Resources for Interpreting Variants in Precision Genomic Oncology Applications

Assigning clinical meaning to somatic and germ-line whole-exome sequencing data in a prospective cancer precision medicine study

(2017) Arezou A. Ghazani et al.   GENETICS IN MEDICINE

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

(2017) Malachi Griffith et al.   NATURE GENETICS

Key Lessons Learned from Moffitt's Molecular Tumor Board: The Clinical Genomics Action Committee Experience

(2017) Todd C. Knepper et al.   ONCOLOGIST

In a major shift, cancer drugs go ‘tissue-agnostic’

(2017) Ken Garber   SCIENCE

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

(2017) Dung T. Le et al.   SCIENCE

Experience with precision genomics and tumor board, indicates frequent target identification, but barriers to delivery

(2017) Alan H. Bryce et al.   Oncotarget

A variant by any name: quantifying annotation discordance across tools and clinical databases

(2017) Jennifer L. Yen et al.   Genome Medicine

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Genomic Alteration–Driven Clinical Trial Designs in Oncology

(2016) Richard Simon   ANNALS OF INTERNAL MEDICINE

Immune targets and neoantigens for cancer immunotherapy and precision medicine

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

HGVS Recommendations for the Description of Sequence Variants: 2016 Update

(2016) Johan T. den Dunnen et al.   HUMAN MUTATION

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Generating a neoantigen map of advanced urothelial carcinoma by whole exome sequencing.

(2016) Bishoy Faltas et al.   JOURNAL OF CLINICAL ONCOLOGY

The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations

(2016) Linda Huang et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Toward a Shared Vision for Cancer Genomic Data

(2016) Robert L. Grossman et al.   NEW ENGLAND JOURNAL OF MEDICINE

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Development and clinical application of an integrative genomic approach to personalized cancer therapy

(2016) Andrew V. Uzilov et al.   Genome Medicine

Next-Generation Sequencing in Oncology in the Era of Precision Medicine

(2016) Gideon M. Blumenthal et al.   JAMA Oncology

Unified representation of genetic variants

(2015) Adrian Tan et al.   BIOINFORMATICS

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

Abstract 2983: In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals novel targeting opportunities

(2015) Carlota Rubio-Perez et al.   CANCER RESEARCH

The Molecular Taxonomy of Primary Prostate Cancer

(2015) Adam Abeshouse et al.   CELL

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

Molecular Profiling and Targeted Therapy for Advanced Thoracic Malignancies: A Biomarker-Derived, Multiarm, Multihistology Phase II Basket Trial

(2015) Ariel Lopez-Chavez et al.   JOURNAL OF CLINICAL ONCOLOGY

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)

(2015) Donavan T. Cheng et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Cancer Driver Log (CanDL)

(2015) Senthilkumar Damodaran et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Prospective Clinical Study of Precision Oncology in Solid Tumors

(2015) Davendra P. S. Sohal et al.   JNCI-Journal of the National Cancer Institute

Pharmacogenomics in the clinic

(2015) Mary V. Relling et al.   NATURE

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

(2015) Hui Yang et al.   Nature Protocols

DGIdb 2.0: mining clinically relevant drug–gene interactions

(2015) Alex H. Wagner et al.   NUCLEIC ACIDS RESEARCH

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Prospective Clinical Study of Precision Oncology in Solid Tumors

(2015) Davendra P. S. Sohal et al.   JNCI-Journal of the National Cancer Institute

Whole-Exome Sequencing of Metastatic Cancer and Biomarkers of Treatment Response

(2015) Himisha Beltran et al.   JAMA Oncology

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

MutationTaster2: mutation prediction for the deep-sequencing age

(2014) Jana Marie Schwarz et al.   NATURE METHODS

My Cancer Genome

(2014) Christine M. Micheel et al.   Cancer Genetics

Genomics-Driven Oncology: Framework for an Emerging Paradigm

(2013) Levi A. Garraway   JOURNAL OF CLINICAL ONCOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

Chimeric Antigen Receptor–Modified T Cells for Acute Lymphoid Leukemia

(2013) Stephan A. Grupp et al.   NEW ENGLAND JOURNAL OF MEDICINE

Crizotinib versus Chemotherapy in Advanced ALK-Positive Lung Cancer

(2013) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features

(2013) Yong Mao et al.   PLoS One

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

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

(2012) Pablo Cingolani et al.   FLY

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The Pediatric Cancer Genome Project

(2012) James R Downing et al.   NATURE GENETICS

Cancer pharmacogenomics: strategies and challenges

(2012) Heather E. Wheeler et al.   NATURE REVIEWS GENETICS

Combined BRAF and MEK Inhibition in Melanoma with BRAF V600 Mutations

(2012) Keith T. Flaherty et al.   NEW ENGLAND JOURNAL OF MEDICINE

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

(2011) J. Zhang et al.   Database-The Journal of Biological Databases and Curation

Gefitinib or Chemotherapy for Non–Small-Cell Lung Cancer with Mutated EGFR

(2010) Makoto Maemondo et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements

(2010) M. Masso et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH

Functional annotations improve the predictive score of human disease-related mutations in proteins

(2009) Remo Calabrese et al.   HUMAN MUTATION

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE