Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

(2019) Robert M. Samstein et al.   NATURE GENETICS

Biomarker analyses from JAVELIN Renal 101: Avelumab + axitinib (A+Ax) versus sunitinib (S) in advanced renal cell carcinoma (aRCC).

(2019) Toni K. Choueiri et al.   JOURNAL OF CLINICAL ONCOLOGY

Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer

(2018) Matthew D. Hellmann et al.   CANCER CELL

Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

Host expression of PD-L1 determines efficacy of PD-L1 pathway blockade–mediated tumor regression

(2018) Heng Lin et al.   JOURNAL OF CLINICAL INVESTIGATION

Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma

(2018) David F. McDermott et al.   NATURE MEDICINE

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

(2018) Diana Miao et al.   SCIENCE

An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors

(2018) Tao Wang et al.   Cancer Discovery

Anti-PD-1 and Anti-CTLA-4 Therapies in Cancer: Mechanisms of Action, Efficacy, and Limitations

(2018) Judith A. Seidel et al.   Frontiers in Oncology

Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors

(2018) Diana Miao et al.   NATURE GENETICS

Publisher Correction: Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer

(2017) Vinod P. Balachandran et al.   NATURE

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

The problem with neoantigen prediction

(2017)   NATURE BIOTECHNOLOGY

The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia

(2017) Yu Liu et al.   NATURE GENETICS

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

(2017) Ahmet Zehir et al.   NATURE MEDICINE

FDA Approval Summary: Nivolumab for the Treatment of Relapsed or Progressive Classical Hodgkin Lymphoma

(2017) Yvette L. Kasamon et al.   ONCOLOGIST

High somatic mutation and neoantigen burden are correlated with decreased progression-free survival in multiple myeloma

(2017) A Miller et al.   Blood Cancer Journal

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

Neoantigen Targeting—Dawn of a New Era in Cancer Immunotherapy?

(2017) Thomas C. Wirth et al.   Frontiers in Immunology

Accuracy of Programs for the Determination of Human Leukocyte Antigen Alleles from Next-Generation Sequencing Data

(2017) Antti Larjo et al.   Frontiers in Immunology

The frequency of neoantigens per somatic mutation rather than overall mutational load or number of predicted neoantigens per se is a prognostic factor in ovarian clear cell carcinoma

(2017) Hirokazu Matsushita et al.   OncoImmunology

Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer

(2016) Elena Cherkasova et al.   CANCER RESEARCH

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

(2016) Willy Hugo et al.   CELL

Immune targets and neoantigens for cancer immunotherapy and precision medicine

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

Neoantigen landscape dynamics during human melanoma–T cell interactions

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

Pembrolizumab versus Chemotherapy for PD-L1–Positive Non–Small-Cell Lung Cancer

(2016) Martin Reck 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

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

(2016) Solveig K. Sieberts et al.   Nature Communications

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

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

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

(2016) Valsamo Anagnostou et al.   Cancer Discovery

Neoantigen Load, Antigen Presentation Machinery, and Immune Signatures Determine Prognosis in Clear Cell Renal Cell Carcinoma

(2016) H. Matsushita et al.   Cancer Immunology Research

Immunotherapy in hepatocellular carcinoma: Primed to make a difference?

(2015) James J. Harding et al.   CANCER

Genomic Classification of Cutaneous Melanoma

(2015) Rehan Akbani et al.   CELL

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

(2015) Massimo Andreatta et al.   IMMUNOGENETICS

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

Epigenetic silencing of TH1-type chemokines shapes tumour immunity and immunotherapy

(2015) Dongjun Peng et al.   NATURE

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

PD-1 Blockade with Nivolumab in Relapsed or Refractory Hodgkin's Lymphoma

(2015) Stephen M. Ansell 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

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

(2015) N. A. Rizvi et al.   SCIENCE

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

(2015) Nicholas McGranahan et al.   Science Translational Medicine

2015: The Year of Anti-PD-1/PD-L1s Against Melanoma and Beyond

(2015) Paolo A. Ascierto et al.   EBioMedicine

Ultra-low Dose Interleukin-2 Promotes Immune-modulating Function of Regulatory T Cells and Natural Killer Cells in Healthy Volunteers

(2014) Sawa Ito et al.   MOLECULAR THERAPY

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

A vaccine targeting mutant IDH1 induces antitumour immunity

(2014) Theresa Schumacher et al.   NATURE

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

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

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

CTLA-4 and PD-1/PD-L1 Blockade: New Immunotherapeutic Modalities with Durable Clinical Benefit in Melanoma Patients

(2013) P. A. Ott et al.   CLINICAL CANCER RESEARCH

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Integrated molecular analysis of clear-cell renal cell carcinoma

(2013) Yusuke Sato et al.   NATURE GENETICS

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

(2013) Chang Liu et al.   NUCLEIC ACIDS RESEARCH

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

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

Immunotherapy of hepatocellular carcinoma

(2012) Angela D. Pardee et al.   OncoImmunology

The Confluence of Stereotactic Ablative Radiotherapy and Tumor Immunology

(2011) Steven Eric Finkelstein et al.   Clinical & Developmental Immunology

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

(2011) Mark A DePristo et al.   NATURE GENETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) David A. Barbie et al.   NATURE