Evolutionary divergence of HLA class I genotype impacts efficacy of cancer immunotherapy

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

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

Neoantigen-directed immune escape in lung cancer evolution

(2019) Rachel Rosenthal et al.   NATURE

Divergent Allele Advantage at Human MHC Genes: Signatures of Past and Ongoing Selection

(2018) Federica Pierini et al.   MOLECULAR BIOLOGY AND EVOLUTION

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

Evolutionary Pressure against MHC Class II Binding Cancer Mutations

(2018) Rachel Marty et al.   CELL

Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

(2018) David Gfeller et al.   Frontiers in Immunology

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

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

(2017) Ahmet Zehir et al.   NATURE MEDICINE

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy

(2017) Diego Chowell et al.   SCIENCE

Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles

(2017) James Robinson et al.   PLoS Genetics

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

(2016) Willy Hugo et al.   CELL

HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection

(2016) Stéphane Buhler et al.   IMMUNOGENETICS

MHC class I–associated peptides derive from selective regions of the human genome

(2016) Hillary Pearson et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2016) Ronglai Shen et al.   NUCLEIC ACIDS RESEARCH

Heterozygous colon cancer-associated mutations ofSAMHD1have functional significance

(2016) Matilda Rentoft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) N. McGranahan et al.   SCIENCE

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

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

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

(2015) E. M. Van Allen et al.   SCIENCE

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

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

(2015) N. A. Rizvi et al.   SCIENCE

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

The IPD and IMGT/HLA database: allele variant databases

(2014) James Robinson et al.   NUCLEIC ACIDS RESEARCH

Episodic Positive Selection in the Evolution of Avian Toll-Like Receptor Innate Immunity Genes

(2014) Catherine E. Grueber et al.   PLoS One

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

HLA Class I Alleles Are Associated with Peptide-Binding Repertoires of Different Size, Affinity, and Immunogenicity

(2013) S. Paul et al.   JOURNAL OF IMMUNOLOGY

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

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

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

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

(2011) David E. Larson et al.   BIOINFORMATICS

COMPUTATIONAL PREDICTION OF MHC II-ANTIGEN BINDING SUPPORTS DIVERGENT ALLELE ADVANTAGE AND EXPLAINS TRANS-SPECIES POLYMORPHISM

(2011) Tobias L. Lenz   EVOLUTION

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

Comprehensive assessment of T-cell receptor  -chain diversity in    T cells

(2009) H. S. Robins et al.   BLOOD