Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer

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

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

Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer

(2018) Janos L. Tanyi et al.   Science Translational Medicine

Sensitive and frequent identification of high avidity neo-epitope specific CD8+ T cells in immunotherapy-naive ovarian cancer

(2018) Sara Bobisse et al.   Nature Communications

Rapid Construction of Antitumor T-cell Receptor Vectors from Frozen Tumors for Engineered T-cell Therapy

(2018) Takemasa Tsuji et al.   Cancer Immunology Research

A Pilot Trial of the Combination of Transgenic NY-ESO-1-reactive Adoptive Cellular Therapy with Dendritic Cell Vaccination With or Without Ipilimumab

(2018) Theodore S Nowicki et al.   CLINICAL CANCER RESEARCH

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

(2018) Derin B. Keskin et al.   NATURE

Intratumoral and Intertumoral Genomic Heterogeneity of Multifocal Localized Prostate Cancer Impacts Molecular Classifications and Genomic Prognosticators

(2017) Lei Wei et al.   EUROPEAN UROLOGY

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

Is It Possible to Develop Cancer Vaccines to Neoantigens, What Are the Major Challenges, and How Can These Be Overcome?

(2017) Stephen P. Schoenberger   Cold Spring Harbor Perspectives in Biology

Cancer statistics, 2016

(2016) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy

(2016) Jianjun Gao et al.   CELL

Lack of Immunomodulatory Interleukin-27 Enhances Oncogenic Properties of Mutant p53 In Vivo

(2016) D. Dibra et al.   CLINICAL CANCER RESEARCH

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

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

Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma

(2016) Jesse M. Zaretsky et al.   NEW ENGLAND JOURNAL OF MEDICINE

MYC regulates the antitumor immune response through CD47 and PD-L1

(2016) S. C. Casey et al.   SCIENCE

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

(2016) N. McGranahan et al.   SCIENCE

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

(2016) Valsamo Anagnostou et al.   Cancer Discovery

Proteomic analysis uncovers common effects of IFN-γ and IL-27 on the HLA class I antigen presentation machinery in human cancer cells

(2016) Andrea Petretto et al.   Oncotarget

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

Low Mutation Burden in Ovarian Cancer May Limit the Utility of Neoantigen-Targeted Vaccines

(2016) Spencer D. Martin et al.   PLoS One

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

(2015) Massimo Andreatta et al.   IMMUNOGENETICS

Synergistic anti-tumor effect of combined inhibition of EGFR and JAK/STAT3 pathways in human ovarian cancer

(2015) Wei Wen et al.   Molecular Cancer

Targeted Blockade of JAK/STAT3 Signaling Inhibits Ovarian Carcinoma Growth

(2015) G. Gritsina et al.   MOLECULAR CANCER THERAPEUTICS

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher 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

Direct tumor recognition by a human CD4+ T-cell subset potently mediates tumor growth inhibition and orchestrates anti-tumor immune responses

(2015) Junko Matsuzaki et al.   Scientific Reports

The antitumor potential of Interleukin-27 in prostate cancer

(2015) Emma Di Carlo et al.   Oncotarget

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) M. Rajasagi et al.   BLOOD

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

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

Immunotherapy for ovarian cancer

(2014) Emese Zsiros et al.   CURRENT OPINION IN ONCOLOGY

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

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

Targeting JAK1/STAT3 Signaling Suppresses Tumor Progression and Metastasis in a Peritoneal Model of Human Ovarian Cancer

(2014) W. Wen et al.   MOLECULAR CANCER THERAPEUTICS

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

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

(2014) E. Tran et al.   SCIENCE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

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

The genomic landscape of hypodiploid acute lymphoblastic leukemia

(2013) Linda Holmfeldt 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

CD4+ T Effectors Specific for the Tumor Antigen NY-ESO-1 Are Highly Enriched at Ovarian Cancer Sites and Coexist with, but Are Distinct from, Tumor-Associated Treg

(2013) M. Ayyoub et al.   Cancer Immunology Research

Nonclassical Antigen-Processing Pathways Are Required for MHC Class II-Restricted Direct Tumor Recognition by NY-ESO-1-Specific CD4+ T Cells

(2013) J. Matsuzaki et al.   Cancer Immunology Research

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

High-Risk Ovarian Cancer Based on 126-Gene Expression Signature Is Uniquely Characterized by Downregulation of Antigen Presentation Pathway

(2012) Kosuke Yoshihara et al.   CLINICAL CANCER RESEARCH

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

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

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Efficacy of vaccination with recombinant vaccinia and fowlpox vectors expressing NY-ESO-1 antigen in ovarian cancer and melanoma patients

(2012) K. Odunsi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

(2011) M. N. Edmonson et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Antigen-Presenting Cell (APC) Subsets in Ovarian Cancer

(2011) Cailin Moira Wilke et al.   INTERNATIONAL REVIEWS OF IMMUNOLOGY

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

(2011) Steven A. Rosenberg   Nature Reviews Clinical Oncology

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

Refinement of cytogenetic classification in acute myeloid leukemia: determination of prognostic significance of rare recurring chromosomal abnormalities among 5876 younger adult patients treated in the United Kingdom Medical Research Council trials

(2010) D. Grimwade et al.   BLOOD

Antibody-Targeted NY-ESO-1 to Mannose Receptor or DEC-205 In Vitro Elicits Dual Human CD8+ and CD4+ T Cell Responses with Broad Antigen Specificity

(2010) T. Tsuji et al.   JOURNAL OF IMMUNOLOGY

The t(6;9) associated DEK/CAN fusion protein targets a population of long-term repopulating hematopoietic stem cells for leukemogenic transformation

(2010) C Oancea et al.   LEUKEMIA

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Tumor-infiltrating NY-ESO-1–specific CD8+T cells are negatively regulated by LAG-3 and PD-1 in human ovarian cancer

(2010) Junko Matsuzaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Characterization of Preexisting MAGE-A3-Specific CD4+ T Cells in Cancer Patients and Healthy Individuals and Their Activation by Protein Vaccination

(2009) T. Tsuji et al.   JOURNAL OF IMMUNOLOGY

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

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

(2008) Ilka Hoof et al.   IMMUNOGENETICS