Genomic predictors of response to PD-1 inhibition in children with germline DNA replication repair deficiency

Very low mutation burden is a feature of inflamed recurrent glioblastomas responsive to cancer immunotherapy

(2021) Matthias Gromeier et al.   Nature Communications

Surgical outcomes and survival rates of colon cancer in children and young adults

(2021) Adesola C. Akinkuotu et al.   AMERICAN JOURNAL OF SURGERY

Mutations in the RAS/MAPK pathway drive replication repair deficient hypermutated tumors and confer sensitivity to MEK inhibition

(2021) Brittany B. Campbell et al.   Cancer Discovery

High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types

(2021) D.J. McGrail et al.   ANNALS OF ONCOLOGY

A vaccine targeting mutant IDH1 in newly diagnosed glioma

(2021) Michael Platten et al.   NATURE

The Spectrum of Benefit from Checkpoint Blockade in Hypermutated Tumors

(2021) Benoit Rousseau et al.   NEW ENGLAND JOURNAL OF MEDICINE

Colon Cancer in Patients Under 25 Years Old: A Different Disease?

(2020) Andrea A. Hayes-Jordan et al.   JOURNAL OF THE AMERICAN COLLEGE OF SURGEONS

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Contributions of Age-Related Thymic Involution to Immunosenescence and Inflammaging

(2020) Rachel Thomas et al.   Immunity & Ageing

Evidence of pseudoprogression in patients treated with PD1/PDL1 antibodies across tumor types

(2020) Patricia Martin‐Romano et al.   Cancer Medicine

Expression of TIM3/VISTA checkpoints and the CD68 macrophage-associated marker correlates with anti-PD1/PDL1 resistance: implications of immunogram heterogeneity

(2020) Shumei Kato et al.   OncoImmunology

Nivolumab in children and young adults with relapsed or refractory solid tumours or lymphoma (ADVL1412): a multicentre, open-label, single-arm, phase 1–2 trial

(2020) Kara L Davis et al.   LANCET ONCOLOGY

Mechanisms and therapeutic implications of hypermutation in gliomas

(2020) Mehdi Touat et al.   NATURE

PD-1 inhibitors: Do they have a future in the treatment of glioblastoma?

(2020) Mustafa Khasraw et al.   CLINICAL CANCER RESEARCH

Role of POLE and POLD1 in familial cancer

(2020) Pilar Mur et al.   GENETICS IN MEDICINE

Immune profiling of pediatric solid tumors

(2020) Rachael L. Terry et al.   JOURNAL OF CLINICAL INVESTIGATION

European guidelines from the EHTG and ESCP for Lynch syndrome: an updated third edition of the Mallorca guidelines based on gene and gender

(2020) T. T. Seppälä et al.   BRITISH JOURNAL OF SURGERY

Association of tumour mutational burden with outcomes in patients with advanced solid tumours treated with pembrolizumab: prospective biomarker analysis of the multicohort, open-label, phase 2 KEYNOTE-158 study

(2020) Aurélien Marabelle et al.   LANCET ONCOLOGY

Pembrolizumab in Microsatellite-Instability–High Advanced Colorectal Cancer

(2020) Thierry André et al.   NEW ENGLAND JOURNAL OF MEDICINE

DNA polymerase and mismatch repair exert distinct microsatellite instability signatures in normal and malignant human cells

(2020) Jiil Chung et al.   Cancer Discovery

The first-week proliferative response of peripheral blood PD-1+CD8+ T cells predicts the response to anti-PD-1 therapy in solid tumors

(2019) Kyung Hwan Kim et al.   CLINICAL CANCER RESEARCH

An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE)

(2019) Derek L. Clouthier et al.   Journal for ImmunoTherapy of Cancer

Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma

(2019) Timothy F. Cloughesy et al.   NATURE MEDICINE

Tumor mutational burden is predictive of response to immune checkpoint inhibitors in MSI-high metastatic colorectal cancer

(2019) A B Schrock et al.   ANNALS OF ONCOLOGY

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Genetic diversity of tumors with mismatch repair deficiency influences anti–PD-1 immunotherapy response

(2019) Rajarsi Mandal et al.   SCIENCE

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

(2019) Gregor Sturm et al.   BIOINFORMATICS

Replication-Coupled DNA Repair

(2019) David Cortez   MOLECULAR CELL

Five-Year Survival and Correlates Among Patients With Advanced Melanoma, Renal Cell Carcinoma, or Non–Small Cell Lung Cancer Treated With Nivolumab

(2019) Suzanne L. Topalian et al.   JAMA Oncology

Nivolumab Is Effective in Mismatch Repair–Deficient Noncolorectal Cancers: Results From Arm Z1D—A Subprotocol of the NCI-MATCH (EAY131) Study

(2019) Nilofer S. Azad et al.   JOURNAL OF CLINICAL ONCOLOGY

Efficacy of Pembrolizumab in Patients With Noncolorectal High Microsatellite Instability/Mismatch Repair–Deficient Cancer: Results From the Phase II KEYNOTE-158 Study

(2019) Aurelien Marabelle et al.   JOURNAL OF CLINICAL ONCOLOGY

Atezolizumab for children and young adults with previously treated solid tumours, non-Hodgkin lymphoma, and Hodgkin lymphoma (iMATRIX): a multicentre phase 1–2 study

(2019) Birgit Geoerger et al.   LANCET ONCOLOGY

Metastatic patterns and survival outcomes in patients with stage IV colon cancer: A population‐based analysis

(2019) Jiwei Wang et al.   Cancer Medicine

Pembrolizumab in paediatric patients with advanced melanoma or a PD-L1-positive, advanced, relapsed, or refractory solid tumour or lymphoma (KEYNOTE-051): interim analysis of an open-label, single-arm, phase 1–2 trial

(2019) Birgit Geoerger et al.   LANCET ONCOLOGY

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

(2019) David Liu et al.   NATURE MEDICINE

Harmonization of PD-L1 testing in oncology: a Canadian pathology perspective

(2018) D.N. Ionescu et al.   Current Oncology

Deviations of the immune cell landscape between healthy liver and hepatocellular carcinoma

(2018) Nataliya Rohr-Udilova et al.   Scientific Reports

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

Risk of tumor flare after nivolumab treatment in patients with irradiated field recurrence

(2017) Tatsuya Yoshida et al.   MEDICAL ONCOLOGY

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

Analysis of somatic microsatellite indels identifies driver events in human tumors

(2017) Yosef E Maruvka et al.   NATURE BIOTECHNOLOGY

Detection of immune responses after immunotherapy in glioblastoma using PET and MRI

(2017) Joseph P. Antonios et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

(2017) Dung T. Le et al.   SCIENCE

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Immune Checkpoint Inhibition for Hypermutant Glioblastoma Multiforme Resulting From Germline Biallelic Mismatch Repair Deficiency

(2016) Eric Bouffet et al.   JOURNAL OF CLINICAL ONCOLOGY

Pembrolizumab: first experience with recurrent primary central nervous system (CNS) tumors

(2016) Deborah T. Blumenthal et al.   JOURNAL OF NEURO-ONCOLOGY

FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

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

(2016) N. McGranahan et al.   SCIENCE

Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples

(2016) Joseph Kaplinsky et al.   Nature Communications

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

(2016) Jasreet Hundal et al.   Genome Medicine

Phase I Clinical Trial of Ipilimumab in Pediatric Patients with Advanced Solid Tumors

(2015) M. S. Merchant et al.   CLINICAL CANCER RESEARCH

High frequency of mismatch repair deficiency among pediatric high grade gliomas in Jordan

(2015) Nisreen Amayiri et al.   INTERNATIONAL JOURNAL OF CANCER

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers

(2015) Adam Shlien et al.   NATURE GENETICS

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

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

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

Pembrolizumab for the Treatment of Non–Small-Cell Lung Cancer

(2015) Edward B. Garon et al.   NEW ENGLAND JOURNAL OF MEDICINE

Going back to class I: MHC and immunotherapies for childhood cancer

(2014) Kellie B. Haworth et al.   PEDIATRIC BLOOD & CANCER

The Vigorous Immune Microenvironment of Microsatellite Instable Colon Cancer Is Balanced by Multiple Counter-Inhibitory Checkpoints

(2014) Nicolas J. Llosa et al.   Cancer Discovery

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Derivation of HLA types from shotgun sequence datasets

(2012) René L Warren et al.   Genome Medicine

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Risk of recurrence and survival after relapse in patients with Ewing sarcoma

(2011) Martin Stahl et al.   PEDIATRIC BLOOD & CANCER

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

(2010) A. McKenna et al.   GENOME RESEARCH

Updated Response Assessment Criteria for High-Grade Gliomas: Response Assessment in Neuro-Oncology Working Group

(2010) Patrick Y. Wen et al.   JOURNAL OF CLINICAL ONCOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1)

(2008) E.A. Eisenhauer et al.   EUROPEAN JOURNAL OF CANCER