Neoantigen identification strategies enable personalized immunotherapy in refractory solid tumors

Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies

(2018) Lena Gorgannezhad et al.   LAB ON A CHIP

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

(2018) Nikolaos Zacharakis et al.   NATURE MEDICINE

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

Natural Killer T-cell Immunotherapy in Combination with Chemotherapy-Induced Immunogenic Cell Death Targets Metastatic Breast Cancer

(2017) Simon Gebremeskel et al.   Cancer Immunology Research

Breast Cancer Neoantigens Can Induce CD8 + T-Cell Responses and Antitumor Immunity

(2017) Xiuli Zhang et al.   Cancer Immunology Research

Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA

(2016) J. C. Thompson et al.   CLINICAL CANCER RESEARCH

Immune activation and response to pembrolizumab in POLE-mutant endometrial cancer

(2016) Janice M. Mehnert et al.   JOURNAL OF CLINICAL INVESTIGATION

Identification of Individual Cancer-Specific Somatic Mutations for Neoantigen-Based Immunotherapy of Lung Cancer

(2016) Takahiro Karasaki et al.   Journal of Thoracic Oncology

Pembrolizumab for patients with PD-L1-positive advanced gastric cancer (KEYNOTE-012): a multicentre, open-label, phase 1b trial

(2016) Kei Muro et al.   LANCET ONCOLOGY

Neoantigen landscape dynamics during human melanoma–T cell interactions

(2016) Els M. E. Verdegaal et al.   NATURE

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

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

Cancer immunotherapy targeting neoantigens

(2016) Yong-Chen Lu et al.   SEMINARS IN IMMUNOLOGY

Combination of radiotherapy and vaccination overcomes checkpoint blockade resistance

(2016) Wenxin Zheng et al.   Oncotarget

Mutational profiling of non-small-cell lung cancer patients resistant to first-generation EGFR tyrosine kinase inhibitors using next generation sequencing

(2016) Ying Jin et al.   Oncotarget

The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine

(2016) Andrea Garofalo et al.   Genome Medicine

NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets

(2016) Morten Nielsen et al.   Genome Medicine

Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade

(2016) D. B. Johnson et al.   Cancer Immunology Research

HLA class I-restricted MYD88 L265P-derived peptides as specific targets for lymphoma immunotherapy

(2016) Annika Nelde et al.   OncoImmunology

CRISPR-Cas9-mediated disruption of PD-1 on human T cells for adoptive cellular therapies of EBV positive gastric cancer

(2016) Shu Su et al.   OncoImmunology

Genomic Alterations in Cell-Free DNA and Enzalutamide Resistance in Castration-Resistant Prostate Cancer

(2016) Alexander W. Wyatt et al.   JAMA Oncology

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Toward Personalized Lymphoma Immunotherapy: Identification of Common Driver Mutations Recognized by Patient CD8+ T Cells

(2015) J. S. Nielsen et al.   CLINICAL CANCER RESEARCH

Clinical Actionability Enhanced through Deep Targeted Sequencing of Solid Tumors

(2015) K. Chen et al.   CLINICAL CHEMISTRY

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

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

Suppressive effects of gemcitabine plus cisplatin chemotherapy on regulatory T cells in nonsmall-cell lung cancer

(2015) Cheng Chen et al.   JOURNAL OF INTERNATIONAL MEDICAL RESEARCH

Prospective Clinical Study of Precision Oncology in Solid Tumors

(2015) Davendra P. S. Sohal et al.   JNCI-Journal of the National Cancer Institute

Activity and safety of nivolumab, an anti-PD-1 immune checkpoint inhibitor, for patients with advanced, refractory squamous non-small-cell lung cancer (CheckMate 063): a phase 2, single-arm trial

(2015) Naiyer A Rizvi et al.   LANCET ONCOLOGY

Chimeric antigen receptor-modified T cells derived from defined CD8+ and CD4+ subsets confer superior antitumor reactivity in vivo

(2015) D Sommermeyer et al.   LEUKEMIA

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

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

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

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

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

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

(2015) N. A. Rizvi et al.   SCIENCE

Prospective Clinical Study of Precision Oncology in Solid Tumors

(2015) Davendra P. S. Sohal et al.   JNCI-Journal of the National Cancer Institute

HLA ligandomics identifies histone deacetylase 1 as target for ovarian cancer immunotherapy

(2015) Janet Kerstin Peper et al.   OncoImmunology

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution

(2014) Aaron M. Newman et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Survival, Durable Tumor Remission, and Long-Term Safety in Patients With Advanced Melanoma Receiving Nivolumab

(2014) Suzanne L. Topalian et al.   JOURNAL OF CLINICAL ONCOLOGY

Radiation-Induced CXCL16 Release by Breast Cancer Cells Attracts Effector T Cells

(2014) S. Matsumura et al.   JOURNAL OF IMMUNOLOGY

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

A vaccine targeting mutant IDH1 induces antitumour immunity

(2014) Theresa Schumacher et al.   NATURE

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

(2014) Thomas Powles 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

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations

(2014) Faviel F. González-Galarza 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

Low-Dose Irradiation Programs Macrophage Differentiation to an iNOS+/M1 Phenotype that Orchestrates Effective T Cell Immunotherapy

(2013) Felix Klug et al.   CANCER CELL

Dendritic cell immunotherapy combined with gemcitabine chemotherapy enhances survival in a murine model of pancreatic carcinoma

(2013) Tomar Ghansah et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Oncology Meets Immunology: The Cancer-Immunity Cycle

(2013) Daniel S. Chen et al.   IMMUNITY

Mutated PPP1R3B Is Recognized by T Cells Used To Treat a Melanoma Patient Who Experienced a Durable Complete Tumor Regression

(2013) Y.-C. Lu et al.   JOURNAL OF IMMUNOLOGY

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

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 Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Mechanisms and insights into drug resistance in cancer

(2013) Hiba Zahreddine et al.   Frontiers in Pharmacology

Personalized peptide vaccination: a new approach for advanced cancer as therapeutic cancer vaccine

(2012) Masanori Noguchi et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

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

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

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

(2012) Hirokazu Matsushita et al.   NATURE

Durable Complete Responses in Heavily Pretreated Patients with Metastatic Melanoma Using T-Cell Transfer Immunotherapy

(2011) S. A. Rosenberg et al.   CLINICAL CANCER RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Cell transfer immunotherapy for metastatic solid cancer—what clinicians need to know

(2011) Steven A. Rosenberg   Nature Reviews Clinical Oncology

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

(2011) Nikhil Wagle et al.   Cancer Discovery

HLA-A2-restricted T-cell epitopes specific for prostatic acid phosphatase

(2010) Brian M. Olson et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Complete molecular response in CML after p210 BCR–ABL1-derived peptide vaccination

(2010) Monica Bocchia et al.   Nature Reviews Clinical Oncology

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

(2009) Morten Nielsen et al.   BMC BIOINFORMATICS

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

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