Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers

Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers

(2022) Frank J. Lowery et al.   SCIENCE

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

(2021) Kevin Bi et al.   CANCER CELL

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

(2021) Kevin Litchfield et al.   CELL

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

(2021) Ayse Bassez et al.   NATURE MEDICINE

The role of GPR56/ADGRG1 in health and disease

(2021) Abhishek Kumar Singh et al.   Biomedical Journal

Spatially organized multicellular immune hubs in human colorectal cancer

(2021) Karin Pelka et al.   CELL

Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

(2021) Justina X. Caushi et al.   NATURE

Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

(2021) Giacomo Oliveira et al.   NATURE

A transcriptionally distinct CXCL13+CD103+CD8+ T-cell population is associated with B-cell recruitment and neoantigen load in human cancer

(2019) Hagma H Workel et al.   Cancer Immunology Research

HLA*LA—HLA typing from linearly projected graph alignments

(2019) Alexander T Dilthey et al.   BIOINFORMATICS

Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4+ memory T cells

(2019) Kim-Long Truong et al.   Nature Communications

Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers

(2019) Maria R. Parkhurst et al.   Cancer Discovery

MHC-II neoantigens shape tumour immunity and response to immunotherapy

(2019) Elise Alspach et al.   NATURE

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes

(2018) Marvin H. Gee et al.   CELL

Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations

(2018) Christopher P. Wardell et al.   JOURNAL OF HEPATOLOGY

A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade

(2018) Daniela S. Thommen et al.   NATURE MEDICINE

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors

(2018) Thomas Duhen et al.   Nature Communications

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

Cancer Neoantigens

(2018) Ton N. Schumacher et al.   Annual Review of Immunology

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

(2018) Hanjie Li et al.   CELL

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

Maftools: efficient and comprehensive analysis of somatic variants in cancer

(2018) Anand Mayakonda et al.   GENOME RESEARCH

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

(2018) Wouter Scheper et al.   NATURE MEDICINE

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

(2017) Chao Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Association of Distinct Mutational Signatures With Correlates of Increased Immune Activity in Pancreatic Ductal Adenocarcinoma

(2017) Ashton A. Connor et al.   JAMA Oncology

Genomic analyses identify molecular subtypes of pancreatic cancer

(2016) Peter Bailey et al.   NATURE

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

(2016) Eric Tran et al.   NEW ENGLAND JOURNAL OF MEDICINE

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

(2016) Valsamo Anagnostou et al.   Cancer Discovery

Genomic spectra of biliary tract cancer

(2015) Hiromi Nakamura et al.   NATURE GENETICS

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

Granzyme A activates another way to die

(2015) Judy Lieberman   IMMUNOLOGICAL REVIEWS

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads

(2014) Yu Bai et al.   BMC GENOMICS

Efficient Identification of Mutated Cancer Antigens Recognized by T Cells Associated with Durable Tumor Regressions

(2014) Y.-C. Lu et al.   CLINICAL CANCER RESEARCH

CCR4 and its ligands: from bench to bedside

(2014) O. Yoshie et al.   INTERNATIONAL IMMUNOLOGY

PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors

(2014) Alena Gros et al.   JOURNAL OF CLINICAL INVESTIGATION

Cancer Immunotherapy Based on Mutation-Specific CD4+ T Cells in a Patient with Epithelial Cancer

(2014) E. Tran et al.   SCIENCE

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

(2014) Christopher A. Miller et al.   PLoS Computational Biology

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Specific expression of GPR56 by human cytotoxic lymphocytes

(2011) Yen-Ming Peng et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Persistence of effector memory Th1 cells is regulated by Hopx

(2010) Inka Albrecht et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Both CD4 and CD8 T Cells Mediate Equally Effective In Vivo Tumor Treatment When Engineered with a Highly Avid TCR Targeting Tyrosinase

(2010) T. L. Frankel et al.   JOURNAL OF IMMUNOLOGY

IL-7 Receptor Expression Provides the Potential for Long-Term Survival of Both CD62Lhigh Central Memory T Cells and Th1 Effector Cells during Leishmania major Infection

(2009) S. L. Colpitts et al.   JOURNAL OF IMMUNOLOGY