of displaced labeled polynucleotide. Determination of displaced labeled polynucleotide (L) gives a value which is a function of the presence and concentration of target nucleotide sequence (G) in the sample.

Displacement polynucleotide assay employing polyether and diagnostic kit

A diagnostic reagent is disclosed containing a complex of a probe polynucleotide (P) bound via purine/pyrimidine hydrogen bonding to a labeled polynucleotide (L). The probe (P) contains a target binding region (TBR) capable of binding to a target nucleotide sequence (G) of a biological sample. A method is disclosed in which contact with a sample containing the target nucleotide sequence (G) causes binding, initially between G and a single-stranded portion (IBR) of the target binding region (TBR). Thereafter the labeled polynucleotide (L) is displaced from the complex by branch migration of (G) into the (P)/(L) binding region. Determination of displaced labeled polynucleotide (L) gives a value which is a function of the presence and concentration of target nucleotide sequence (G) in the sample.

Displacement polynucleotide assay method and polynucleotide complex

The protein having factor VIII:C procoagulant activity has been produced by culturing a cell transformed with a recombinant expression vector encoding the gene for that activity.

Human factor VIII:C gene and recombinant methods for production

A target nucleotide sequence having a half-restriction site is determined in the nucleic acid of a biological sample. It is contacted with a reagent complex of:

Assay, reagent and kit employing nucleic acid strand displacement and

Reagent complexes containing a probe polynucleotide with at least two target binding regions. A labeled polynucleotide is bound to at least a portion of each target binding region. In one method, sample nucleic acid displaces labeled polynucleotide from one target binding region; after washing, a reagent polynucleotide displaces labeled polynucleotide from the other target binding region. In a second method, sample nucleic acid strands having two target nucleic acid sequences in proximity (e.g., sequences translocated in certain cancers) displace the labeled polynucleotide from both target binding region.

Growing community of inventors

Concord, MA, United States of America

Edward F Fritsch