Personalized neoantigen vaccine NEO-PV-01 with chemotherapy and anti-PD-1 as first-line treatment for non-squamous non-small cell lung cancer

Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

(2021) Zhuting Hu et al.   NATURE MEDICINE

Pemetrexed Plus Platinum With or Without Pembrolizumab in Patients With Previously Untreated Metastatic Nonsquamous NSCLC: Protocol-Specified Final Analysis From KEYNOTE-189

(2021) D. Rodríguez-Abreu et al.   ANNALS OF ONCOLOGY

ctDNA guiding adjuvant immunotherapy in urothelial carcinoma

(2021) Thomas Powles et al.   NATURE

Toward personalized treatment approaches for non-small-cell lung cancer

(2021) Meina Wang et al.   NATURE MEDICINE

Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps

(2021) Junjie Ma et al.   Science Immunology

CD29 Enriches for Cytotoxic Human CD4+ T Cells

(2021) Benoît P. Nicolet et al.   JOURNAL OF IMMUNOLOGY

First-Line Nivolumab Plus Ipilimumab in Advanced NSCLC: 4-Year Outcomes From the Randomized, Open-Label, Phase 3 CheckMate 227 Part 1 Trial

(2021) Luis G. Paz-Ares et al.   Journal of Thoracic Oncology

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

(2020) Rita Cabrita et al.   NATURE

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

Updated Analysis From KEYNOTE-189: Pembrolizumab or Placebo Plus Pemetrexed and Platinum for Previously Untreated Metastatic Nonsquamous Non–Small-Cell Lung Cancer

(2020) Shirish Gadgeel et al.   JOURNAL OF CLINICAL ONCOLOGY

T‐cell receptor immunosequencing reveals altered repertoire diversity and disease‐associated clonal expansions in ankylosing spondylitis patients

(2020) Aimee L. Hanson et al.   Arthritis & Rheumatology

Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer

(2020) David Y. Oh et al.   CELL

Pembrolizumab plus chemotherapy versus chemotherapy alone in patients with advanced non–small cell lung cancer without tumor PD‐L1 expression: A pooled analysis of 3 randomized controlled trials

(2020) Hossein Borghaei et al.   CANCER

A Phase Ib Trial of Personalized Neoantigen Therapy Plus Anti-PD-1 in Patients with Advanced Melanoma, Non-small Cell Lung Cancer, or Bladder Cancer

(2020) Patrick A. Ott et al.   CELL

Long-Term Overall Survival From KEYNOTE-021 Cohort G: Pemetrexed and Carboplatin With or Without Pembrolizumab as First-Line Therapy for Advanced Nonsquamous NSCLC

(2020) Mark M. Awad et al.   Journal of Thoracic Oncology

Updated Analysis of KEYNOTE-024: Pembrolizumab Versus Platinum-Based Chemotherapy for Advanced Non–Small-Cell Lung Cancer With PD-L1 Tumor Proportion Score of 50% or Greater

(2019) Martin Reck et al.   JOURNAL OF CLINICAL ONCOLOGY

Immune Profiling and Quantitative Analysis Decipher the Clinical Role of Immune-Checkpoint Expression in the Tumor Immune Microenvironment of DLBCL

(2019) Ziju Y. Xu-Monette et al.   Cancer Immunology Research

Memory T cells targeting oncogenic mutations detected in peripheral blood of epithelial cancer patients

(2019) Gal Cafri et al.   Nature Communications

Personalized detection of circulating tumor DNA antedates breast cancer metastatic recurrence

(2019) R. Charles Coombes et al.   CLINICAL CANCER RESEARCH

Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

(2019) Emil Christensen et al.   JOURNAL OF CLINICAL ONCOLOGY

Endogenous CD4+ T Cells Recognize Neoantigens in Lung Cancer Patients, Including Recurrent Oncogenic KRAS and ERBB2 (Her2) Driver Mutations

(2019) Joshua R. Veatch et al.   Cancer Immunology Research

Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer

(2019) Thomas Reinert et al.   JAMA Oncology

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Use of Circulating Tumor DNA for Cancer Immunotherapy

(2019) Alexandra Snyder et al.   CLINICAL CANCER RESEARCH

Nivolumab plus Ipilimumab in Advanced Non–Small-Cell Lung Cancer

(2019) Matthew D. Hellmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

CD4+ T-cell Immunity in the Peripheral Blood Correlates with Response to Anti-PD-1 Therapy

(2019) Hiroshi Kagamu et al.   Cancer Immunology Research

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

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

Cancer immunotherapy efficacy and patients' sex: a systematic review and meta-analysis

(2018) Fabio Conforti et al.   LANCET ONCOLOGY

Pembrolizumab plus Chemotherapy in Metastatic Non–Small-Cell Lung Cancer

(2018) Leena Gandhi et al.   NEW ENGLAND JOURNAL OF MEDICINE

Actively personalized vaccination trial for newly diagnosed glioblastoma

(2018) Norbert Hilf et al.   NATURE

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

(2018) Derin B. Keskin et al.   NATURE

Application of Cell-free DNA Analysis to Cancer Treatment

(2018) Ryan B. Corcoran et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2017) Jennifer G. Abelin et al.   IMMUNITY

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

(2017) Ugur Sahin et al.   NATURE

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

(2017) Christopher Abbosh et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

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

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

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

T-cell receptor profiling in cancer

(2015) Ilan Kirsch et al.   Molecular Oncology

Mutant MHC class II epitopes drive therapeutic immune responses to cancer

(2015) Sebastian Kreiter et al.   NATURE

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

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

(2015) N. A. Rizvi et al.   SCIENCE

Diversity index of mucosal resident T lymphocyte repertoire predicts clinical prognosis in gastric cancer

(2015) Qingzhu Jia et al.   OncoImmunology

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs

(2013) Alexis Christoforides et al.   BMC GENOMICS

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhancement of Tumor-Reactive Cytotoxic CD4+ T-cell Responses after Ipilimumab Treatment in Four Advanced Melanoma Patients

(2013) S. Kitano et al.   Cancer Immunology Research

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

An integrative variant analysis suite for whole exome next-generation sequencing data

(2012) Danny Challis et al.   BMC BIOINFORMATICS

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

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

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis 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 Spreading Contributes to MAGE Vaccination-Induced Regression of Melanoma Metastases

(2011) Véronique Corbière et al.   CANCER RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS