Best practices for bioinformatic characterization of neoantigens for clinical utility

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas

(2019) Susan K. Rathe et al.   Scientific Reports

A Synthetic DNA, Multi-Neoantigen Vaccine Drives Predominately MHC Class I CD8+ T-cell Responses, Impacting Tumor Challenge

(2019) Elizabeth K. Duperret et al.   Cancer Immunology Research

ScanNeo: identifying indel derived neoantigens using RNA-Seq data

(2019) Ting-You Wang et al.   BIOINFORMATICS

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

(2019) Francesca Finotello et al.   Genome Medicine

NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline

(2019) Ryan O. Schenck et al.   BMC BIOINFORMATICS

Attacking Tumors From All Sides: Personalized Multiplex Vaccines to Tackle Intratumor Heterogeneity

(2019) Felix L. Fennemann et al.   Frontiers in Immunology

Quantifying tumor-infiltrating immune cells from transcriptomics data

(2018) Francesca Finotello et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

(2018) Pauline Robbe et al.   GENETICS IN MEDICINE

Improved methods for predicting peptide binding affinity to MHC class II molecules

(2018) Kamilla Kjaergaard Jensen et al.   IMMUNOLOGY

The perfect personalized cancer therapy: cancer vaccines against neoantigens

(2018) Luigi Aurisicchio et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors

(2018) Yong-Chen Lu et al.   MOLECULAR THERAPY

Personalized vaccines for cancer immunotherapy

(2018) Ugur Sahin et al.   SCIENCE

Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different

(2018) Chung-Han Lee et al.   TRENDS IN IMMUNOLOGY

Genetic Mechanisms of Immune Evasion in Colorectal Cancer

(2018) Catherine S. Grasso et al.   Cancer Discovery

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

(2018) Reyka G. Jayasinghe et al.   Cell Reports

Neoantigen Vaccine Delivery for Personalized Anticancer Immunotherapy

(2018) Yugang Guo et al.   Frontiers in Immunology

MHCflurry: Open-Source Class I MHC Binding Affinity Prediction

(2018) Timothy J. O'Donnell et al.   Cell Systems

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data

(2018) Chang Xu   Computational and Structural Biotechnology Journal

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

(2018) André Kahles et al.   CANCER CELL

Heterogeneous mutation pattern in tumor tissue and circulating tumor DNA warrants parallel NGS panel testing

(2018) Qiaomei Guo et al.   Molecular Cancer

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

(2018) K. G. Paulson et al.   Nature Communications

Determination of a Predictive Cleavage Motif for Eluted Major Histocompatibility Complex Class II Ligands

(2018) Sinu Paul et al.   Frontiers in Immunology

B cell lymphomas present immunoglobulin neoantigens

(2018) Michael S. Khodadoust et al.   BLOOD

Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples

(2018) Erica K. Barnell et al.   GENETICS IN MEDICINE

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

(2018) Derin B. Keskin et al.   NATURE

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

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

Accounting for proximal variants improves neoantigen prediction

(2018) Jasreet Hundal et al.   NATURE GENETICS

The Immune Epitope Database (IEDB): 2018 update

(2018) Randi Vita et al.   NUCLEIC ACIDS RESEARCH

Noncoding regions are the main source of targetable tumor-specific antigens

(2018) Céline M. Laumont et al.   Science Translational Medicine

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

(2018) Weilong Zhao et al.   PLoS Computational Biology

Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

(2018) Aaron S. Mansfield et al.   Journal of Thoracic Oncology

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes

(2017) Jin Zhang et al.   EXPERIMENTAL HEMATOLOGY

HLA-HD: An accurate HLA typing algorithm for next-generation sequencing data

(2017) Shuji Kawaguchi et al.   HUMAN MUTATION

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction

(2017) Jennifer G. Abelin et al.   IMMUNITY

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

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

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

(2017) Ugur Sahin et al.   NATURE

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens

(2017) Michael S. Khodadoust et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Antigen receptor repertoire profiling from RNA-seq data

(2017) Dmitriy A Bolotin et al.   NATURE BIOTECHNOLOGY

Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA–seq data

(2017) Bo Li et al.   NATURE GENETICS

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

(2017) Chao Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impaired HLA Class I Antigen Processing and Presentation as a Mechanism of Acquired Resistance to Immune Checkpoint Inhibitors in Lung Cancer

(2017) Scott Gettinger et al.   Cancer Discovery

GFusion: an Effective Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data

(2017) Jian Zhao et al.   Scientific Reports

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

(2017) Pornpimol Charoentong et al.   Cell Reports

The neoepitope landscape in pediatric cancers

(2017) Ti-Cheng Chang et al.   Genome Medicine

Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

(2017) Maurizio Callari et al.   Genome Medicine

Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia

(2017) Stacy A. Malaker et al.   Cancer Immunology Research

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

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

Comprehensive benchmarking of SNV callers for highly admixed tumor data

(2017) Regina Bohnert et al.   PLoS One

Variations in MHC Class II Antigen Processing and Presentation in Health and Disease

(2016) Emil R. Unanue et al.   Annual Review of Immunology

VDJviz: a versatile browser for immunogenomics data

(2016) Dmitriy V. Bagaev et al.   BMC GENOMICS

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

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

Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

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

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

(2016) Anne Bruun Krøigård et al.   PLoS One

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

EpiToolKit—a web-based workbench for vaccine design

(2015) Benjamin Schubert et al.   BIOINFORMATICS

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

(2015) Massimo Andreatta et al.   BIOINFORMATICS

HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data

(2015) Naoki Nariai et al.   BMC GENOMICS

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

(2015) Jin Zhang et al.   GENOME RESEARCH

Advances in DNA sequencing technologies for high resolution HLA typing

(2015) Nezih Cereb et al.   HUMAN IMMUNOLOGY

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

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

Tumor neoantigens: building a framework for personalized cancer immunotherapy

(2015) Matthew M. Gubin et al.   JOURNAL OF CLINICAL INVESTIGATION

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

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data

(2015) Silvia Liu et al.   NUCLEIC ACIDS RESEARCH

LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins

(2015) Yaxuan Yu et al.   NUCLEIC ACIDS RESEARCH

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

(2015) E. M. Van Allen 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

JAFFA: High sensitivity transcriptome-focused fusion gene detection

(2015) Nadia M Davidson et al.   Genome Medicine

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

(2015) Mikhail Shugay et al.   PLoS Computational Biology

Frameshift mutations, neoantigens and tumor-specific CD8+T cells in microsatellite unstable colorectal cancers

(2015) Pauline Maby et al.   OncoImmunology

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples

(2015) Ensel Oh et al.   PLoS One

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

(2014) Jason A. Vander Heiden et al.   BIOINFORMATICS

Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions

(2014) Yohan Kim et al.   BMC BIOINFORMATICS

Comparison of somatic mutation calling methods in amplicon and whole exome sequence data

(2014) Huilei Xu et al.   BMC GENOMICS

Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs

(2014) Jorg J. A. Calis et al.   IMMUNOGENETICS

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

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

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

A vaccine targeting mutant IDH1 induces antitumour immunity

(2014) Theresa Schumacher 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

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

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

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

HLA-Binding Properties of Tumor Neoepitopes in Humans

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

Downregulation of MHC-I Expression Is Prevalent but Reversible in Merkel Cell Carcinoma

(2014) K. G. Paulson et al.   Cancer Immunology Research

Pathways of Antigen Processing

(2013) Janice S. Blum et al.   Annual Review of Immunology

Shimmer: detection of genetic alterations in tumors using next-generation sequence data

(2013) Nancy F. Hansen et al.   BIOINFORMATICS

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

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

Predictor for the effect of amino acid composition on CD4+ T cell epitopes preprocessing

(2013) Ehud Hoze et al.   JOURNAL OF IMMUNOLOGICAL METHODS

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

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

(2013) Paul F Robbins et al.   NATURE MEDICINE

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

(2013) Chang Liu et al.   NUCLEIC ACIDS RESEARCH

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data

(2013) Yuichi Shiraishi et al.   NUCLEIC ACIDS RESEARCH

An effective and effecient peptide binding prediction approach for a broad set of HLA-DR molecules based on ordered weighted averaging of binding pocket profiles

(2013) Wen-Jun Shen et al.   Proteome Science

MHC Class I-Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia

(2013) M. Cobbold et al.   Science Translational Medicine

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

(2013) Jorg J. A. Calis et al.   PLoS Computational Biology

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

(2013) Wenlong Jia et al.   GENOME BIOLOGY

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

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

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

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

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

TEPITOPEpan: Extending TEPITOPE for Peptide Binding Prediction Covering over 700 HLA-DR Molecules

(2012) Lianming Zhang et al.   PLoS One

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

(2012) Moritz Gerstung et al.   Nature Communications

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

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Definitions of histocompatibility typing terms

(2011) E. Nunes et al.   BLOOD

Expression of antigen processing and presenting molecules in brain metastasis of breast cancer

(2011) Yan Liu et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Viral Vector-Based Therapeutic Cancer Vaccines

(2011) Cecilia Larocca et al.   CANCER JOURNAL

The Present and Future of Peptide Vaccines for Cancer

(2011) Craig L. Slingluff   CANCER JOURNAL

ELISpot for measuring human immune responses to vaccines

(2011) Meredith Slota et al.   Expert Review of Vaccines

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

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

(2011) Edita Karosiene et al.   IMMUNOGENETICS

FurinDB: A Database of 20-Residue Furin Cleavage Site Motifs, Substrates and Their Associated Drugs

(2011) Sun Tian et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

(2011) Massimo Andreatta et al.   PLoS One

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

(2011) N. Stransky et al.   SCIENCE

MultiRTA: A simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes

(2010) Andrew J. Bordner et al.   BMC BIOINFORMATICS

GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection

(2010) Y. Xue et al.   PROTEIN ENGINEERING DESIGN & SELECTION

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding

(2009) Hao Zhang et al.   BIOINFORMATICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

(2009) Yohan Kim et al.   BMC BIOINFORMATICS

Vaccination against HPV-16 Oncoproteins for Vulvar Intraepithelial Neoplasia

(2009) Gemma G. Kenter et al.   NEW ENGLAND JOURNAL OF MEDICINE

Induction of Tumor-Specific CD4+ and CD8+ T-Cell Immunity in Cervical Cancer Patients by a Human Papillomavirus Type 16 E6 and E7 Long Peptides Vaccine

(2008) M. J.P. Welters et al.   CLINICAL CANCER RESEARCH

Superior induction of anti-tumor CTL immunity by extended peptide vaccines involves prolonged, DC-focused antigen presentation

(2008) Martijn S. Bijker et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

The anticancer immune response: indispensable for therapeutic success?

(2008) Laurence Zitvogel et al.   JOURNAL OF CLINICAL INVESTIGATION