Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens

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

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Integrated analysis of somatic mutations and immune microenvironment of multiple regions in breast cancers

(2017) Taigo Kato et al.   Oncotarget

Metastatic Melanoma Patient Had a Complete Response with Clonal Expansion after Whole Brain Radiation and PD-1 Blockade

(2017) Cara L. Haymaker et al.   Cancer Immunology Research

Integrated analysis of somatic mutations and immune microenvironment in malignant pleural mesothelioma

(2017) Kazuma Kiyotani et al.   OncoImmunology

TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection

(2017) Zhan Zhou et al.   Royal Society Open Science

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

Targeting human melanoma neoantigens by T cell receptor gene therapy

(2016) Matthias Leisegang et al.   JOURNAL OF CLINICAL INVESTIGATION

Comparison of exome-based HLA class I genotyping tools: identification of platform-specific genotyping errors

(2016) Kazuma Kiyotani et al.   JOURNAL OF HUMAN GENETICS

Sampling From the Proteome to the Human Leukocyte Antigen-DR (HLA-DR) Ligandome ProceedsViaHigh Specificity

(2016) Geert P. M. Mommen et al.   MOLECULAR & CELLULAR PROTEOMICS

Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes

(2016) Amalie Kai Bentzen et al.   NATURE BIOTECHNOLOGY

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

(2016) Alena Gros et al.   NATURE 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

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens

(2016) Shelly Kalaora et al.   Oncotarget

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

(2016) Marios Giannakis et al.   Cell Reports

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

(2016) Jasreet Hundal et al.   Genome Medicine

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

Intratumoral expression levels of PD-L1, GZMA, and HLA-A along with oligoclonal T cell expansion associate with response to nivolumab in metastatic melanoma

(2016) Hiroyuki Inoue et al.   OncoImmunology

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Eradication of Large Solid Tumors by Gene Therapy with a T-Cell Receptor Targeting a Single Cancer-Specific Point Mutation

(2015) M. Leisegang et al.   CLINICAL CANCER RESEARCH

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

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

Immune Checkpoint Blockade in Cancer Therapy

(2015) Michael A. Postow et al.   JOURNAL OF CLINICAL ONCOLOGY

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

(2015) Michal Bassani-Sternberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry

(2015) Etienne Caron et al.   MOLECULAR & CELLULAR PROTEOMICS

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

NY-ESO-1–specific TCR–engineered T cells mediate sustained antigen-specific antitumor effects in myeloma

(2015) Aaron P Rapoport et al.   NATURE MEDICINE

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

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

Adoptive cell transfer as personalized immunotherapy for human cancer

(2015) S. A. Rosenberg et al.   SCIENCE

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

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

HLAreporter: a tool for HLA typing from next generation sequencing data

(2015) Yazhi Huang et al.   Genome Medicine

Association of Polymerase e–Mutated and Microsatellite-Instable Endometrial Cancers With Neoantigen Load, Number of Tumor-Infiltrating Lymphocytes, and Expression of PD-1 and PD-L1

(2015) Brooke E. Howitt et al.   JAMA Oncology

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia

(2014) M. Rajasagi et al.   BLOOD

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

(2014) Yu Bai et al.   BMC GENOMICS

Whole-Exome Sequencing of Muscle-Invasive Bladder Cancer Identifies Recurrent Mutations of UNC5C and Prognostic Importance of DNA Repair Gene Mutations on Survival

(2014) K. L. Yap et al.   CLINICAL CANCER RESEARCH

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

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

Phase II Clinical Trial of Multiple Peptide Vaccination for Advanced Head and Neck Cancer Patients Revealed Induction of Immune Responses and Improved OS

(2014) Y. Yoshitake et al.   CLINICAL CANCER RESEARCH

Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival

(2014) S. D. Brown et al.   GENOME RESEARCH

A phase ΙI study of five peptides combination with oxaliplatin-based chemotherapy as a first-line therapy for advanced colorectal cancer (FXV study)

(2014) Shoichi Hazama et al.   Journal of Translational Medicine

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma

(2014) Carsten Linnemann et al.   NATURE MEDICINE

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

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

The immune epitope database (IEDB) 3.0

(2014) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

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

(2014) E. Tran et al.   SCIENCE

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

MHC Class I Antigen Processing and Presenting Machinery: Organization, Function, and Defects in Tumor Cells

(2013) P. Leone et al.   JNCI-Journal of the National Cancer Institute

The Human Leukocyte Antigen–presented Ligandome of B Lymphocytes

(2013) Chopie Hassan et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Paul F Robbins et al.   NATURE MEDICINE

HLA Haplotyping from RNA-seq Data Using Hierarchical Read Weighting

(2013) Hyunsung John Kim et al.   PLoS One

Immunotype and Immunohistologic Characteristics of Tumor-Infiltrating Immune Cells Are Associated with Clinical Outcome in Metastatic Melanoma

(2012) G. Erdag et al.   CANCER RESEARCH

Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity

(2012) Mikkel Harndahl et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Safety and Activity of Anti–PD-L1 Antibody in Patients with Advanced Cancer

(2012) Julie R. Brahmer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Safety, Activity, and Immune Correlates of Anti–PD-1 Antibody in Cancer

(2012) Suzanne L. Topalian et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

Tumor Regression in Patients With Metastatic Synovial Cell Sarcoma and Melanoma Using Genetically Engineered Lymphocytes Reactive With NY-ESO-1

(2011) Paul F. Robbins et al.   JOURNAL OF CLINICAL ONCOLOGY

Nomenclature for factors of the HLA system, 2010

(2010) S. G. E. Marsh et al.   TISSUE ANTIGENS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH