Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy

Long-Term Outcomes in BRAF-Mutated Melanoma Treated with Combined Targeted Therapy or Immune Checkpoint Blockade: Are We Approaching a True Cure?

(2020) Patrick Schummer et al.   AMERICAN JOURNAL OF CLINICAL DERMATOLOGY

Human Anti-tumor Immunity: Insights from Immunotherapy Clinical Trials

(2020) Jackson G. Egen et al.   IMMUNITY

Resistance to Checkpoint Inhibition in Cancer Immunotherapy

(2020) Luisa Barrueto et al.   Translational Oncology

TCR Convergence in Individuals Treated With Immune Checkpoint Inhibition for Cancer

(2020) Timothy John Looney et al.   Frontiers in Immunology

Association of Tumor Microenvironment T-Cell Repertoire and Mutational Load With Clinical Outcome After Sequential Checkpoint Blockade in Melanoma

(2019) Erik Yusko et al.   Cancer Immunology Research

Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition

(2019) Philip Bradley et al.   Annual Review of Immunology

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

The evolving landscape of ‘next-generation’ immune checkpoint inhibitors: A review

(2019) Luca Mazzarella et al.   EUROPEAN JOURNAL OF CANCER

PD-L1 Distribution and Perspective for Cancer Immunotherapy—Blockade, Knockdown, or Inhibition

(2019) Yilun Wu et al.   Frontiers in Immunology

The impact of CTLA-4 blockade and interferon-α on clonality of T-cell repertoire in the tumor microenvironment and peripheral blood of metastatic melanoma patients

(2019) Arjun Khunger et al.   OncoImmunology

Characterization of Distinct T Cell Receptor Repertoires in Tumor and Distant Non-tumor Tissues from Lung Cancer Patients

(2019) Xiang Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Compartmental analysis of T cell clonal dynamics as a function of pathologic response to neoadjuvant PD-1 blockade in resectable non-small cell lung cancer

(2019) Jiajia Zhang et al.   CLINICAL CANCER RESEARCH

Immune checkpoint inhibitors: a promising anticancer therapy

(2019) Sima Singh et al.   DRUG DISCOVERY TODAY

TCR Repertoire Diversity of Peripheral PD-1+CD8+ T Cells Predicts Clinical Outcomes after Immunotherapy in Patients with Non–Small Cell Lung Cancer

(2019) Jiefei Han et al.   Cancer Immunology Research

Neoadjuvant PD-1 Blockade in Resectable Lung Cancer

(2018) Patrick M. Forde et al.   NEW ENGLAND JOURNAL OF MEDICINE

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

The Mutation-Associated Neoantigen Functional Expansion of Specific T Cells (MANAFEST) Assay: A Sensitive Platform for Monitoring Antitumor Immunity

(2018) Ludmila Danilova et al.   Cancer Immunology Research

Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification

(2018) Ke-Yue Ma et al.   Frontiers in Immunology

Dynamics of tumor and immune responses during immune checkpoint blockade in non-small cell lung cancer

(2018) Valsamo Anagnostou et al.   CANCER RESEARCH

Peripheral Blood TCR Repertoire Profiling May Facilitate Patient Stratification for Immunotherapy against Melanoma

(2018) Sabrina A. Hogan et al.   Cancer Immunology Research

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

(2017) Whijae Roh et al.   Science Translational Medicine

Regulation of PD-1/PD-L1 pathway and resistance to PD-1/PDL1 blockade

(2017) Jie Bai et al.   Oncotarget

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis

(2017) Alexandra Snyder et al.   PLOS MEDICINE

ImmunoMap: A Bioinformatics Tool for T-cell Repertoire Analysis

(2017) John-William Sidhom et al.   Cancer Immunology Research

Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile

(2017) Theres Oakes et al.   Frontiers in Immunology

RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data

(2016) Bram Gerritsen et al.   BIOINFORMATICS

TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences

(2016) Sheng-Jou Hung et al.   BMC BIOINFORMATICS

The role of neoantigens in response to immune checkpoint blockade

(2016) Nadeem Riaz et al.   INTERNATIONAL IMMUNOLOGY

How many TCR clonotypes does a body maintain?

(2016) Grant Lythe et al.   JOURNAL OF THEORETICAL BIOLOGY

Evidence of shared epitopic reactivity among independent B-cell clones in chronic lymphocytic leukemia patients

(2016) S Mimmi et al.   LEUKEMIA

Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire

(2016) Jennifer S. Sims et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clonal expansion of CD8 T cells in the systemic circulation precedes development of ipilimumab-induced toxicities

(2016) Sumit K. Subudhi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Validation of biomarkers to predict response to immunotherapy in cancer: Volume I — pre-analytical and analytical validation

(2016) Giuseppe V. Masucci et al.   Journal for ImmunoTherapy of Cancer

IMSEQ—a fast and error aware approach to immunogenetic sequence analysis

(2015) Leon Kuchenbecker et al.   BIOINFORMATICS

Anti–PD-1/PD-L1 therapy of human cancer: past, present, and future

(2015) Lieping Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Nivolumab versus chemotherapy in patients with advanced melanoma who progressed after anti-CTLA-4 treatment (CheckMate 037): a randomised, controlled, open-label, phase 3 trial

(2015) Jeffrey S Weber et al.   LANCET ONCOLOGY

T-cell receptor profiling in cancer

(2015) Ilan Kirsch et al.   Molecular Oncology

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires

(2015) Victor Greiff et al.   TRENDS IN IMMUNOLOGY

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

(2015) Mikhail Shugay et al.   PLoS Computational Biology

A high density of tertiary lymphoid structure B cells in lung tumors is associated with increased CD4+T cell receptor repertoire clonality

(2015) Wei Zhu et al.   OncoImmunology

Peripheral T cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma

(2015) Michael A. Postow et al.   Journal for ImmunoTherapy of Cancer

Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing

(2014) Mathieu Giraud et al.   BMC GENOMICS

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice

(2014) Victor Greiff et al.   BMC IMMUNOLOGY

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

(2014) Michael E. Birnbaum et al.   CELL

The Future of Cancer Therapy: Selecting Patients Likely to Respond to PD1/L1 Blockade

(2014) A. Ribas et al.   CLINICAL CANCER RESEARCH

CTLA4 Blockade Broadens the Peripheral T-Cell Receptor Repertoire

(2014) L. Robert et al.   CLINICAL CANCER RESEARCH

Nivolumab for the treatment of cancer

(2014) Anasuya Gunturi et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

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

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

MPDL3280A (anti-PD-L1) treatment leads to clinical activity in metastatic bladder cancer

(2014) Thomas Powles et al.   NATURE

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Improved Survival with T Cell Clonotype Stability After Anti-CTLA-4 Treatment in Cancer Patients

(2014) E. Cha et al.   Science Translational Medicine

Quantification of HTLV-1 Clonality and TCR Diversity

(2014) Daniel J. Laydon et al.   PLoS Computational Biology

MiTCR: software for T-cell receptor sequencing data analysis

(2013) Dmitriy A Bolotin et al.   NATURE METHODS

Breathing new life into immunotherapy: review of melanoma, lung and kidney cancer

(2013) Charles G. Drake et al.   Nature Reviews Clinical Oncology

Ecological analysis of antigen-specific CTL repertoires defines the relationship between naive and immune T-cell populations

(2013) P. G. Thomas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using synthetic templates to design an unbiased multiplex PCR assay

(2013) Christopher S. Carlson et al.   Nature Communications

Sequence analysis of T-cell repertoires in health and disease

(2013) Daniel J Woodsworth et al.   Genome Medicine

Next generation sequencing for TCR repertoire profiling: Platform-specific features and correction algorithms

(2012) Dmitry A. Bolotin et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

High Frequency of Herpesvirus-Specific Clonotypes in the Human T Cell Repertoire Can Remain Stable over Decades with Minimal Turnover

(2012) M. A. Neller et al.   JOURNAL OF VIROLOGY

Subtle changes in TCRα CDR1 profoundly increase the sensitivity of CD4 T cells

(2012) Jennifer N. Lynch et al.   MOLECULAR IMMUNOLOGY

Natural Innate and Adaptive Immunity to Cancer

(2011) Matthew D. Vesely et al.   Annual Review of Immunology

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

(2011) R. L. Warren et al.   GENOME RESEARCH

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Trans-Endocytosis of CD80 and CD86: A Molecular Basis for the Cell-Extrinsic Function of CTLA-4

(2011) O. S. Qureshi et al.   SCIENCE

On the Composition of the Preimmune Repertoire of T Cells Specific for Peptide–Major Histocompatibility Complex Ligands

(2010) Marc K. Jenkins et al.   Annual Review of Immunology

Improved Survival with Ipilimumab in Patients with Metastatic Melanoma

(2010) F. Stephen Hodi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

(2009) J. D. Freeman et al.   GENOME RESEARCH

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

(2009) S. D. Boyd et al.   Science Translational Medicine