Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial

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

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Genomic analysis of 63,220 tumors reveals insights into tumor uniqueness and targeted cancer immunotherapy strategies

(2017) Ryan J. Hartmaier et al.   Genome Medicine

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis

(2017) Alexandra Snyder et al.   PLOS MEDICINE

Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation sequencing

(2016) Lei Wei et al.   BMC Medical Genomics

Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations

(2016) Zhifu Sun et al.   BRIEFINGS IN BIOINFORMATICS

Assessment of the latest NGS enrichment capture methods in clinical context

(2016) Gema García-García et al.   Scientific Reports

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

(2016) Jasreet Hundal et al.   Genome Medicine

Advances in DNA sequencing technologies for high resolution HLA typing

(2015) Nezih Cereb et al.   HUMAN IMMUNOLOGY

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes

(2015) A Sveen et al.   ONCOGENE

Poly(I:C) as cancer vaccine adjuvant: Knocking on the door of medical breakthroughs

(2015) Rachid Ammi et al.   PHARMACOLOGY & THERAPEUTICS

Systematic pan-cancer analysis of tumour purity

(2015) Dvir Aran et al.   Nature Communications

Performance comparison of four commercial human whole-exome capture platforms

(2015) Daichi Shigemizu et al.   Scientific Reports

A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

(2015) Adam Cornish et al.   Biomed Research International

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

(2015) Ensel Oh et al.   PLoS One

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

HLA-Binding Properties of Tumor Neoepitopes in Humans

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

Dendritic cells process synthetic long peptides better than whole protein, improving antigen presentation and T-cell activation

(2013) Rodney A. Rosalia et al.   EUROPEAN 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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Exploiting the Mutanome for Tumor Vaccination

(2012) J. C. Castle et al.   CANCER RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

HLA typing from RNA-Seq sequence reads

(2012) Sebastian Boegel et al.   Genome Medicine

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

(2011) Edita Karosiene et al.   IMMUNOGENETICS

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

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

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH