Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy

Mutation position is an important determinant for predicting cancer neoantigens

(2020) Aude-Hélène Capietto et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

(2020) Daniel K. Wells et al.   CELL

Neoantigen identification strategies enable personalized immunotherapy in refractory solid tumors

(2019) Fangjun Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction

(2019) Jennifer G. Abelin et al.   IMMUNITY

T-cell responses toTP53"hotspot" mutations and unique neoantigens expressed by human ovarian cancers

(2018) Drew C Deniger et al.   CLINICAL CANCER RESEARCH

Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer

(2018) Nikolaos Zacharakis et al.   NATURE MEDICINE

Combined analysis of antigen presentation and T cell recognition reveals restricted immune responses in melanoma

(2018) Shelly Kalaora et al.   Cancer Discovery

Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification

(2018) Brendan Bulik-Sullivan et al.   NATURE BIOTECHNOLOGY

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

Cancer: Precision T-cell therapy targets tumours

(2017) Cornelis J. M. Melief   NATURE

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Neoantigen prediction and the need for validation

(2017) Antonella Vitiello et al.   NATURE BIOTECHNOLOGY

The problem with neoantigen prediction

(2017)   NATURE BIOTECHNOLOGY

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

(2017) InYoung Song et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Landscape of immunogenic tumor antigens in successful immunotherapy of virally induced epithelial cancer

(2017) Sanja Stevanović et al.   SCIENCE

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

(2017) Dung T. Le et al.   SCIENCE

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope

(2017) InYoung Song et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TCR Signal Strength and T Cell Development

(2016) Nicholas R.J. Gascoigne et al.   Annual Review of Cell and Developmental Biology

Immune targets and neoantigens for cancer immunotherapy and precision medicine

(2016) Rong-Fu Wang et al.   CELL RESEARCH

Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 Expression

(2016) Maria Parkhurst et al.   CLINICAL CANCER RESEARCH

Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

(2016) Alena Gros et al.   NATURE MEDICINE

Drugging the Undruggable Ras — Immunotherapy to the Rescue?

(2016) Carl H. June   NEW ENGLAND JOURNAL OF MEDICINE

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

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

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

(2016) N. McGranahan et al.   SCIENCE

Targeting of cancer neoantigens with donor-derived T cell receptor repertoires

(2016) E. Stronen et al.   SCIENCE

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

(2016) Valsamo Anagnostou et al.   Cancer Discovery

Durable Complete Response from Metastatic Melanoma after Transfer of Autologous T Cells Recognizing 10 Mutated Tumor Antigens

(2016) T. D. Prickett et al.   Cancer Immunology Research

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Isolation of neoantigen-specific T cells from tumor and peripheral lymphocytes

(2015) Cyrille J. Cohen et al.   JOURNAL OF CLINICAL INVESTIGATION

TCR contact residue hydrophobicity is a hallmark of immunogenic CD8+T cell epitopes

(2015) Diego Chowell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neoantigens in cancer immunotherapy

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

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

(2015) B. M. Carreno et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

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

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

Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

(2014) Fei Duan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA-Binding Properties of Tumor Neoepitopes in Humans

(2014) E. F. Fritsch et al.   Cancer Immunology Research

Surveillance of the Tumor Mutanome by T Cells during Progression from Primary to Recurrent Ovarian Cancer

(2013) Darin A. Wick et al.   CLINICAL CANCER RESEARCH

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

(2012) Hirokazu Matsushita et al.   NATURE

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

(2012) Martin Christen Frølund Thomsen et al.   NUCLEIC ACIDS RESEARCH

T Cell Receptor    Diversity Inversely Correlates with Pathogen-Specific Antibody Levels in Human Cytomegalovirus Infection

(2012) G. C. Wang et al.   Science Translational Medicine

iMOSFLM: a new graphical interface for diffraction-image processing withMOSFLM

(2011) T. Geoff G. Battye et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Natural Innate and Adaptive Immunity to Cancer

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

A Single T Cell Receptor Bound to Major Histocompatibility Complex Class I and Class II Glycoproteins Reveals Switchable TCR Conformers

(2011) Lei Yin et al.   IMMUNITY

T Cell Allorecognition via Molecular Mimicry

(2009) Whitney A. Macdonald et al.   IMMUNITY

UV-Induced Ligand Exchange in MHC Class I Protein Crystals

(2009) Patrick H. N. Celie et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Age-associated decline in T cell repertoire diversity leads to holes in the repertoire and impaired immunity to influenza virus

(2008) Eric J. Yager et al.   JOURNAL OF EXPERIMENTAL MEDICINE